# 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/Haloarcula_hispanica_ATCC_33960_uid72475/NC_015944.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/Haloarcula_hispanica_ATCC_33960_uid72475/NC_015944.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Haloarcula_hispanica_ATCC_33960_uid72475/NC_015944.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|344209943|ref|YP_004786119.1|  [L=414]
Description: cell division control protein 6 [Haloarcula hispanica ATCC 33960]
Scores for 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-22   77.7   0.0    1.7e-21   76.0   0.0    2.0  1  Cdc6_C        CDC6, C terminal winged helix domain
    3.3e-10   40.4   0.0    7.6e-10   39.2   0.0    1.5  1  AAA_22        AAA domain
    1.2e-09   38.8   0.3    1.4e-08   35.3   0.0    2.5  2  AAA_16        AAA ATPase domain
     0.0021   17.3   0.0     0.0035   16.5   0.0    1.3  1  DUF815        Protein of unknown function (DUF815)
     0.0053   17.2   0.0      0.013   15.9   0.0    1.7  1  AAA           ATPase family associated with various cellular 
     0.0072   16.3   0.0      0.015   15.2   0.0    1.5  2  NACHT         NACHT domain
     0.0088   16.0   0.0      0.014   15.3   0.0    1.4  1  ATPase_2      ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.035   14.5   0.0      0.072   13.5   0.0    1.6  1  RNA_helicase  RNA helicase
      0.054   13.0   0.0      0.097   12.2   0.0    1.3  1  AAA_7         P-loop containing dynein motor region
      0.083   12.7   0.3        5.4    6.8   0.0    2.3  2  DEAD          DEAD/DEAH box 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 !   76.0   0.0   9.3e-25   1.7e-21       2      83 ..     303     383 ..     302     384 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 9.3e-25
                                       HHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSC CS
                            Cdc6_C   2 calvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdp 78 
                                       +a+v l + +gk++++t+++  +Y++ +e+ g+dpl  r+++d+l eL+mlgi+++ ++++Grr+g +r++sL +dp
  gi|344209943|ref|YP_004786119.1| 303 YAMVTLDQ-EGKTPARTRDIRPRYTNFAEKAGIDPLVPRRMRDHLGELSMLGIISAIERNEGRRGGTYREYSLEMDP 378
                                       89999999.******************************************************************** PP

                                       HHHHH CS
                            Cdc6_C  79 ddvle 83 
                                       + +l+
  gi|344209943|ref|YP_004786119.1| 379 EMILA 383
                                       *9986 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   4.2e-13   7.6e-10       5     126 ..      49     177 ..      45     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 4.2e-13
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrellralglelka...erlssee 77 
                                        + ++++G +G+GKT   r l + l+e+a+  e  + +v   ++ +++ss +++++l++++ +e++     +  +  
  gi|344209943|ref|YP_004786119.1|  49 PNNIFLYGKTGVGKTAGTRYLIDHLEEDAAKYEDIDLTVkMLNCDGLSSSYQIATRLVNEFRDETSQistTGYPRAT 125
                                       56799********************76655444444444699***********************999988888888 PP

                            AAA_22  78 llealeqalraravielliiDEaqhlrs.eealeeL.rsllnl..srkgvqli 126
                                       ++++l+  l++++ +  +++DE++h+ + + +l +L r ++n+  s+ ++ +i
  gi|344209943|ref|YP_004786119.1| 126 VYDMLWTELDSCGGTIYIVLDEVDHI-EdDSILYQLpRARANDnlSSAKIGII 177
                                       99************************.65999999999999985555555544 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   7.7e-12   1.4e-08       1      91 [.      25     107 ..      25     172 .. 0.61
   2 ?   -2.0   0.1       2.3   4.1e+03      88     106 ..     239     257 ..     194     290 .. 0.46

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 7.7e-12
                            AAA_16   1 rlvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqal 76 
                                       +lvGR+ el++ ++al++v  g+  ++++l+G  GvGK++  r l ++le+d     ++k+++ +  ++    +++ 
  gi|344209943|ref|YP_004786119.1|  25 NLVGRDTELNRYRAALQPVINGEQpNNIFLYGKTGVGKTAGTRYLIDHLEED-----AAKYEDID--LTVK-MLNCD 93 
                                       59*****************999999***************************.....44444442..2221.22222 PP

                            AAA_16  77 areellrqlldeaes 91 
                                          +   q+++++ +
  gi|344209943|ref|YP_004786119.1|  94 -GLSSSYQIATRLVN 107
                                       .22344444444333 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.3
                            AAA_16  88 eaesaeleawrekleeala 106
                                       +  +++++++r+ l+  ++
  gi|344209943|ref|YP_004786119.1| 239 AYGAKDAGDARQSLDLLMK 257
                                       2233334444443333333 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     2e-06    0.0035      25      81 ..      21      77 ..       6      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2e-06
                            DUF815 25 vklddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg 81
                                       + ++Lvg d++ ++  +  +  ++g++ nn++L+G+ G+GK +  + l+ +++e+ 
  gi|344209943|ref|YP_004786119.1| 21 YQPENLVGRDTELNRYRAALQPVINGEQPNNIFLYGKTGVGKTAGTRYLIDHLEEDA 77
                                      567899**************************************9999999887765 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 !   15.9   0.0   7.5e-06     0.013       2     131 ..      53     205 ..      52     206 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.5e-06
                                       EEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS......STTHHHHHHHHHHHHHHHTS..... CS
                               AAA   2 llyGppGtGKTllakavakel..........gvefleisgsellsk......yvgesekkirelfkeakeka..... 57 
                                        lyG  G+GKT+  + ++ +l          + ++  +++  l s+      +v e  ++++++ ++    a     
  gi|344209943|ref|YP_004786119.1|  53 FLYGKTGVGKTAGTRYLIDHLeedaakyediDLTVKMLNCDGLSSSyqiatrLVNEFRDETSQISTTGYPRAtvydm 129
                                       79******************844444333333556777777777555566664444444444444443333333333 PP

                                       .........TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...GGGSTHHHHST CS
                               AAA  58 .........kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...pdkldpallrg 122
                                                ++  +++DE+d +          e+++++ qL ++  + + +++k+ +ig++n+    d+l+p++ ++
  gi|344209943|ref|YP_004786119.1| 130 lwteldscgGTIYIVLDEVDHI----------EDDSILYQLPRARANDNLSSAKIGIIGISNDfsfRDDLSPKVKSS 196
                                       4444444544455666666666..........4556999**999999999999**********98889999999888 PP

                                       TSSEEEETT CS
                               AAA 123 Rfdrkieie 131
                                        ++++i+++
  gi|344209943|ref|YP_004786119.1| 197 LCEEEIQFP 205
                                       999988876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   8.6e-06     0.015       3      96 ..      52     154 ..      50     171 .. 0.84
   2 ?   -2.9   0.1         3   5.4e+03      70     109 ..     210     252 ..     188     280 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.6e-06
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC.-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C....... CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqga.fklvFflslrelsrsgnarsladllfsqlpepaapvse....... 71 
                                       ++l G+ G+GKT+  + l++ + e+  + +     v +l++  ls s   + +a+ l+ ++ ++ +++s+       
  gi|344209943|ref|YP_004786119.1|  52 IFLYGKTGVGKTAGTRYLIDHLEEDAAKYEDiDLTVKMLNCDGLSSS---YQIATRLVNEFRDETSQISTtgyprat 125
                                       789*********************99888764455566677776666...799*****************9999999 PP

                                       ....CHHHHCCSCCCEEEEEE-STT-SS- CS
                             NACHT  72 ....vwavllelperlLlilDglDelvtd 96 
                                            w++l +    + ++lD +D +++d
  gi|344209943|ref|YP_004786119.1| 126 vydmLWTELDSCGGTIYIVLDEVDHIEDD 154
                                       88888888888888888*******99975 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3
                                       -CCHHHHCCSCCCEE...EEEE-STT-SS-TCH.........H CS
                             NACHT  70 sevwavllelperlL...lilDglDelvtdlgqkekqpvrtlL 109
                                       +e +++l+++++ +     + Dg+ el++  g+k++  +r+ L
  gi|344209943|ref|YP_004786119.1| 210 KELIQILQQRADVAFhdgVLEDGVIELCAAYGAKDAGDARQSL 252
                                       4555566666655556666667777777777776666666555 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 !   15.3   0.0   7.8e-06     0.014       4      47 ..      29      76 ..      26     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.8e-06
                          ATPase_2  4 Rekelke....leeilerepneiyfiYGpegsGKtaLlkeiienledk 47
                                      R++el++    l+ +++ e+ + +f+YG  g+GKta  + +i  le+ 
  gi|344209943|ref|YP_004786119.1| 29 RDTELNRyraaLQPVINGEQPNNIFLYGKTGVGKTAGTRYLIDHLEED 76
                                      66666642222777889999999*******************999653 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     4e-05     0.072       1      28 [.      52      79 ..      52     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklkl 28
                                      i+lyG++g+GK+  +++L+++l+++  +
  gi|344209943|ref|YP_004786119.1| 52 IFLYGKTGVGKTAGTRYLIDHLEEDAAK 79
                                      79********************977633 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 ?   12.2   0.0   5.4e-05     0.097      21      69 ..      35      85 ..      19      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.4e-05
                             AAA_7 21 rysyllelllknk..kpvllvGptGtGKtviikdllkkldkekylsltinf 69
                                      ry+  l+ +++ +  ++++l+G+tG+GKt+ ++ l+++l+++  ++  i +
  gi|344209943|ref|YP_004786119.1| 35 RYRAALQPVINGEqpNNIFLYGKTGVGKTAGTRYLIDHLEEDAAKYEDIDL 85
                                      6666666666544115799********************998887777665 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.018        33      13      29 ..      48      64 ..      35      79 .. 0.74
   2 ?    6.8   0.0     0.003       5.4     106     141 ..     124     159 ..      64     180 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.018
                                      TTCEEEEEESTTSSHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                              DEAD 13 gggdvlvaaeTGsGKTl 29
                                      + +++++ ++TG GKT+
  gi|344209943|ref|YP_004786119.1| 48 QPNNIFLYGKTGVGKTA 64
                                      337999**********7 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.003
                                       HHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 106 grlddllstgklnlsqvrflVlDEadrlldqgfsdf 141
                                         + d+l+t+  ++    ++VlDE+d + d++   +
  gi|344209943|ref|YP_004786119.1| 124 ATVYDMLWTELDSCGGTIYIVLDEVDHIEDDSILYQ 159
                                       456678887777799999**********99865554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 2700.98
//
Query:       gi|344209944|ref|YP_004786120.1|  [L=118]
Description: hypothetical protein HAH_5002 [Haloarcula hispanica ATCC 33960]
Scores for 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-15   55.5   0.3    6.5e-15   55.2   0.3    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 !   55.2   0.3   3.6e-19   6.5e-15       2      73 ..      34     107 ..      33     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 3.6e-19
                            HalOD1   2 eespstaVveavaavegvdptelepLydaiDpdALdaLfasradge..aradgsvsFtyegyeVtVrsdgeieV 73 
                                       ++++ t +v+ava+ +g++p   +pL+d+iD dA+++L+  ++ ++  ++a+ +++F+y++  VtVr+dg i+ 
  gi|344209944|ref|YP_004786120.1|  34 DQELATVIVQAVADQSGTEPYRESPLHDYIDVDAIETLLFGTQPDQsiGSASQNITFRYRNIIVTVRADGVIQL 107
                                       78999********************************998876666457888******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.56
# Mc/sec: 637.87
//
Query:       gi|344209945|ref|YP_004786121.1|  [L=226]
Description: hypothetical protein HAH_5003 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   1.1       0.11   12.5   0.5    2.5  2  Hemopexin  Hemopexin
       0.29   11.0   0.5        0.6   10.0   0.5    1.5  1  TnpW       Transposon-encoded protein TnpW


Domain annotation for each model (and alignments):
>> Hemopexin  Hemopexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.5   1.2e-05      0.11      14      37 ..      84     108 ..      83     112 .. 0.87
   2 ?    0.5   0.0     0.065   5.9e+02      29      36 ..     180     187 ..     173     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                                       EEETTEEEEEETT.EETTTEEEEHH CS
                         Hemopexin  14 FFkGdkYWrfdpq.kvepgypklis 37 
                                       F++Gd YW fd q +++ +y+ + s
  gi|344209945|ref|YP_004786121.1|  84 FYQGDMYWSFDQQgQQMEMYRIGNS 108
                                       9*************99999987655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.065
                                       TTTEEEEH CS
                         Hemopexin  29 epgypkli 36 
                                       ++gyp++i
  gi|344209945|ref|YP_004786121.1| 180 DSGYPRRI 187
                                       89****99 PP

>> TnpW  Transposon-encoded protein TnpW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.5   6.6e-05       0.6       2      13 ..     102     113 ..     102     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.6e-05
                              TnpW   2 ekkIGgTTYvVr 13 
                                       +++IG+ TY+V 
  gi|344209945|ref|YP_004786121.1| 102 MYRIGNSTYTVT 113
                                       69*********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1366.17
//
Query:       gi|344209946|ref|YP_004786122.1|  [L=132]
Description: transcription regulator [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-13   49.7   0.2    4.3e-13   49.5   0.2    1.1  1  TetR_C_6   BetI-type transcriptional repressor, C-terminal
    6.9e-06   26.2   0.0    8.7e-06   25.9   0.0    1.2  1  TetR_C_31  Tetracyclin repressor-like, C-terminal domain
    1.3e-05   25.2   0.1    1.7e-05   24.8   0.1    1.5  1  TetR_C_27  Tetracyclin repressor-like, C-terminal domain
    0.00017   21.8   0.3    0.00032   21.0   0.1    1.6  2  TetR_C_24  Tetracyclin repressor-like, C-terminal domain
      0.003   17.6   0.1      0.004   17.2   0.1    1.3  1  TetR_C_7   AefR-like transcriptional repressor, C-terminal do
  ------ inclusion threshold ------
      0.049   13.7   0.0      0.065   13.3   0.0    1.3  1  TetR_C_17  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 !   49.5   0.2   1.4e-16   4.3e-13       1     114 [.      16     129 ..      16     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 1.4e-16
                                       HHHHHHHHHHCCSTHSHHHH.HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCTTSTHHHHH CS
                          TetR_C_6   1 prerlraileallpldqerr.aelavwlafwaeaardpelaelqrenyarlrsnlrallaelaegglradadaeaaA 76 
                                       p+e ++ i+++++ ++ +++ +++++ +++ a+aa+d+++ +l+r++++ +r ++++++++++++g ++ +d+ + A
  gi|344209946|ref|YP_004786122.1|  16 PEEYIEIIVDEIFGTSSNSDvEFSQAVIELRAQAAHDDDYNRLFRRSDDFIRKQIARVIRAGVDAGAFDVEDPSQTA 92 
                                       5677788999999976666637999**************************************************** PP

                                       HHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHHT CS
                          TetR_C_6  77 erlaAlidGLwlraalapeeldaeraralvrrhldall 114
                                       +  + ++ G+  + +++ +e + + +ra  rr+++ +l
  gi|344209946|ref|YP_004786122.1|  93 ALFHTVLVGIQAERITS-DEETIDDVRAEFRRYVENCL 129
                                       **************999.89999***********9887 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 !   25.9   0.0   2.9e-09   8.7e-06      20     103 ..      35     127 ..      14     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.9e-09
                                       THHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHHHH......HHCSS-HHHHHHHHHHHHHHHHHHHHHSG. CS
                         TetR_C_31  20 drertlAryelfleaarrPeLraalarlrralrealaalla......alGlpdpeeaarllvaaldGllldrLagp. 89 
                                       d e   A +el+ +aa++++  ++++r+ + +r ++a++ +      a+ ++dp ++a+l++ +l G+  +r++ + 
  gi|344209946|ref|YP_004786122.1|  35 DVEFSQAVIELRAQAAHDDDYNRLFRRSDDFIRKQIARVIRagvdagAFDVEDPSQTAALFHTVLVGIQAERITSDe 111
                                       666667899********************999999999999777555555579999*******************95 PP

                                       .TS-H.HHHHHHHHHH CS
                         TetR_C_31  90 .aadp.raevrellra 103
                                        + d+ rae+r++++ 
  gi|344209946|ref|YP_004786122.1| 112 eTIDDvRAEFRRYVEN 127
                                       4223368888888876 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 !   24.8   0.1   5.8e-09   1.7e-05      47      84 ..      65     102 ..      37     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 5.8e-09
                                       HHHHHHHHHHHHHHHCT-STT--HHHHHHHHHHHSGGG CS
                         TetR_C_27  47 eleeqlaeIireGvaaGeFkaadpeaaaravfdatarf 84 
                                        +++q+a++ir+Gv+aG+F ++dp+++a ++ ++++ +
  gi|344209946|ref|YP_004786122.1|  65 FIRKQIARVIRAGVDAGAFDVEDPSQTAALFHTVLVGI 102
                                       5789************************9998887755 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 !   21.0   0.1   1.1e-07   0.00032      23      85 ..      38     100 ..      14     104 .. 0.87
   2 ?   -1.5   0.0      0.97   2.9e+03      38      52 ..     111     125 ..      96     129 .. 0.50

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB-SS-HHHHHHHHHHHHH CS
                         TetR_C_24  23 reeaavllrelraLspehreeiralrreyerllrdlieeGvaagefedldpklaalailgmln 85 
                                       +++a++ lr   a ++++ + +r+  + ++++++++i++Gv+ag f+++dp+ +a ++ ++l 
  gi|344209946|ref|YP_004786122.1|  38 FSQAVIELRAQAAHDDDYNRLFRRSDDFIRKQIARVIRAGVDAGAFDVEDPSQTAALFHTVLV 100
                                       6778888888888899999999999999************************99988877766 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.97
                                       HHHHHHHHHHHHHHH CS
                         TetR_C_24  38 pehreeiralrreye 52 
                                       +e  + +ra  r+y 
  gi|344209946|ref|YP_004786122.1| 111 EETIDDVRAEFRRYV 125
                                       333344444444443 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 !   17.2   0.1   1.3e-06     0.004      38      83 ..      57     101 ..      36     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-06
                                       CCHHHT.T----HHHHHHHHHHHHTTSB-SS-HHHHHHHHHHHHHH CS
                          TetR_C_7  38 rafyeagpgrveealaayLeaavaaGrLridDpelAAeqflgllkg 83 
                                       r f ++     ++++a++++a v+aG+ +++Dp ++A+ f+  l g
  gi|344209946|ref|YP_004786122.1|  57 RLFRRS-DDFIRKQIARVIRAGVDAGAFDVEDPSQTAALFHTVLVG 101
                                       444444.6778999**************************988765 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 ?   13.3   0.0   2.2e-05     0.065      14      96 ..      32     113 ..      17     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.2e-05
                                       TTGGGSSHHHHHHHHHGGGG-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS---SS-HHHHHHHHHHHHHHHHHHHH CS
                         TetR_C_17  14 eeideslllakyEyfltsyreeerrayleeRyerlvealkellqeGvergEfkPqlplesiakylisfldGliletl 90 
                                        ++d  ++ a +E   ++ ++++ ++++ +  + + +++ +++ +Gv+ g f  + p ++ a  +  +l G+  e++
  gi|344209946|ref|YP_004786122.1|  32 SNSDVEFSQAVIELRAQAAHDDDYNRLFRRSDDFIRKQIARVIRAGVDAGAFDVEDPSQTAAL-FHTVLVGIQAERI 107
                                       56667778888888878888888888887777778899***************9999887665.5678889999999 PP

                                       HS-HHH CS
                         TetR_C_17  91 algeek 96 
                                       + +ee+
  gi|344209946|ref|YP_004786122.1| 108 TSDEET 113
                                       988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 828.59
//
Query:       gi|344209947|ref|YP_004786123.1|  [L=644]
Description: sialidase [Haloarcula hispanica ATCC 33960]
Scores for complete 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   54.0  25.7     0.0023   18.1   0.1    5.5  5  CARDB            CARDB
    1.7e-13   50.6  18.6    9.5e-05   22.6   0.4    7.9  6  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
    3.2e-07   30.5  37.6      0.069   13.5   1.2    7.0  5  DUF11            Domain of unknown function DUF11
    1.5e-05   25.1  10.6      0.066   13.4   0.0    5.3  5  ASH              Abnormal spindle-like microcephaly-assoc'd, 
    5.5e-05   23.2  12.5       0.95    9.6   0.2    7.3  8  Fn3-like         Fibronectin type III-like domain
    0.00017   22.3   2.3        5.7    7.7   0.1    5.2  6  N_BRCA1_IG       Ig-like domain from next to BRCA1 gene
    0.00094   19.3   0.2         12    6.1   0.0    4.5  5  Transglut_C      Transglutaminase family, C-terminal ig like 
     0.0028   17.5   4.9         11    5.7   0.0    4.9  5  DUF4832          Domain of unknown function (DUF4832)
  ------ inclusion threshold ------
      0.025   14.4   0.0       0.14   11.9   0.0    2.3  1  FAS_meander      Fatty acid synthase meander beta sheet domai
      0.032   14.5   3.3       0.24   11.6   0.0    3.2  4  AP3B1_C          Clathrin-adaptor complex-3 beta-1 subunit C-
      0.036   13.8   0.5       0.13   12.0   0.1    2.1  2  BppU_N           BppU N-terminal domain
       0.04   14.2   1.1        2.2    8.6   0.0    3.1  3  Alpha_adaptinC2  Adaptin C-terminal domain
      0.056   14.0   0.4      0.056   14.0   0.4    4.9  5  MBG              MBG domain
        3.7    8.5  19.1        6.5    7.7   0.1    5.1  5  Pilin            Pilin (bacterial filament)


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 !   13.0   0.3   7.2e-05     0.092       9      92 ..      36     142 ..      30     149 .. 0.82
   2 !   13.1   0.6     7e-05     0.089       9      88 ..     171     259 ..     160     261 .. 0.79
   3 !   12.3   2.4   0.00012      0.16      11      88 ..     287     373 ..     278     379 .. 0.87
   4 !   11.9   0.4   0.00015       0.2      10      71 ..     400     465 ..     393     493 .. 0.87
   5 !   18.1   0.1   1.8e-06    0.0023      10      72 ..     512     577 ..     505     597 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-05
                                       EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.EEEEE..................SEE-CTEEEEEE CS
                             CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv.gtvtv..................psLaagesttvs 66 
                                       tl+ +++ +ge+ ti++++ N+G+ +sg+t+     ++ ++ +  tv                    L+ag +ttv 
  gi|344209947|ref|YP_004786123.1|  36 TLEDDTVAPGEQKTIEISLVNSGELDSGSTRNPALNNEVTTaKGLTVslgsgdapisvknskrslGTLQAGPKTTVP 112
                                       77889999***********************999999988875566677888888899999999999********** PP

                                       EEEE-S..-S-CEEE..EEEEESTT-SS-- CS
                             CARDB  67 ftwtte..ategevt..ltvvvDpdnevaE 92 
                                       f + ++  a++g+++  l+++   +++++E
  gi|344209947|ref|YP_004786123.1| 113 FEISVDedASSGTYDaqLRLNYKHTSYISE 142
                                       **9999888899998555555555555555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7e-05
                                       EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.......EEEEESEE-CTEEEEEEEEEE-S..-S-C CS
                             CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv.......gtvtvpsLaagesttvsftwtte..ateg 76 
                                       t   s+a v ++ t+ v+v+N+G+ a+++  v+l    +         ++  v + ++ge +t ++ +  +  a++ 
  gi|344209947|ref|YP_004786123.1| 171 TDIDSNARVASTGTVAVSVENTGDSAARDAAVTLQSQNQDLavsggdaTSRFVDEWEPGEVRTFNYRVSSAeaAEPE 247
                                       56678899999*******************99998776665578877677778999999999999999888755555 PP

                                       EEEEEEEESTT- CS
                             CARDB  77 evtltvvvDpdn 88 
                                       ++ ++++v  dn
  gi|344209947|ref|YP_004786123.1| 248 SYGFELSVAFDN 259
                                       555776665555 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00012
                                       C-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.......EEEEESEE-CTEEEEEEEEEE-S..-S-CEE CS
                             CARDB  11 npseafvgeentitvtvkNqGtaasgatkvalyldgelv.......gtvtvpsLaagesttvsftwtte..ategev 78 
                                       + s++ v ++ t +v+++N+G  +  +++v+++ +           +t++v + ++g+ +tv++  t++  a+  ++
  gi|344209947|ref|YP_004786123.1| 287 SSSSVAVSNTGTYEVQLRNTGPLTVNDSSVTFVSENADItfgksssTTAYVGEWEPGAVRTVRVDTTASpdAEDRSY 363
                                       567888999999************9999999988776667899999999**************99999988999999 PP

                                       EEEEEESTT- CS
                             CARDB  79 tltvvvDpdn 88 
                                       +l+++v  ++
  gi|344209947|ref|YP_004786123.1| 364 ALSANVQYED 373
                                       9999987765 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.00015
                                       EC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEEEEEEEEE- CS
                             CARDB  10 lnpseafvgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagesttvsftwtt 71 
                                         ++++ +ge+ ++++t++N+Gt + +++ +a    +++     ++  v  L+age+++ +f + +
  gi|344209947|ref|YP_004786123.1| 400 NVETSLQAGEDGSLSATLTNTGTRDVENVVIAWESQQSTLspkeSQYAVGDLDAGETANFNFGVDV 465
                                       567889999***********************999999989999999************9997655 PP

  == domain 5  score: 18.1 bits;  conditional E-value: 1.8e-06
                                       EC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE-S CS
                             CARDB  10 lnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtte 72 
                                       ++ s++ vg++ +it+t++N+ +++ ++++ + ++++ l    +++ +++La+g+s+tvs++  + 
  gi|344209947|ref|YP_004786123.1| 512 VENSTLGVGQDRSITFTITNTKNKTLTSIEGKAFVNDPLSssdDETFIAELAPGASETVSVQLSAG 577
                                       6778888999***************************9998889999**************99876 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 ?    1.0   0.0      0.39     5e+02       2      18 ..      43      59 ..      42      66 .. 0.90
   2 !   10.6   0.0    0.0004      0.51      38      78 ..      94     134 ..      69     135 .. 0.91
   3 ?    3.1   0.7     0.091   1.2e+02       5      30 ..     181     206 ..     177     258 .. 0.63
   4 ?    5.9   0.3     0.012        15      40      78 ..     333     371 ..     328     372 .. 0.84
   5 !   22.6   0.4   7.5e-08   9.5e-05       2      77 ..     406     481 ..     405     483 .. 0.84
   6 !   12.9   0.0   7.5e-05     0.096       4      76 ..     520     591 ..     518     594 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.39
                       NPCBM_assoc  2 epGetvtltltvtndgt 18
                                       pGe++t++++++n+g+
  gi|344209947|ref|YP_004786123.1| 43 APGEQKTIEISLVNSGE 59
                                      79************995 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0004
                       NPCBM_assoc  38 evspasaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                       + s +s+ +l++G ++++ +++++ ++a  G+y+ ++++++
  gi|344209947|ref|YP_004786123.1|  94 KNSKRSLGTLQAGPKTTVPFEISVDEDASSGTYDAQLRLNY 134
                                       56788999**************************9999876 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.091
                       NPCBM_assoc   5 etvtltltvtndgtaaatnvslslsl 30 
                                       +t t+ ++v n+g++aa++  ++l+ 
  gi|344209947|ref|YP_004786123.1| 181 STGTVAVSVENTGDSAARDAAVTLQS 206
                                       57899999999999999999998875 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.012
                       NPCBM_assoc  40 spasaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                       ++a + + +pG+  ++ v+ t++++a+   y + a++++
  gi|344209947|ref|YP_004786123.1| 333 TTAYVGEWEPGAVRTVRVDTTASPDAEDRSYALSANVQY 371
                                       344445889***************************987 PP

  == domain 5  score: 22.6 bits;  conditional E-value: 7.5e-08
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaa.slapGetveatvkVtppagaaaGdyevtakar 77 
                                       ++Ge+ +l +t+tn+gt+ ++nv ++ +  ++ t + ++ + a  +l++Get+ +++ V ++++a+aG ++  + ++
  gi|344209947|ref|YP_004786123.1| 406 QAGEDGSLSATLTNTGTRDVENVVIAWES-QQSTLSPKESQYAVgDLDAGETANFNFGVDVSNSAEAGARQFDFGVS 481
                                       79************************887.444545555555558***********************987666655 PP

  == domain 6  score: 12.9 bits;  conditional E-value: 7.5e-05
                       NPCBM_assoc   4 GetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtaka 76 
                                       G++ ++t+t+tn+ ++++t+++ ++ + +  + ++ + + +a+lapG++ ++ v+++++++a   +y++ +  
  gi|344209947|ref|YP_004786123.1| 520 GQDRSITFTITNTKNKTLTSIEGKAFVNDPLS-SSDDETFIAELAPGASETVSVQLSAGSDALDKTYPLNLDF 591
                                       899999**************999999977667.778999999*********************9999998765 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.8    0.0097        12       7      86 ..      39     125 ..      12     131 .. 0.66
   2 !    8.0   3.8    0.0028       3.6       8      84 ..     175     246 ..     153     250 .. 0.73
   3 !    9.7   4.8   0.00083       1.1       8      85 ..     289     361 ..     281     369 .. 0.78
   4 !   13.5   1.2   5.4e-05     0.069       9      86 ..     404     473 ..     393     477 .. 0.80
   5 !    9.4   0.2   0.00099       1.3       6      58 ..     513     582 ..     510     613 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0097
                             DUF11   7 ksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsv.sasqgtasaltsv.......gsLeagesatlsft 75 
                                         +v+pG++ t  + + N+g  ++ g + +  l   +++ ++ + s g+++a  sv       g+L+ag ++t+ f+
  gi|344209947|ref|YP_004786123.1|  39 DDTVAPGEQKTIEISLVNSGELDS-GSTRNPALNNEVTTAKGlTVSLGSGDAPISVknskrslGTLQAGPKTTVPFE 114
                                       447888888888888888888777.3333333322222221112224455555555555566699999999999999 PP

                             DUF11  76 vrvtrtaasga 86 
                                       ++v   a+sg+
  gi|344209947|ref|YP_004786123.1| 115 ISVDEDASSGT 125
                                       99988888775 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0028
                             DUF11   8 sevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas..qgtasaltsv.gsLeagesatlsftvrvtrt 81 
                                       s++r   t t+ + v Ntg ++a ++ v        +++s       + ++a++++  + e+ge +t++++v+ + +
  gi|344209947|ref|YP_004786123.1| 175 SNARVASTGTVAVSVENTGDSAARDAAV--------TLQSQNQDlaVSGGDATSRFvDEWEPGEVRTFNYRVSSAEA 243
                                       36778889***************55555........4444444443333456666679999********99999888 PP

                             DUF11  82 aas 84 
                                       a+ 
  gi|344209947|ref|YP_004786123.1| 244 AEP 246
                                       775 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00083
                             DUF11   8 sevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrtaas 84 
                                       s v+   t ty + ++Ntgp + n+  vt  + ++  +  +++s    s++ +vg+ e+g+ +t+++  ++++ a++
  gi|344209947|ref|YP_004786123.1| 289 SSVAVSNTGTYEVQLRNTGPLTVNDSSVTF-VSENADITFGKSS----STTAYVGEWEPGAVRTVRVDTTASPDAED 360
                                       468888999***********9998888885.6655555555555....4466779***************9999986 PP

                             DUF11  85 g 85 
                                        
  gi|344209947|ref|YP_004786123.1| 361 R 361
                                       5 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 5.4e-05
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrtaasg 85 
                                        +++G+  +   t+tNtg+++ ++vv+   + ++ ++ s + s      ++ vg+L age+a ++f v v+++a+ g
  gi|344209947|ref|YP_004786123.1| 404 SLQAGEDGSLSATLTNTGTRDVENVVIA--WESQQSTLSPKES------QYAVGDLDAGETANFNFGVDVSNSAEAG 472
                                       477888888889**********999995..4444444555555......7888********************9977 PP

                             DUF11  86 a 86 
                                       a
  gi|344209947|ref|YP_004786123.1| 473 A 473
                                       4 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.00099
                             DUF11   6 dksevrpGdtvtytltvtNtgpasa....ngvvvtDtl.............Paglayvsvsasqgtasal 58 
                                       ++s++  G+  + t t tNt ++++     ++ v+D+l             P + ++vsv+ s g+   +
  gi|344209947|ref|YP_004786123.1| 513 ENSTLGVGQDRSITFTITNTKNKTLtsieGKAFVNDPLsssddetfiaelaPGASETVSVQLSAGSDALD 582
                                       5666777887777778888888777446667889999988888888888888888888888886665554 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 ?    0.5   0.0      0.57   7.3e+02      60      78 ..      40      58 ..      31      67 .. 0.76
   2 ?   -0.7   0.1       1.3   1.7e+03      19      41 ..     177     199 ..     175     216 .. 0.71
   3 ?    4.6   0.2     0.029        37      44      91 ..     273     321 ..     257     326 .. 0.83
   4 !   13.4   0.0   5.2e-05     0.066      40      85 ..     383     428 ..     374     437 .. 0.87
   5 !    8.0   0.1    0.0025       3.3      17      75 ..     515     575 ..     498     580 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.57
                                      XXXXXXXXXXXXXXXXXXX CS
                               ASH 60 levqpgesvtltvtwtPte 78
                                       +v+pge+ t+++++ ++ 
  gi|344209947|ref|YP_004786123.1| 40 DTVAPGEQKTIEISLVNSG 58
                                      5889999999999887764 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                                       ---EEEEEEE-EEESS-SS--EE CS
                               ASH  19 vkvGssaerlLtveNpseepaev 41 
                                        +v s+ +  + veN+++ +a+ 
  gi|344209947|ref|YP_004786123.1| 177 ARVASTGTVAVSVENTGDSAARD 199
                                       578899999999***99988543 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.029
                                       EEEE--XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXX CS
                               ASH  44 skvpaaekgfsveetelevqpgesvtltvtwtPteegavr.evLqflvn 91 
                                         +p++e++fsv +++  v+   + t +v++ +t   +v+ + ++f+++
  gi|344209947|ref|YP_004786123.1| 273 AVTPDPEQQFSVVNSSSSVAVSNTGTYEVQLRNTGPLTVNdSSVTFVSE 321
                                       456888***************************9998865156777766 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 5.2e-05
                                       EEEEEEEE--XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               ASH  40 evkvskvpaaekgfsveetelevqpgesvtltvtwtPteegavrev 85 
                                        v +s +pa+e++f v++ e+ +q+ge+ +l+ t+t+t +  v  v
  gi|344209947|ref|YP_004786123.1| 383 DVRLSLSPAPEQNFDVSNVETSLQAGEDGSLSATLTNTGTRDVENV 428
                                       57889999*****************************987766665 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.0025
                                       -----EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXX...XXXXXXXXXXXXXXXX CS
                               ASH  17 gdvkvGssaerlLtveNpseepaevkvskvpaaekgfsveete...levqpgesvtltvtwt 75 
                                        +  vG+ ++ + t++N+++++++ + +k+   +  +s + +e    e++pg s t++v+++
  gi|344209947|ref|YP_004786123.1| 515 STLGVGQDRSITFTITNTKNKTLTSIEGKAF-VNDPLSSSDDEtfiAELAPGASETVSVQLS 575
                                       5678999999999*******99555555555.45555555555579999*******999976 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 ?    0.8   0.0      0.42   5.3e+02      29      41 ..      42      54 ..      40      65 .. 0.89
   2 ?    1.3   0.0      0.29   3.7e+02      29      47 ..     103     122 ..      99     144 .. 0.81
   3 !    9.6   0.2   0.00075      0.95      33      69 ..     152     191 ..     149     193 .. 0.86
   4 ?    5.4   0.1     0.015        19      36      67 ..     271     303 ..     266     306 .. 0.83
   5 ?   -3.6   0.0        10   1.3e+04      27      43 ..     403     419 ..     402     425 .. 0.82
   6 ?    0.2   0.0      0.62     8e+02      28      45 ..     450     467 ..     437     505 .. 0.73
   7 ?   -1.9   0.0       2.9   3.8e+03      28      44 ..     516     532 ..     513     540 .. 0.82
   8 ?    5.7   0.0     0.012        16      28      43 ..     561     576 ..     559     602 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.42
                                      E-TT-EEEEEEEE CS
                          Fn3-like 29 LapGesktvtftl 41
                                      +apGe+kt++++l
  gi|344209947|ref|YP_004786123.1| 42 VAPGEQKTIEISL 54
                                      89********987 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.29
                                       E-TT-EEEEEEEEEC.GGG- CS
                          Fn3-like  29 LapGesktvtftldr.kdls 47 
                                       L++G ++tv f++++ +d s
  gi|344209947|ref|YP_004786123.1| 103 LQAGPKTTVPFEISVdEDAS 122
                                       99***********9845555 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00075
                                       -EEEEEEEEECGG...G-EEETTTTEEE--SCEEEEEEES CS
                          Fn3-like  33 esktvtftldrkd...lsvwdeekqkwvvepGeytvlvgt 69 
                                       +++tv +++d++d   + v d +++++v+ +G++ v v +
  gi|344209947|ref|YP_004786123.1| 152 KTRTVDIEIDVTDdatFNVTDIDSNARVASTGTVAVSVEN 191
                                       699*******988677777888999***********9975 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.015
                                       EEEEEEEC.GGG-EEETTTTEEE--SCEEEEEE CS
                          Fn3-like  36 tvtftldr.kdlsvwdeekqkwvvepGeytvlv 67 
                                        v +t d+ +++sv++  ++  v  +G+y+v+ 
  gi|344209947|ref|YP_004786123.1| 271 SVAVTPDPeQQFSVVNSSSSVAVSNTGTYEVQL 303
                                       56666665489*******************986 PP

  == domain 5  score: -3.6 bits;  conditional E-value: 10
                                       EEE-TT-EEEEEEEEEC CS
                          Fn3-like  27 veLapGesktvtftldr 43 
                                       ++L++Ge   ++ tl+ 
  gi|344209947|ref|YP_004786123.1| 403 TSLQAGEDGSLSATLTN 419
                                       68999999998888875 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 0.62
                                       EE-TT-EEEEEEEEECGG CS
                          Fn3-like  28 eLapGesktvtftldrkd 45 
                                       +L +Ge++  +f +d+++
  gi|344209947|ref|YP_004786123.1| 450 DLDAGETANFNFGVDVSN 467
                                       69999*999999999876 PP

  == domain 7  score: -1.9 bits;  conditional E-value: 2.9
                                       EE-TT-EEEEEEEEECG CS
                          Fn3-like  28 eLapGesktvtftldrk 44 
                                       +L  G+ + +tft++ +
  gi|344209947|ref|YP_004786123.1| 516 TLGVGQDRSITFTITNT 532
                                       5778999******9964 PP

  == domain 8  score: 5.7 bits;  conditional E-value: 0.012
                                       EE-TT-EEEEEEEEEC CS
                          Fn3-like  28 eLapGesktvtftldr 43 
                                       eLapG+s+tv+++l++
  gi|344209947|ref|YP_004786123.1| 561 ELAPGASETVSVQLSA 576
                                       69***********986 PP

>> N_BRCA1_IG  Ig-like domain from next to BRCA1 gene
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       7.4   9.5e+03      52      70 ..      37      55 ..      19      62 .. 0.69
   2 ?    2.0   0.0      0.28   3.5e+02      29      89 ..      77     137 ..      64     148 .. 0.82
   3 ?   -1.5   0.0       3.4   4.4e+03      20      69 ..     189     238 ..     184     254 .. 0.60
   4 !    7.7   0.1    0.0045       5.7      18      77 ..     301     361 ..     284     376 .. 0.78
   5 ?    4.1   0.0     0.061        78       8      69 ..     405     463 ..     400     494 .. 0.74
   6 ?    3.0   0.0      0.13   1.7e+02      18      72 ..     527     577 ..     512     602 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7.4
                        N_BRCA1_IG 52 vsvpavapgeevevsvelk 70
                                      ++ + vapge+ +++++l+
  gi|344209947|ref|YP_004786123.1| 37 LEDDTVAPGEQKTIEISLV 55
                                      4456677777777776654 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.28
                        N_BRCA1_IG  29 pagtklvfvgGdkmgsasaeessvsvpavapgeevevsvelkaPskpgryisywrlatedg 89 
                                        +g ++ + +Gd+ +s++++++s+ + ++ p+ +v +++++   ++ g+y ++ rl  ++ 
  gi|344209947|ref|YP_004786123.1|  77 AKGLTVSLGSGDAPISVKNSKRSLGTLQAGPKTTVPFEISVDEDASSGTYDAQLRLNYKHT 137
                                       46778888888888765767888889999999999999999999***********988765 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.4
                        N_BRCA1_IG  20 lrNtGseaW.pagtklvfvgGdkmgsasaeessvsvpavapgeevevsvel 69 
                                       ++NtG++a  +a ++l+ ++ d   ++  +++s  v++ +pge+ +++ ++
  gi|344209947|ref|YP_004786123.1| 189 VENTGDSAArDAAVTLQSQNQDLA-VSGGDATSRFVDEWEPGEVRTFNYRV 238
                                       678888775233344443333333.32334455667888888877776655 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0045
                        N_BRCA1_IG  18 WrlrNtGseaWpagtklvfvgGdkmg.sasaeessvsvpavapgeevevsvelka.Pskpgr 77 
                                        +lrNtG+ +  +++++ fv++++ +  +++++++  v + +pg + +v v+ +a P+ + r
  gi|344209947|ref|YP_004786123.1| 301 VQLRNTGPLTV-NDSSVTFVSENADItFGKSSSTTAYVGEWEPGAVRTVRVDTTAsPDAEDR 361
                                       579******96.999******8888745677788888**************66651665554 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.061
                        N_BRCA1_IG   8 vppgteftktWrlrNtGseaWpagtklvfvgGdkmgsasaeessvsvpavapgeevevsvel 69 
                                       +++g+    + +l+NtG+++  +++ +++ + ++    s +es++ v ++ +ge+++++  +
  gi|344209947|ref|YP_004786123.1| 405 LQAGEDGSLSATLTNTGTRDV-ENVVIAWESQQST--LSPKESQYAVGDLDAGETANFNFGV 463
                                       55555555566899*****96.8888888886666..568899************9997644 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.13
                        N_BRCA1_IG  18 WrlrNtGseaWpagtklvfvgGdkmgs..asaeessvsvpavapgeevevsvelkaP 72 
                                       ++++Nt      ++ +l  ++G+++++   s+++++  + ++apg + +vsv+l a 
  gi|344209947|ref|YP_004786123.1| 527 FTITNT------KNKTLTSIEGKAFVNdpLSSSDDETFIAELAPGASETVSVQLSAG 577
                                       555555......3445666666666633646677888899************99886 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 ?   -0.1   0.0      0.82     1e+03      56      75 ..      36      55 ..      24      61 .. 0.82
   2 ?   -2.9   0.0         6   7.7e+03      54      75 ..      95     116 ..      71     119 .. 0.76
   3 ?   -0.2   0.0      0.84   1.1e+03       8      38 ..     174     204 ..     171     239 .. 0.88
   4 ?    5.8   0.0     0.012        15       7      73 ..     401     462 ..     398     473 .. 0.88
   5 !    6.1   0.0    0.0096        12       3      74 ..     508     574 ..     507     580 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.82
                                      EEEEEEE-TTEEEEEEEEE- CS
                       Transglut_C 56 ksleltLePkeeksvrlkil 75
                                      + +  t+ P+e+k+++++++
  gi|344209947|ref|YP_004786123.1| 36 TLEDDTVAPGEQKTIEISLV 55
                                      567889********999874 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6
                                       EEEEEEEEE-TTEEEEEEEEE- CS
                       Transglut_C  54 kkksleltLePkeeksvrlkil 75 
                                       ++k   +tL+++ + +v+++i+
  gi|344209947|ref|YP_004786123.1|  95 NSKRSLGTLQAGPKTTVPFEIS 116
                                       4556678899999999998886 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.84
                                       SSCEBTTSEEEEEEEEEE-SSS-BEEEEEEE CS
                       Transglut_C   8 lesavlgqdltvsvllkNplseelkdvklnl 38 
                                        ++a++ +  tv v++ N+ +++ +d+ + l
  gi|344209947|ref|YP_004786123.1| 174 DSNARVASTGTVAVSVENTGDSAARDAAVTL 204
                                       5789999999********9999988876665 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.012
                                       ESSCEBTTSEEEEEEEEEE-SSS-BEEEEEEEEEEEEECTTTEEEEEEEEEEEEEE-TTEEEEEEEE CS
                       Transglut_C   7 vlesavlgqdltvsvllkNplseelkdvklnlcaqtveynGvlaaefkkksleltLePkeeksvrlk 73 
                                       v  s++ g d ++s++l+N+ ++ +++     ++++ e++  + + ++++++ ++L+++e++++ + 
  gi|344209947|ref|YP_004786123.1| 401 VETSLQAGEDGSLSATLTNTGTRDVEN-----VVIAWESQQSTLSPKESQYAVGDLDAGETANFNFG 462
                                       66678899****************999.....788889999999999*************9999876 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.0096
                                       EEEEESS.CEBTTSEEEEEEEEEE-SSS-BEEEEEEEEEEEEECTTTEEEEEEEEEEEEEE-TTEEEEEEEEE CS
                       Transglut_C   3 lkievle.savlgqdltvsvllkNplseelkdvklnlcaqtveynGvlaaefkkksleltLePkeeksvrlki 74 
                                       ++iev + ++ +gqd +++ +++N+  ++l+ ++    + +   + +  +++  +++  +L P+++++v++++
  gi|344209947|ref|YP_004786123.1| 508 FDIEVENsTLGVGQDRSITFTITNTKNKTLTSIE----GKAFVNDPL--SSSDDETFIAELAPGASETVSVQL 574
                                       678886415789*************999988755....333333333..467777788888888888777766 PP

>> DUF4832  Domain of unknown function (DUF4832)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0089        11     160     203 ..      95     138 ..      36     143 .. 0.75
   2 ?    2.6   0.0      0.08     1e+02     114     191 ..     173     249 ..     168     267 .. 0.65
   3 ?    4.7   0.1     0.018        23     111     203 ..     286     375 ..     281     387 .. 0.77
   4 ?    1.5   0.0      0.18   2.3e+02     114     189 ..     401     472 ..     396     492 .. 0.65
   5 ?   -0.1   0.0      0.55     7e+02     112     204 ..     495     581 ..     482     603 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0089
                           DUF4832 160 kldadprkwlpgttttitiklklpselakGkykvyLnlpdpseg 203
                                       +++ ++ +++ g +tt+  +++++++ ++G+y+  L+l  ++++
  gi|344209947|ref|YP_004786123.1|  95 NSKRSLGTLQAGPKTTVPFEISVDEDASSGTYDAQLRLNYKHTS 138
                                       36777888999999************************999876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.08
                           DUF4832 114 lskkvkaggtlsleltlkNeGfAalynerkvelvlrdeegeekyklkldadprkwlpgttttitiklklpselakGk 190
                                       ++++++ ++t ++ ++++N+G +a+ ++  v l  ++++  ++   +++  + +w pg+  t++  ++  +  + ++
  gi|344209947|ref|YP_004786123.1| 173 IDSNARVASTGTVAVSVENTGDSAA-RDAAVTLQSQNQDLAVSGGDATSRFVDEWEPGEVRTFNYRVSSAEAAEPES 248
                                       4555666799999********8864.444455555555555544456888899999999777666655555555555 PP

                           DUF4832 191 y 191
                                       y
  gi|344209947|ref|YP_004786123.1| 249 Y 249
                                       5 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.018
                           DUF4832 111 ssslskkvkaggtlsleltlkNeGfAalynerkvelvlrdeegeekyklkldadprkwlpgttttitiklklpsela 187
                                       +ss   +v+ ++t ++e++l+N+G    +n+ +v +v ++ + +   +  ++a + +w pg   t+ ++++   + +
  gi|344209947|ref|YP_004786123.1| 286 NSSS--SVAVSNTGTYEVQLRNTGPL-TVNDSSVTFVSENADITFGKSSSTTAYVGEWEPGAVRTVRVDTTASPDAE 359
                                       4444..44456999**********64.568999999998888887767789999*******9999999966666888 PP

                           DUF4832 188 kGkykvyLnlpdpseg 203
                                       + +y ++ n++ ++++
  gi|344209947|ref|YP_004786123.1| 360 DRSYALSANVQYEDQE 375
                                       8888888888777665 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.18
                           DUF4832 114 lskkvkaggtlsleltlkNeGfAalynerkvelvlrdeegee..kyklkldadprkwlpgttttitiklklpselak 188
                                       ++++ +ag++ sl+ tl+N+G         ve v++  e+++   +  ++++ + ++  g+t +++  +++ ++ ++
  gi|344209947|ref|YP_004786123.1| 401 VETSLQAGEDGSLSATLTNTGTRD------VENVVIAWESQQstLSPKESQYAVGDLDAGETANFNFGVDVSNSAEA 471
                                       56677889999*********9743......33333333333311233347788888888887777777777777777 PP

                           DUF4832 189 G 189
                                       G
  gi|344209947|ref|YP_004786123.1| 472 G 472
                                       7 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.55
                           DUF4832 112 sslskkvkaggtlsleltlkNeGfAalynerkvelvlrdeegeekyklkldadprkwlpgttttitiklklpselak 188
                                        +++++v+ g++ +++++++N+    + ++r++ ++++++++++ ++++ +a +++ l++++ +  i     +ela 
  gi|344209947|ref|YP_004786123.1| 495 LEVRSQVA-GSQDEFDIEVENSTL-GVGQDRSITFTITNTKNKTLTSIEGKAFVNDPLSSSDDETFI-----AELAP 564
                                       55655554.788888888888754.467889999999999998855555444444444433333222.....23333 PP

                           DUF4832 189 G.kykvyLnlpdpsegl 204
                                       G + +v+++l+ +s+ l
  gi|344209947|ref|YP_004786123.1| 565 GaSETVSVQLSAGSDAL 581
                                       43444444444444443 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 ?   11.9   0.0   0.00011      0.14      52     124 ..     525     602 ..     518     607 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                       FAS_meander  52 qlveieeadspektvvtvke....ake.sgelkkaveiklsedkeIsvtlieertaegesvpLeleFeYkpetglap 123
                                        +++i+++++++ t+++ k+    + + s++++ ++e+   +++++sv+l   ++a +++ pL+l+F+Y+   g  +
  gi|344209947|ref|YP_004786123.1| 525 ITFTITNTKNKTLTSIEGKAfvndPLSsSDDETFIAELAPGASETVSVQLSAGSDALDKTYPLNLDFQYETPDGEKR 601
                                       55667766666656555443333333404455566899999999*************************98776665 PP

                       FAS_meander 124 I 124
                                       +
  gi|344209947|ref|YP_004786123.1| 602 V 602
                                       5 PP

>> AP3B1_C  Clathrin-adaptor complex-3 beta-1 subunit C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       8.2     1e+04      91     100 ..      49      58 ..      16      82 .. 0.64
   2 ?   -2.1   0.0       3.2     4e+03      91     104 ..     184     197 ..     153     214 .. 0.56
   3 ?   11.6   0.0   0.00019      0.24      94     147 ..     415     469 ..     410     470 .. 0.91
   4 ?    1.8   0.1       0.2   2.6e+02      91     138 ..     524     571 ..     520     575 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 8.2
                           AP3B1_C  91 sveltltNts 100
                                       ++e+ l N++
  gi|344209947|ref|YP_004786123.1|  49 TIEISLVNSG 58 
                                       4444444444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.2
                           AP3B1_C  91 sveltltNtsdsei 104
                                       +v +  +Nt+ds +
  gi|344209947|ref|YP_004786123.1| 184 TVAVSVENTGDSAA 197
                                       34444555555555 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00019
                           AP3B1_C  94 ltltNtsdseiknihigekklqagmeihefa.eiesLepgasttvvlGidFnDst 147
                                        tltNt++++++n+ i  +++q+ ++ +e++  +  L++g++++   G+d ++s 
  gi|344209947|ref|YP_004786123.1| 415 ATLTNTGTRDVENVVIAWESQQSTLSPKESQyAVGDLDAGETANFNFGVDVSNSA 469
                                       69************************9999846999**************99985 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.2
                           AP3B1_C  91 sveltltNtsdseiknihigekklqagmeihefaeiesLepgasttvv 138
                                       s+  t+tNt +++++ i+ +    +   +  + + i++L+pgas tv+
  gi|344209947|ref|YP_004786123.1| 524 SITFTITNTKNKTLTSIEGKAFVNDPLSSSDDETFIAELAPGASETVS 571
                                       79999************9776644444555667778888888887776 PP

>> BppU_N  BppU N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1    0.0001      0.13       3      58 ..     126     182 ..     124     242 .. 0.80
   2 ?   -1.9   0.1       1.9   2.5e+03     101     123 ..     511     533 ..     496     551 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                            BppU_N   3 kdieldltkdnnkvisqgiqfrsgDtgtaklnikl.tkngspldLtgltarlefkke 58 
                                       +d++l+l+ + +++is+g+ +r +D++t++++i++ + ++  ++ t++  + ++ ++
  gi|344209947|ref|YP_004786123.1| 126 YDAQLRLNYKHTSYISEGTGARDEDRKTRTVDIEIdVTDDATFNVTDIDSNARVAST 182
                                       678899999999********************************9996555555454 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.9
                            BppU_N 101 yidkndeslittgrFtFeikksl 123
                                       ++++++  + + +++tF+i +  
  gi|344209947|ref|YP_004786123.1| 511 EVENSTLGVGQDRSITFTITNTK 533
                                       44444455555555555554433 PP

>> Alpha_adaptinC2  Adaptin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2       5.3   6.8e+03      20      42 ..     291     313 ..     279     332 .. 0.73
   2 ?    2.8   0.0      0.11   1.4e+02      22      61 ..     407     443 ..     394     493 .. 0.73
   3 ?    8.6   0.0    0.0017       2.2       9      97 ..     506     597 ..     499     609 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.3
                                       TTSTTEEEEEEEEEE-SSS-EEE CS
                   Alpha_adaptinC2  20 perpgqiritlsftNkssqpisn 42 
                                          ++++++++++ N+ + ++++
  gi|344209947|ref|YP_004786123.1| 291 VAVSNTGTYEVQLRNTGPLTVND 313
                                       45667788888888888877776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.11
                                       STTEEEEEEEEEE-SSS-EEEEEEEEEEBTTCEEEEEEES CS
                   Alpha_adaptinC2  22 rpgqiritlsftNkssqpisnfsfqaavpkslklqlqpps 61 
                                        ++++ + +++tN+ + +++n+++    ++s    l+p  
  gi|344209947|ref|YP_004786123.1| 407 AGEDGSLSATLTNTGTRDVENVVIAWESQQST---LSPKE 443
                                       567899****************9986554443...55544 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0017
                                       TTEEEEEEEEETTSTTEEEEEEEEEE-SSS-EEEEEEEEEEBTTCEEEEEEES-S-B-TTCEEEEEEEEEEES...C CS
                   Alpha_adaptinC2   9 ddlqIgfkfekperpgqiritlsftNkssqpisnfsfqaavpkslklqlqppsstvlppnpggqitqvllien...p 82 
                                       d++ I+++ +  + +++  it ++tN+ +++++++  +a v+++l  +  +    +l+p  g++ t ++ +++   +
  gi|344209947|ref|YP_004786123.1| 506 DEFDIEVENSTLGVGQDRSITFTITNTKNKTLTSIEGKAFVNDPLSSSDDETFIAELAP--GASETVSVQLSAgsdA 580
                                       5666666666666777889**************************88888888888888..8888888888877899 PP

                                       TTS-EEEEEEEEEE..C CS
                   Alpha_adaptinC2  83 skkplrmrlrisyk..v 97 
                                        +k+ +++l+++y+  +
  gi|344209947|ref|YP_004786123.1| 581 LDKTYPLNLDFQYEtpD 597
                                       99999*******99533 PP

>> MBG  MBG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.7       2.2   2.9e+03      51      63 ..     118     130 ..      61     172 .. 0.55
   2 ?   -1.9   2.7         4   5.2e+03      52      67 ..     178     193 ..     123     245 .. 0.54
   3 ?   14.0   0.4   4.4e-05     0.056      38      85 ..     279     333 ..     255     337 .. 0.76
   4 ?    0.1   0.2      0.98   1.3e+03       3      39 ..     380     420 ..     364     470 .. 0.71
   5 ?    0.5   0.4      0.75   9.6e+02      14      80 ..     530     591 ..     519     603 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.2
                               MBG  51 taptnvGtYtvkL 63 
                                       ++    GtY+ +L
  gi|344209947|ref|YP_004786123.1| 118 DEDASSGTYDAQL 130
                                       3444556665543 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4
                               MBG  52 aptnvGtYtvkLtaag 67 
                                            Gt  v+  ++g
  gi|344209947|ref|YP_004786123.1| 178 RVASTGTVAVSVENTG 193
                                       2233333333333333 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 4.4e-05
                               MBG  38 agDfewktadgnttaptnvGtYtvkLtaaglaklkaa.......npNytf.tdakt 85 
                                        + f++++++++  a  n GtY+v+L ++g  ++++        n+++tf ++++t
  gi|344209947|ref|YP_004786123.1| 279 EQQFSVVNSSSS-VAVSNTGTYEVQLRNTGPLTVNDSsvtfvseNADITFgKSSST 333
                                       578888777777.899********************99999977777777433333 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.98
                               MBG   3 tYdGqaatldd...snsnnkitti.ttngkdatktytltag 39 
                                       tYd+   +l++   +n++ +++ + +++g+d++ + tlt++
  gi|344209947|ref|YP_004786123.1| 380 TYDDVRLSLSPapeQNFDVSNVETsLQAGEDGSLSATLTNT 420
                                       55555555443111233222222257777777777777754 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.75
                               MBG  14 snsnnkittittngkdatktytlta.gDfewktadgnttaptnvGtYtvkLtaaglaklkaanp.Nytf 80 
                                       +n++ ++t + ++gk + ++  l++ +D ++  a     ap    t  v+L+ ag ++l++  p N++f
  gi|344209947|ref|YP_004786123.1| 530 TNTK-NKTLTSIEGKAFVNDP-LSSsDDETF-IA-E--LAPGASETVSVQLS-AGSDALDKTYPlNLDF 591
                                       2222.2333466777666666.665144444.33.2..25777777777777.6777776663335554 PP

>> Pilin  Pilin (bacterial filament)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.85   1.1e+03      52      81 ..      17      53 ..       2      97 .. 0.69
   2 ?    3.7   0.8     0.094   1.2e+02      36      86 ..     152     210 ..     128     225 .. 0.70
   3 ?    1.5   0.3      0.45   5.7e+02      47      91 ..     282     327 ..     254     356 .. 0.69
   4 ?    7.7   0.1     0.005       6.5      26      85 ..     375     437 ..     362     457 .. 0.69
   5 ?    5.2   0.1     0.032        41      37      79 ..     502     546 ..     469     582 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.85
                                      ECCCEEC.......CEEEEEECCCSSTCCTTEEEEEE CS
                             Pilin 52 tveaatg.......gtitatfggnaaakikgktltlt 81
                                      tv+++t+         i at+   ++a+  +kt++++
  gi|344209947|ref|YP_004786123.1| 17 TVTSGTAtaavvgsPDIAATLEDDTVAPGEQKTIEIS 53
                                      4444333445555566777777777766666666654 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.094
                                       C.......TTBSTCSCCTC.EEEEECCCEECCEEEEEECCCSSTCCTTEEEEEEEECTT CS
                             Pilin  36 d.......iGlasstaicg.visvtveaatggtitatfggnaaakikgktltltrtads 86 
                                       +       i ++++++ +   i++++  a++gt+ + + +++ +++  + +tl+ ++++
  gi|344209947|ref|YP_004786123.1| 152 KtrtvdieIDVTDDATFNVtDIDSNARVASTGTVAVSVENTGDSAARDAAVTLQSQNQD 210
                                       23333344666666665445555555566669999999999999999999999998774 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.45
                                       C...EEEEECCCEECCEEEEEECCCSSTCCTTEEEEEEEECTTSCEEE CS
                             Pilin  47 g...visvtveaatggtitatfggnaaakikgktltltrtadsgsgkW 91 
                                           ++s++v+ +++gt ++++++++  +++   +t++  ++   +++
  gi|344209947|ref|YP_004786123.1| 282 FsvvNSSSSVAVSNTGTYEVQLRNTGPLTVNDSSVTFVSENA--DITF 327
                                       245666777777778999999999998889999999988855..2333 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.005
                                       CSSSCTCCCCCTTBSTCSCCTC..EEEEECCCEEC..CEEEEEECCCSSTCCTTEEEEEEEECT CS
                             Pilin  26 egktpttaaadiGlasstaicg..visvtveaatg..gtitatfggnaaakikgktltltrtad 85 
                                       eg t+t ++  + l+++ ++ +  v++v+ + ++g  g+++at+++++  ++ + ++ +  +++
  gi|344209947|ref|YP_004786123.1| 375 EGDTSTYDDVRLSLSPAPEQ-NfdVSNVETSLQAGedGSLSATLTNTGTRDVENVVIAWESQQS 437
                                       34444444444555554443.2365555555544466************99********98866 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.032
                                       TTBSTCSCCTCEEEEECCCEECCEEEEEECCCSSTC...CTTEEEE CS
                             Pilin  37 iGlasstaicgvisvtveaatggtitatfggnaaak...ikgktlt 79 
                                       +G ++  +i +v+++t + +++ +it+t++++++++   i gk ++
  gi|344209947|ref|YP_004786123.1| 502 AGSQDEFDI-EVENSTLGVGQDRSITFTITNTKNKTltsIEGKAFV 546
                                       444444444.2666666666669*********99888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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):              14  [number of targets reported over threshold]
# CPU time: 0.74u 0.33s 00:00:01.07 Elapsed: 00:00:00.51
# Mc/sec: 3814.69
//
Query:       gi|344209948|ref|YP_004786124.1|  [L=830]
Description: hypothetical protein HAH_5006 [Haloarcula hispanica ATCC 33960]
Scores for 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   96.0  26.0    4.7e-20   71.8   1.7    2.7  2  MMPL            MMPL family
    8.5e-08   30.8  12.8    5.8e-07   28.0   5.9    2.4  2  Patched         Patched family
    1.2e-06   28.4   4.4    0.00032   20.6   0.5    2.7  2  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ


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 !   71.8   1.7   7.9e-24   4.7e-20      11     301 ..      98     391 ..      88     402 .. 0.83
   2 !   28.8  16.8   9.3e-11   5.6e-07      85     299 ..     601     807 ..     479     824 .. 0.74

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 7.9e-24
                              MMPL  11 kamdrleaafpe.eadsdkiivvvlaegdealgsaaaeaavdelvdelkkdt.khvgevsdf...........lsdp 74 
                                       ka  rle++ ++ + ++++++++v     ++l+   +++++ e++d +++ + ++++++  +           ls++
  gi|344209948|ref|YP_004786124.1|  98 KAQHRLEQRESQdVVGTTSVAQAVA----QTLN--PDAETLPEQIDTVEAASqTEIKSATRTtlerqpavaglLSND 168
                                       4444444444443333333333333....4443..477777777777755430344444444777777777764555 PP

                              MMPL  75 d.vaaafvSkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlkliev 150
                                          ++   S+  ++++  v+   +++ te+ + ++ i++ +e  +   + +++v G++++ a+l+ + + +l+l++ 
  gi|344209948|ref|YP_004786124.1| 169 LnREEPSASATLTTVTHEVSGVSSSAGTEGSSPLTPIQQEAEFIVSSVDGDISVFGSGLISAELNSVISDSLGLVVP 245
                                       4588888888899999999999999**************************************************** PP

                              MMPL 151 vtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyr 227
                                       +++v+il  L+i+yr +   l+ l++ ++ ++ ++g+ + +a + + ++  +v++l    l+a+G+D+ +  v Ryr
  gi|344209948|ref|YP_004786124.1| 246 AAVVLILFFLIIAYRDPFDLLIGLVSLAMAIIWTFGF-MGWASIPFTQMLITVPPL----LLAIGIDFGIHAVNRYR 317
                                       *********************9999999999999999.99****999999999997....6899************* PP

                              MMPL 228 eelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvl 301
                                       ee+ +  +   a+ +a  +  ++ ++ + t ++ +++  +++l+ ++ +G+++++G+++++li   +lP++  +
  gi|344209948|ref|YP_004786124.1| 318 EERIEDVEPTPAMRTATDQLLPAFFIVTGTTVLGFAANGTSQLGPIRDLGFVASVGIIFTFLIFGIFLPSFKHF 391
                                       ***************************************************************99999987665 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 9.3e-11
                              MMPL  85 gkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLl 161
                                            + + +    +s++++++v++ ++av++      +++  tG+ ++l+ ++d+ ++++ +  +++++  ++ L+
  gi|344209948|ref|YP_004786124.1| 601 YAR--TRIVYS--VESDASQQEVTDDTRAVADEF---RMEATATGSVVVLKAVSDVIAESAYISLALAILASAAFLF 670
                                       433..334444..234455555555555544444...4666677777777776666666666665555555555555 PP

                              MMPL 162 ivy....rSl...vaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreela 231
                                        +y    r +   +a l+p+l  +  l+a++         l +  +  +   +  ++i+ G+DY   Lv R+ ee +
  gi|344209948|ref|YP_004786124.1| 671 FAYwlleRRPglgAANLVPILLTIAALAATMRY-------LDIPFNVLTG-TTLSIGIGLGIDYSAHLVHRFSEEYR 739
                                       555222255433345555555555555555554.......5677766655.45679********************* PP

                              MMPL 232 agedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAll 299
                                             ea+   v++tg++ +++ +t    +  Lv+a +p+l+q+G+ ia++vl ++ +++ +lP  +
  gi|344209948|ref|YP_004786124.1| 740 GDTGLLEALDISVRGTGGALAGSMVTTTSGTGVLVLAVVPILGQFGLLIAVSVLYSFVASILVLPTSI 807
                                       ***999****************************************************9999997644 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   5.9   9.7e-11   5.8e-07     254     372 ..     262     381 ..     247     398 .. 0.89
   2 !    6.5   0.6   0.00032       1.9     719     776 ..     718     779 ..     707     811 .. 0.62

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 9.7e-11
                           Patched 254 pilailgvlspvlAivsslGlllwlGfrfnsivtvtPFLvLaiGvDdmflmvaawkrteakls.vkkrigealseag 329
                                       p+  ++g++s  +Ai+  +G++ w  ++f +++  +P L LaiG+D    +v+++++ + ++      +  a  +  
  gi|344209948|ref|YP_004786124.1| 262 PFDLLIGLVSLAMAIIWTFGFMGWASIPFTQMLITVPPLLLAIGIDFGIHAVNRYREERIEDVePTPAMRTATDQLL 338
                                       556689****************************************887788887777666554667899999999* PP

                           Patched 330 vaitiTslTdvlsFgiGaittlpaiqlFciytavailfdfiYq 372
                                       +a +i + T vl F++  +++l  i     +++v i+f+f+  
  gi|344209948|ref|YP_004786124.1| 339 PAFFIVTGTTVLGFAANGTSQLGPIRDLGFVASVGIIFTFLIF 381
                                       ****************************************754 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00032
                           Patched 719 msiGfsvdlsaHiayafvrsekd......dakeRvvealealgwPvvqgalSTilgvlvLlfvd 776
                                       + iG  +d+saH  ++f++++          +  v+ +  al+  +v   + T  gvlvL++v+
  gi|344209948|ref|YP_004786124.1| 718 IGIGLGIDYSAHLVHRFSEEYRGdtglleALDISVRGTGGALAGSMVTTTSGT--GVLVLAVVP 779
                                       56899*************99875343333233344444455555555555554..566666666 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 !   20.6   0.5   5.4e-08   0.00032      10     131 ..     266     387 ..     265     406 .. 0.84
   2 !    8.4   0.2   0.00029       1.7       3     129 ..     677     803 ..     675     821 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.4e-08
                                       HHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCH.HHHHHHHHHHHCCCC CS
                    Sterol-sensing  10 lagviivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrslde.seriaealgevgpsi 85 
                                       l g++ ++++++ ++g++ +  +++t + +  +P l+la+g+d     v+ +++   +  e    +  a  +  p+ 
  gi|344209948|ref|YP_004786124.1| 266 LIGLVSLAMAIIWTFGFMGWASIPFTQMLI-TVPPLLLAIGIDFGIHAVNRYREERIEDVEpTPAMRTATDQLLPAF 341
                                       5689999***********************.677799******877777777766555444588899999999**** PP

                                       HHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHH CS
                    Sterol-sensing  86 lltsltellalllgaltdvpavqeFclfaavavlvdFllqitfFva 131
                                       ++ + t +l ++    +++  ++   + a v+++++Fl+  +f  +
  gi|344209948|ref|YP_004786124.1| 342 FIVTGTTVLGFAANGTSQLGPIRDLGFVASVGIIFTFLIFGIFLPS 387
                                       ************888**********************998777555 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00029
                                       HHHHHHHHHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCH.HHHHHHHH CS
                    Sterol-sensing   3 kskfgLglagviivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrslde.seriaeal 78 
                                       + + gLg+a ++ +ll++a+    + yl+++++ ++      + +  g+d +  lv+ + +  r  +   e +   +
  gi|344209948|ref|YP_004786124.1| 677 ERRPGLGAANLVPILLTIAALAATMRYLDIPFNVLTG-TTLSIGIGLGIDYSAHLVHRFSEEYRGDTGlLEALDISV 752
                                       56899******************************99.566699999***********9987776655589999999 PP

                                       HHHCCCCHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHH CS
                    Sterol-sensing  79 gevgpsilltsltellalllgaltdvpavqeFclfaavavlvdFllqitfF 129
                                       + +g ++  +++t +    + +l +vp + +F l  av+vl +F+  i++ 
  gi|344209948|ref|YP_004786124.1| 753 RGTGGALAGSMVTTTSGTGVLVLAVVPILGQFGLLIAVSVLYSFVASILVL 803
                                       999999998888888888877788*********************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (830 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); 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):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 5788.36
//
Query:       gi|344209949|ref|YP_004786125.1|  [L=198]
Description: transcription regulator [Haloarcula hispanica ATCC 33960]
Scores for complete 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   50.1   0.0    4.2e-13   49.5   0.0    1.3  1  TetR_C_6   BetI-type transcriptional repressor, C-terminal
    1.4e-10   40.8   0.6    5.4e-10   38.9   0.1    2.1  2  TetR_N     Bacterial regulatory proteins, tetR family
    0.00025   21.3   0.3    0.00056   20.1   0.2    1.7  1  TetR_C_24  Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
      0.016   15.3   0.2      0.032   14.3   0.2    1.7  1  TetR_C_27  Tetracyclin repressor-like, C-terminal domain
      0.018   15.0   0.2      0.028   14.5   0.2    1.2  1  TetR_C_7   AefR-like transcriptional repressor, C-terminal do
       0.04   14.0   0.4      0.089   12.9   0.0    1.8  2  TetR_C_29  Tetracyclin repressor-like, C-terminal domain
      0.053   13.5   0.2       0.17   11.9   0.1    1.8  1  TetR_C_36  Tetracyclin repressor-like, C-terminal domain
      0.055   13.2   0.0       0.15   11.8   0.0    1.7  1  HTH_38     Helix-turn-helix domain
      0.083   13.5   0.1       0.21   12.2   0.0    1.7  3  TetR_C_37  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 !   49.5   0.0   2.1e-16   4.2e-13       1     114 [.      81     196 ..      81     197 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 2.1e-16
                                       HHHHHHHHHHCCST..HSHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCTTSTHHHH CS
                          TetR_C_6   1 prerlraileallp..ldqerraelavwlafwaeaardpelaelqrenyarlrsnlrallaelaegglradadaeaa 75 
                                       p+e l++i+++llp  l++e+r+  +v + +  +a+ ++ ++e++ e + rl + +  +++++ e+ +++d+d+ ++
  gi|344209949|ref|YP_004786125.1|  81 PKEDLHHIITTLLPcqLTEEKRQLHSVLVTLSPQALDQEVFREQFTEIDIRLTAIIEKTVRRGIEADVFRDVDPTHM 157
                                       7899***********9************************************************************* PP

                                       HHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHHT CS
                          TetR_C_6  76 AerlaAlidGLwlraalapeeldaeraralvrrhldall 114
                                       Ae + A+i G   + ++ ++e++  +a a +  ++d++l
  gi|344209949|ref|YP_004786125.1| 158 AEHILAMIKGTMYSRLTTNREAATGAAKASLFSYIDSHL 196
                                       ***********99999999************99999876 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 !   38.9   0.1   2.7e-13   5.4e-10       1      45 [.      15      59 ..      15      61 .. 0.97
   2 ?   -0.6   0.0      0.61   1.2e+03      25      36 ..     180     191 ..     178     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 2.7e-13
                                      HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHH CS
                            TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLle 45
                                      I++a+ + +   Gy++++++ IA+++  +k+++Y+y++sK++Ll 
  gi|344209949|ref|YP_004786125.1| 15 IMHATHRALVNSGYAELSISLIADELDKAKSTIYHYYDSKDDLLI 59
                                      899****************************************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.61
                                       HHTSSHHHHHHH CS
                            TetR_N  25 rAGvskgalYry 36 
                                       + G +k++l+ y
  gi|344209949|ref|YP_004786125.1| 180 ATGAAKASLFSY 191
                                       789999999987 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 !   20.1   0.2   2.8e-07   0.00056      25      87 ..     106     168 ..      78     170 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.8e-07
                                       HHHHHHHHGGGS-HHH.HHHHHHHHHHHHHHHHHHHHHHHHTTSB-SS-HHHHHHHHHHHHHCH CS
                         TetR_C_24  25 eaavllrelraLspeh.reeiralrreyerllrdlieeGvaagefedldpklaalailgmlnwv 87 
                                       +++v+l+  +aL++e  re++++   ++++++++ +++G++a +f+d+dp+ +a  il m+ ++
  gi|344209949|ref|YP_004786125.1| 106 SVLVTLSP-QALDQEVfREQFTEIDIRLTAIIEKTVRRGIEADVFRDVDPTHMAEHILAMIKGT 168
                                       33444444.66666653789999999**********************************9876 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 ?   14.3   0.2   1.6e-05     0.032      47      82 ..     131     166 ..      81     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHHHHHCT-STT--HHHHHHHHHHHSG CS
                         TetR_C_27  47 eleeqlaeIireGvaaGeFkaadpeaaaravfdata 82 
                                       +l++ +++ +r+G++a+ F+  dp  +a+ +++++ 
  gi|344209949|ref|YP_004786125.1| 131 RLTAIIEKTVRRGIEADVFRDVDPTHMAEHILAMIK 166
                                       566777777899*******************99986 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 ?   14.5   0.2   1.4e-05     0.028       1      96 [.      83     180 ..      83     189 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHT..-HHHHCCHHHT.T----HHHHHHHHHHHHTTSB-SS-HHHHHH CS
                          TetR_C_7   1 eqLtalgrallalllspevlalaRlviaeaer..fPelarafyeagpgrveealaayLeaavaaGrLridDpelAAe 75 
                                       e+L+ + ++ll + l +e ++l+ ++++ +++  + e+ r+ +++   r+ + +++ +++  +a   r  Dp   Ae
  gi|344209949|ref|YP_004786125.1|  83 EDLHHIITTLLPCQLTEEKRQLHSVLVTLSPQalDQEVFREQFTEIDIRLTAIIEKTVRRGIEADVFRDVDPTHMAE 159
                                       5789999999999999*******99999998822355666666666666666666666666666689999******* PP

                                       HHHHHHHHHHTHHHHHH---- CS
                          TetR_C_7  76 qflgllkgelfwprlfgveep 96 
                                       + l+++kg++  ++ ++ e++
  gi|344209949|ref|YP_004786125.1| 160 HILAMIKGTMYSRLTTNREAA 180
                                       **********99988776554 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 ?   -3.1   0.1       4.2   8.3e+03       6      18 ..      59      71 ..      56      72 .. 0.79
   2 ?   12.9   0.0   4.5e-05     0.089      41      93 ..     123     174 ..     108     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.2
                                      HHHHHHHHHHHHH CS
                         TetR_C_29  6 rrlveftfdyhaa 18
                                       r+++ft+d+++a
  gi|344209949|ref|YP_004786125.1| 59 IRFLRFTVDRFEA 71
                                      5789999999975 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.5e-05
                                       --SS-.THHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHHHHHHHHHHTHHH CS
                         TetR_C_29  41 esirelnspliekleeilerGqaagvFrpgvdaldlyllisslcffrvsnrht 93 
                                       e+++e+  +l++ +e+ ++rG +a vFr+ vd+ ++   i ++    +  r t
  gi|344209949|ref|YP_004786125.1| 123 EQFTEIDIRLTAIIEKTVRRGIEADVFRD-VDPTHMAEHILAMIKGTMYSRLT 174
                                       5667777889999***************9.99998887777776555555544 PP

>> TetR_C_36  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   8.4e-05      0.17      45     103 ..     128     185 ..     120     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.4e-05
                         TetR_C_36  45 vqrrvvaavaelleeevaageleppldlddlAyllvRiaEsflYadliageepdidkae 103
                                       +  r++a++++ +++ ++a+ ++ ++d++ +A  +  ++  ++Y+ l + +e+ + +a+
  gi|344209949|ref|YP_004786125.1| 128 IDIRLTAIIEKTVRRGIEADVFR-DVDPTHMAEHILAMIKGTMYSRLTTNREAATGAAK 185
                                       6679999**********999776.9**************************99988776 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.6e-05      0.15      20      38 ..      30      48 ..      27      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.6e-05
                            HTH_38 20 GlslreIArrLgrspsTIs 38
                                       ls++ IA +L++++sTI+
  gi|344209949|ref|YP_004786125.1| 30 ELSISLIADELDKAKSTIY 48
                                      58999*************8 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 ?   -2.7   0.0       4.5     9e+03      83      95 ..      23      35 ..      13      60 .. 0.55
   2 ?   -2.2   0.1       3.2   6.4e+03      57      57 ..      64      64 ..      27      96 .. 0.56
   3 ?   12.2   0.0    0.0001      0.21      37      91 ..     118     172 ..     103     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.5
                                      HHHHHHHHHHHHH CS
                         TetR_C_37 83 lvdgaYyylslee 95
                                      lv++ Y  ls++ 
  gi|344209949|ref|YP_004786125.1| 23 LVNSGYAELSISL 35
                                      5555555444422 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.2
                                      H CS
                         TetR_C_37 57 s 57
                                       
  gi|344209949|ref|YP_004786125.1| 64 F 64
                                      2 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.0001
                                       -GGGHHHHHHHHHHHHHHHHHHHHTT--TTTBSS.-HHHHHHHHHHHHHHHHHHH CS
                         TetR_C_37  37 ekeikekykkildsLrevLksklkelneekkiklknkeetaelIfvlvdgaYyyl 91 
                                       ++ ++e++ +i  +L + +++ + +  e + ++  ++ ++ae I+++++g+ y  
  gi|344209949|ref|YP_004786125.1| 118 QEVFREQFTEIDIRLTAIIEKTVRRGIEADVFRDVDPTHMAEHILAMIKGTMYSR 172
                                       6789**********************************************99854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1132.32
//
Query:       gi|344209950|ref|YP_004786126.1|  [L=229]
Description: hypothetical protein HAH_5008 [Haloarcula hispanica ATCC 33960]
Scores for 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-40  136.5   0.1      1e-39  136.2   0.1    1.2  1  LUD_dom      LUD domain
  ------ inclusion threshold ------
      0.016   15.5   0.1      0.044   14.1   0.1    1.8  1  OKR_DC_1_N   Orn/Lys/Arg decarboxylase, N-terminal domain
      0.025   13.8   0.0      0.041   13.2   0.0    1.3  1  YcaO         YcaO cyclodehydratase, ATP-ad Mg2+-binding
      0.027   14.9   1.0      0.096   13.1   0.7    2.2  2  Secretin_N   Bacterial type II/III secretion system short dom
      0.036   14.2   0.1      0.096   12.9   0.1    1.7  1  UPF0180      Uncharacterised protein family (UPF0180)
      0.037   13.9   0.1       0.07   13.0   0.1    1.4  1  RsgA_GTPase  RsgA GTPase
       0.06   13.0   0.1      0.061   13.0   0.1    1.2  1  CHASE2       CHASE2 domain
      0.071   12.7   0.0       0.13   11.8   0.0    1.4  1  PrpR_N       Propionate catabolism activator


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 !  136.2   0.1   4.7e-43     1e-39       1     154 [.      38     195 ..      38     223 .. 0.91

  Alignments for each domain:
  == domain 1  score: 136.2 bits;  conditional E-value: 4.7e-43
                           LUD_dom   1 leefienleangaevyyaktaeealelilellkeksvvseggstdlgeiglapalhsgreevldlfeekl...trea 74 
                                       +e+++enleang++v++++++++al+ +++l++ + +v+ g st+l+eig+ ++l  g++e+  l +e +   ++++
  gi|344209950|ref|YP_004786126.1|  38 IEQTVENLEANGFDVIVVDSTDDALAELQSLIPTEASVMNGHSTTLEEIGFVEYLSDGDHEWESLPDEIWsidDDAE 114
                                       79*************************************************************************** PP

                           LUD_dom  75 reelrekfltadvgitganfaiAetGtlvlvdnegnr.raltflpkvhivvvginkivpdledavkrlkt..aprna 148
                                       r+  r+k+ tad+++ g n +i++tG+lv  d +g r  a+ f+  ++++v g+nkivp+leda++rl++   p ++
  gi|344209950|ref|YP_004786126.1| 115 RQAARRKSQTADYFLGGIN-GISQTGELVAADRSGSRiGAYPFAASNVVIVSGVNKIVPTLEDALDRLENvaYPLEN 190
                                       *******************.**************************************************9989999 PP

                           LUD_dom 149 trlqkk 154
                                       +r++ +
  gi|344209950|ref|YP_004786126.1| 191 ERAK-E 195
                                       8833.3 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 ?   14.1   0.1   1.9e-05     0.044       2      44 ..      34      76 ..      33      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                        OKR_DC_1_N  2 kgaairelaealekegfevvgvtstdDllsvieqnsriaavvl 44
                                      +++ i++ +e le++gf+v+ v+stdD+l+ +++     a v+
  gi|344209950|ref|YP_004786126.1| 34 SEETIEQTVENLEANGFDVIVVDSTDDALAELQSLIPTEASVM 76
                                      67899************************99988776666665 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 ?   13.2   0.0   1.8e-05     0.041     280     308 ..      32      60 ..       4      70 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                              YcaO 280 gdleedletllerlkaagldvlvvdltrp 308
                                          ee +e+ +e l+a+g+dv+vvd t +
  gi|344209950|ref|YP_004786126.1|  32 LASEETIEQTVENLEANGFDVIVVDSTDD 60 
                                       356789*******************9975 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 ?   13.1   0.7   4.3e-05     0.096      31      77 ..      74     182 ..      18     185 .. 0.77
   2 ?   -2.9   0.0       4.1   9.1e+03       3      13 ..     185     195 ..     183     208 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.3e-05
                                       ......................................................................SSTT-TT CS
                        Secretin_N  31 s..............................................................sgassqsgallgkg 45 
                                       s                                                              + ++  +++ +g++
  gi|344209950|ref|YP_004786126.1|  74 SvmnghsttleeigfveylsdgdheweslpdeiwsidddaerqaarrksqtadyflggingisQTGELVAADRSGSR 150
                                       2555567777777777777777777777777777777777777777888888888888888889999999999**** PP

                                       SEEEEETTTTEEEEEECHHHHHHHHHHHHHHC CS
                        Secretin_N  46 grvvadprtNsllvrgspervarirqlikqLD 77 
                                       +   +  ++N ++v+g  + v+++++ +++L+
  gi|344209950|ref|YP_004786126.1| 151 IGAYPFAASNVVIVSGVNKIVPTLEDALDRLE 182
                                       ***************************99996 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.1
                                       EEE-SSS-HHH CS
                        Secretin_N   3 vfpLkyasaad 13 
                                        +pL + +a++
  gi|344209950|ref|YP_004786126.1| 185 AYPLENERAKE 195
                                       58999999988 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   4.3e-05     0.096      23      70 ..      42      86 ..      27      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.3e-05
                           UPF0180 23 VvdleteedaqsvdaiVvtGqdtnvmgied.tetkapvInAsgktaeeI 70
                                      V++le    a+++d+iVv++ d  + + +  + t+a+v n +  t eeI
  gi|344209950|ref|YP_004786126.1| 42 VENLE----ANGFDVIVVDSTDDALAELQSlIPTEASVMNGHSTTLEEI 86
                                      44444....79*************************************9 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   3.1e-05      0.07      58     108 ..      31      80 ..      27      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.1e-05
                                       G--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECST CS
                       RsgA_GTPase  58 lleeeeeleelkeelealgyevllvsaktkegleelkellkdktsvlvGqS 108
                                        l +ee++e++ e+lea g++v++v+++  ++l+el++l+  + sv+ G+S
  gi|344209950|ref|YP_004786126.1|  31 ELASEETIEQTVENLEANGFDVIVVDST-DDALAELQSLIPTEASVMNGHS 80 
                                       4555666******************776.899*****************99 PP

>> CHASE2  CHASE2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.7e-05     0.061      40     114 ..      21      96 ..      19     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.7e-05
                            CHASE2  40 Deeslae..grwpwsravlarllerLeaagakaiglDilfsepeeydealaealak....gpnvvp....aaaglGf 106
                                       D+++++e       s +++ + +e+Lea g  +i++D        +d+alae  ++    + +v++      +++Gf
  gi|344209950|ref|YP_004786126.1|  21 DDADIDEslD-ELASEETIEQTVENLEANGFDVIVVDS-------TDDALAEL-QSliptEASVMNghstTLEEIGF 88 
                                       5555553332.235899*********************.......68888874.443433222322332233999** PP

                            CHASE2 107 vnvvpDaD 114
                                       v++  D D
  gi|344209950|ref|YP_004786126.1|  89 VEYLSDGD 96 
                                       99998886 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.9e-05      0.13      95     135 ..      25      65 ..       9      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.9e-05
                            PrpR_N  95 ldieiytinseeeaeaavkelkaegvevvvGdgvvadlAek 135
                                       +d ++ ++ see++e++v++l a+g++v+v d +   lAe 
  gi|344209950|ref|YP_004786126.1|  25 IDESLDELASEETIEQTVENLEANGFDVIVVDSTDDALAEL 65 
                                       5556667889*********************9999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1331.02
//
Query:       gi|344209951|ref|YP_004786127.1|  [L=390]
Description: putative ABC-type transport system substrate-binding protein ( substrate iron/cobalamin) [Haloarcula hispanica ATCC 33960]
Scores for complete 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-13   49.3   0.0    2.8e-12   46.7   0.0    1.9  2  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 ?    0.3   0.0     0.023   4.1e+02       1      55 [.       2      63 ..       2      92 .. 0.82
   2 !   46.7   0.0   1.5e-16   2.8e-12      94     237 ..     178     337 ..     146     338 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.023
                                      EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT.........TS-BSBESSSB-HHHH CS
                      Peripla_BP_2  1 iaslspsvteillalGatdkvvgvdtttsdpldadklee.......aivevgadgeidvEkl 55
                                      +asl+ ++ +  + +G+t   ++ + t+  ++ ad + +       + ve+  +ge+++E++
  gi|344209951|ref|YP_004786127.1|  2 VASLAGCSSGSSDDGGTTGDGAASAQTDQAEATADTEQStpenstpYTVEIEPHGEFTFEEV 63
                                      67788888888888888888888888888888887766677778778899999999999987 PP

  == domain 2  score: 46.7 bits;  conditional E-value: 1.5e-16
                                       S......HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE....EEE..E-TTS CS
                      Peripla_BP_2  94 g......eslkeqiralgellgledeaeklvaeidsklaaaksaidse..kpkpvlvfggade..ggyvv..agsns 158
                                       g       +l++ ++  + +++++++++++ + +d+ +a+++s+++ e   p+ ++v+ g d+  g +++  ++ ++
  gi|344209951|ref|YP_004786127.1| 178 GyeqetyHELYDVFEKMAAVFQCQARYRAWESLHDEFMANIRSDLPPEdeRPSVIAVWRGVDPtsGQFYLsdIHKYH 254
                                       144444599***************************************98888888888888888444442457899 PP

                                       TTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH.....HHHT-S--HHHHT-SHHHHTSHHHHTT- CS
                      Peripla_BP_2 159 yigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr.....aeadnktgleflkenpllaelpAvkngr 230
                                       + ++ l+ lg+++ ++++   ++++++ E++l+ dpd+i   gr     ++++ + ++e +++np  ++l+Av++g+
  gi|344209951|ref|YP_004786127.1| 255 NQTKPLSRLGLRDGYDAE-IPGGGTVGYEELLNHDPDYIAAVGRlttatHDEFVTNVVEPFENNPNGQDLTAVQEGN 330
                                       99999*********9998.9********************************************************* PP

                                       EEEE-HH CS
                      Peripla_BP_2 231 Vyaldss 237
                                       +++++ +
  gi|344209951|ref|YP_004786127.1| 331 IIRIGGQ 337
                                       **99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2384.05
//
Query:       gi|344209952|ref|YP_004786128.1|  [L=370]
Description: iron/cobalamin ABC transporter permease [Haloarcula hispanica ATCC 33960]
Scores for 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-84  283.2  34.6    2.6e-84  282.9  34.6    1.2  1  FecCD     FecCD transport family
  ------ inclusion threshold ------
       0.26   11.4   6.7       0.56   10.3   0.1    3.6  3  PT-VENN   Pre-toxin domain with VENN motif


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 !  282.9  34.6   2.9e-88   2.6e-84       3     312 .]      36     363 ..      25     363 .. 0.94

  Alignments for each domain:
  == domain 1  score: 282.9 bits;  conditional E-value: 2.9e-88
                             FecCD   3 llllllslllgavkispsevfeallgka....................dsleaeivlelrlprvlaallvGaaLava 59 
                                       l +++l +++ga+++++ e ++ +++ +                       ++ iv++lrlpr+l+++lvGa Lav+
  gi|344209952|ref|YP_004786128.1|  36 LGSTILQVSFGAYPLTLVEAWQTVFDPTvlsslevwrwaflgaavpewLTRQQLIVWNLRLPRILVGVLVGANLAVS 112
                                       557788899999999999999999988788888777777777777776445556*********************** PP

                             FecCD  60 GallQtvtrNpLadPsilGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLa 136
                                       Gal+Q +trN+La+P+ilG+s ga+l+++l+l+ll  +  +  lp++a +g+ la+llv+++a +++g+sp++l+La
  gi|344209952|ref|YP_004786128.1| 113 GALFQIITRNELASPYILGVSDGAGLVVLLTLTLL--TGLVPFLPIFAAAGGGLAFLLVYAIA-WKNGTSPVRLVLA 186
                                       *********************************96..5556679*******************.************* PP

                             FecCD 137 Giavsallsaltsllllll.neealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAks 212
                                       G++v+++++++  +l +++ +   ++s++ wl+G+l +a w +v ++l++++l+++l+++++++ld+lalg++ A s
  gi|344209952|ref|YP_004786128.1| 187 GVVVGTVFGSVQRALFFFIdDLGVAMSAQAWLSGTLMNAGWAEVRIALPFTVLAMALAFAVTQELDVLALGEDRADS 263
                                       *******************7778899*************************************************** PP

                             FecCD 213 lGvnvervrllllllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsp 289
                                       lG++ve+vr++++ + +l ta+a+a++G igFvGLivPh++r lvg+d + ll  + +lG +ll+ ad+ arl+lsp
  gi|344209952|ref|YP_004786128.1| 264 LGMPVEKVRFAIAGIGVLSTAAAIAVAGLIGFVGLIVPHMVRNLVGSDSKLLLAGCLFLGPALLVSADVGARLALSP 340
                                       ***************************************************************************** PP

                             FecCD 290 telpvgivtaliGapffiylllr 312
                                       ++lpvg++t ++G+p+f+yl+++
  gi|344209952|ref|YP_004786128.1| 341 VQLPVGVITGIVGGPYFLYLMRK 363
                                       *********************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 ?   10.3   0.1   6.2e-05      0.56       8      38 ..      17      47 ..      15      48 .. 0.94
   2 ?    0.7   0.1     0.065   5.8e+02      19      34 ..     185     200 ..     182     202 .. 0.72
   3 ?    0.8   0.6     0.061   5.4e+02      14      28 ..     280     294 ..     277     313 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.2e-05
                           PT-VENN  8 EKqtvsalstlaaGlaGgvvggtladavaGa 38
                                      ++ +vs l+ ++aG  + + g t+ +++ Ga
  gi|344209952|ref|YP_004786128.1| 17 DRYEVSKLALIIAGSLAVLLGSTILQVSFGA 47
                                      7899*************************98 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.065
                           PT-VENN  19 aaGlaGgvvggtlada 34 
                                       +aG++ g+v g+ + a
  gi|344209952|ref|YP_004786128.1| 185 LAGVVVGTVFGSVQRA 200
                                       6777777777788877 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.061
                           PT-VENN  14 alstlaaGlaGgvvg 28 
                                        lst+aa +++g++g
  gi|344209952|ref|YP_004786128.1| 280 VLSTAAAIAVAGLIG 294
                                       699999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); 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:                         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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2232.12
//
Query:       gi|344209953|ref|YP_004786129.1|  [L=319]
Description: iron/cobalamin ABC-type transporter ATP-binding protein [Haloarcula hispanica ATCC 33960]
Scores for 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  104.0   0.0    1.3e-29  103.5   0.0    1.2  1  ABC_tran      ABC transporter
    3.7e-13   49.9   1.9    5.4e-06   26.4   0.2    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    5.9e-13   48.8   0.2    1.4e-06   27.9   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    4.5e-07   29.9   0.0    6.6e-05   22.8   0.0    2.1  2  AAA_15        AAA ATPase domain
    5.5e-07   29.2   0.0    1.4e-06   28.0   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
    2.6e-05   23.2   1.3      0.047   12.5   0.0    3.0  2  ABC_ATPase    Predicted ATPase of the ABC class
    7.6e-05   23.0   0.2    0.00045   20.5   0.2    2.0  1  AAA_22        AAA domain
    0.00011   22.6   0.1    0.00024   21.5   0.1    1.9  1  AAA_16        AAA ATPase domain
    0.00023   20.8   0.3      0.013   15.1   0.0    2.6  2  AAA_25        AAA domain
    0.00036   21.1   0.0    0.00061   20.3   0.0    1.3  1  AAA_23        AAA domain
     0.0031   17.3   0.1      0.006   16.3   0.1    1.7  1  AAA_30        AAA domain
     0.0068   16.6   0.1      0.021   15.0   0.1    1.9  1  AAA_33        AAA domain
  ------ inclusion threshold ------
      0.013   15.6   0.1       0.44   10.6   0.0    2.3  2  MMR_HSR1      50S ribosome-binding GTPase
      0.014   14.9   0.1       0.45    9.9   0.1    2.1  2  TniB          Bacterial TniB protein
      0.016   15.1   0.0      0.032   14.0   0.0    1.4  1  MukB          MukB N-terminal
      0.017   15.4   0.0      0.039   14.2   0.0    1.7  1  AAA_28        AAA domain
      0.019   14.9   0.0      0.037   14.0   0.0    1.4  1  NACHT         NACHT domain
       0.02   14.8   0.0      0.044   13.7   0.0    1.6  1  RsgA_GTPase   RsgA GTPase
      0.027   14.5   0.0      0.083   12.9   0.0    1.8  2  AAA_14        AAA domain
       0.03   13.1   0.0        1.2    7.9   0.0    2.1  2  Adeno_IVa2    Adenovirus IVa2 protein
      0.032   14.0   0.1          1    9.1   0.0    2.1  2  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.039   14.4   0.1       0.14   12.6   0.0    1.9  2  AAA           ATPase family associated with various cellular 
      0.063   12.9   0.0       0.11   12.0   0.0    1.4  1  AAA_27        AAA domain
      0.072   13.5   0.0       0.22   11.9   0.0    1.8  1  RNA_helicase  RNA helicase
      0.073   13.0   0.0       0.15   11.9   0.0    1.5  1  ATPase_2      ATPase domain predominantly from Archaea
       0.08   12.2   0.0       0.19   11.0   0.0    1.5  1  Zeta_toxin    Zeta toxin
      0.096   12.4   0.2       0.27   10.9   0.0    1.8  2  AAA_24        AAA domain
      0.098   12.2   0.2       0.19   11.3   0.2    1.7  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
        0.1   12.5   0.2        1.5    8.7   0.0    2.3  2  NTPase_1      NTPase
       0.15   12.1   0.0       0.38   10.7   0.0    1.7  1  AAA_5         AAA domain (dynein-related subfamily)
       0.16   11.7   0.0       0.26   11.0   0.0    1.2  1  VirE          Virulence-associated protein E
       0.17   12.4   0.0       0.47   11.0   0.0    1.9  1  AAA_18        AAA domain
        0.2   11.7   0.0       0.38   10.8   0.0    1.4  1  PAPS_reduct   Phosphoadenosine phosphosulfate reductase famil


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 !  103.5   0.0   2.3e-32   1.3e-29       5     136 ..      60     204 ..      56     205 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.5 bits;  conditional E-value: 2.3e-32
                                       EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                          ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                       s+ + ++e++a++G+nG+GKStLlk++a + +p+ G++ +dg+ ++e   ++l +++g l+qe+ +  +++v++   
  gi|344209953|ref|YP_004786129.1|  60 SIAVPPDEVTALIGPNGSGKSTLLKAMADKISPDDGTVFVDGQTIDEFGSKELARKLGLLSQENVVPTGISVGDLve 136
                                       77899********************************************************************99** PP

                                       ...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                      e+++ +++a++  g+++l+d+ v     sLSgGqkq v +a+a++++ ++lllDEpt
  gi|344209953|ref|YP_004786129.1| 137 rgryphtgffeslsdEDRAAVDDAIQLAGIENLRDRDV----DSLSGGQKQLVWIAMAIAQDTDVLLLDEPT 204
                                       ***********998777777******************....*****************************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 !   26.4   0.2   9.9e-09   5.4e-06       1      20 [.      68      87 ..      68     112 .. 0.78
   2 !   22.7   0.1   1.3e-07   7.2e-05     227     293 ..     167     231 ..     139     237 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 9.9e-09
                            AAA_21  1 lnvliGpNgsGKSnLLdald 20
                                      +++liGpNgsGKS+LL+a+ 
  gi|344209953|ref|YP_004786129.1| 68 VTALIGPNGSGKSTLLKAMA 87
                                      69****************93 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 1.3e-07
                            AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell...kelsrngaQvi 293
                                       ++ +++++++lS G+k+l   +++ ++++   ++ll+DEp ++L+P+ + ++++++   +++s+  + v+
  gi|344209953|ref|YP_004786129.1| 167 ENLRDRDVDSLSGGQKQL-VWIAMAIAQDT--DVLLLDEPTTFLDPQHQLEVMQIVetlRDESQ--ITVV 231
                                       5667788999********.55555555554..**************888666666622255555..5555 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 !   19.2   0.0   1.2e-06   0.00065      24      44 ..      66      86 ..      56      91 .. 0.83
   2 !   27.9   0.0   2.6e-09   1.4e-06     135     208 ..     121     244 ..      87     255 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                                      SSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlldAi 44
                                      +++ta++GpNGSGKs ll A+
  gi|344209953|ref|YP_004786129.1| 66 DEVTALIGPNGSGKSTLLKAM 86
                                      459****************98 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 2.6e-09
                                       T......................................................CS-HHHHHHHHHHHHHHHHCCS CS
                                       x......................................................xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e......................................................lLSgGektLvalaLlfAiqkvk 157
                                       +                                                      +LSgG+k+Lv +a+ +A    +
  gi|344209953|ref|YP_004786129.1| 121 QenvvptgisvgdlvergryphtgffeslsdedraavddaiqlagienlrdrdvdSLSGGQKQLVWIAMAIA----Q 193
                                       44555555555555555555555555555555555555555555555556666669***********99876....5 PP

                                       --SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 158 paplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadkl 208
                                        + + llDe    LD ++  +v +++++ ++++Q+ v+ + +++ + a+  
  gi|344209953|ref|YP_004786129.1| 194 DTDVLLLDEPTTFLDPQHQLEVMQIVETLRDESQITVVLVLHDIAQAARYA 244
                                       67899********************************99988888877544 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.2e-07   6.6e-05      22      73 ..      66     112 ..      59     122 .. 0.76
   2 ?    4.8   0.0     0.037        20     295     358 ..     175     227 ..     167     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.2e-07
                            AAA_15  22 seeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenise 73 
                                       +e +t liG+N+sGKS++l+a+    + k + ++ +++++ + +++f +++ 
  gi|344209953|ref|YP_004786129.1|  66 DE-VTALIGPNGSGKSTLLKAM---AD-KISPDDGTVFVDGQTIDEFGSKEL 112
                                       55.9*****************9...33.333336888888888888877665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.037
                            AAA_15 295 nknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQ 358
                                       +  + G+++l+++++ i+         +++++ll++EP + L pq+q ++++    l +++  Q
  gi|344209953|ref|YP_004786129.1| 175 DSLSGGQKQLVWIAMAIA---------QDTDVLLLDEPTTFLDPQHQLEVMQIVETLRDES--Q 227
                                       566778888888877664.........34789***************99998877766655..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 !   28.0   0.0   2.5e-09   1.4e-06      12      48 ..      56      92 ..      53      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.5e-09
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiqalLvp 48
                                      +dg++i + ++++t l+Gp+GsGKSTll A++  + p
  gi|344209953|ref|YP_004786129.1| 56 IDGESIAVPPDEVTALIGPNGSGKSTLLKAMADKISP 92
                                      578999999999*****************99865555 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 !   12.5   0.0   8.6e-05     0.047     243     279 ..      65      98 ..      55     102 .. 0.80
   2 !    6.3   0.6    0.0066       3.6     324     413 ..     178     252 ..     171     259 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.6e-05
                                       -SSEEEEEE-TTSSHHHHHHHHHHCCSEE-TTSS-TT CS
                        ABC_ATPase 243 pkGvtlIvGggfhGKsTLLeAlekGvynhvpgDGRef 279
                                       p  vt+++G++  GKsTLL+A++  +    p+DG  f
  gi|344209953|ref|YP_004786129.1|  65 PDEVTALIGPNGSGKSTLLKAMADKI---SPDDGTVF 98 
                                       455******************98655...46677655 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0066
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GC CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsgd 400
                                       SG   q ++i+ a+  ++++lL+DE t+   ++  D + q            +++ v+ l+++ +++++lv   + +
  gi|344209953|ref|YP_004786129.1| 178 SGGQKQLVWIAMAIAQDTDVLLLDEPTT---FL--DPQHQLE----------VMQIVETLRDESQITVVLVLHDIAQ 239
                                       7777777788888888888888888765...33..3333322..........3677888888899999999999999 PP

                                       CTTT-SEEEEEET CS
                        ABC_ATPase 401 yldvAdtvilmee 413
                                         + Ad+++++++
  gi|344209953|ref|YP_004786129.1| 240 AARYADNIVALKD 252
                                       9999999998876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.2   8.2e-07   0.00045       7     128 ..      68     233 ..      65     240 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.2e-07
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka........... 70 
                                       +++++G+ G+GK+tll+ ++++         +++++vfv+ +     +sk+l+r+l    +++              
  gi|344209953|ref|YP_004786129.1|  68 VTALIGPNGSGKSTLLKAMADKIS-------PDDGTVFVDGQTIDefGSKELARKLGLLSQENVVPtgisvgdlver 137
                                       689*******************96.......59****9998877667888888888888887766688899999999 PP

                            AAA_22  71 ...............................erlsseellealeqalrarav............ielliiDEaqh.l 103
                                                                       r++  + l+  +       +            + +l++DE    l
  gi|344209953|ref|YP_004786129.1| 138 gryphtgffeslsdedraavddaiqlagienLRDRDVDSLSGGQ-------KqlvwiamaiaqdTDVLLLDEPTTfL 207
                                       99888888888888888888888855555442222222222222.......22444444667778888888888866 PP

                            AAA_22 104 r...seealeeLrsllnlsrkgvqliLv 128
                                       +   + e+++ + +l +  +++++++Lv
  gi|344209953|ref|YP_004786129.1| 208 DpqhQLEVMQIVETLRD--ESQITVVLV 233
                                       67543666666666677..888888887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   4.4e-07   0.00024      25      63 ..      67     106 ..      53     304 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.4e-07
                            AAA_16  25 elvllsGesGvGKsslvrellralekdg.giflrgkcdql 63 
                                       e++ l+G+ G+GKs+l+++ ++ ++ d+  +f+ g++ + 
  gi|344209953|ref|YP_004786129.1|  67 EVTALIGPNGSGKSTLLKAMADKISPDDgTVFVDGQTIDE 106
                                       7889***********************6477799988777 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   2.3e-05     0.013      30      59 ..      63      94 ..      51     165 .. 0.89
   2 ?    3.3   0.4       0.1        55      95     155 ..     239     299 ..     184     304 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.3e-05
                            AAA_25 30 lpagelallaGapgtGKttlaldlalava..t 59
                                      +p +e+++l+G+ g+GK+tl+  +a +++   
  gi|344209953|ref|YP_004786129.1| 63 VPPDEVTALIGPNGSGKSTLLKAMADKISpdD 94
                                      6899*****************99998887544 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.1
                            AAA_25  95 ealrddarllvldlagv.eslpLfakdrggtl.ltadvdaleaaieeveg.vrlvviDplsral 155
                                       +a+r  ++  +l+  ++  + p    +   t+ l adv ++eaa+ e+e  ++++ iDp++ a 
  gi|344209953|ref|YP_004786129.1| 239 QAARYADNIVALKDGSMyARGPP---EEVVTKqLLADVFEIEAAVLETEYgLQVIPIDPVTDAQ 299
                                       33344455555543333222221...22222246677778888888875459999999999875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.1e-06   0.00061      20      39 ..      67      86 ..      56      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.1e-06
                            AAA_23 20 gltlItGpNGaGKTTildAi 39
                                       +t+++GpNG+GK+T+l A+
  gi|344209953|ref|YP_004786129.1| 67 EVTALIGPNGSGKSTLLKAM 86
                                      689**************997 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.1e-05     0.006      13      51 ..      61      99 ..      58     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                            AAA_30 13 lltsgdrvavltGpAGtGKttalkalreaweaaggrvig 51
                                      ++  +d v++l Gp G+GK+t+lka+++ +  + g+v++
  gi|344209953|ref|YP_004786129.1| 61 IAVPPDEVTALIGPNGSGKSTLLKAMADKISPDDGTVFV 99
                                      55667889******************9988888666664 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   3.9e-05     0.021       1      32 [.      68     103 ..      68     245 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.9e-05
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg....avllssdt 32 
                                       ++ l+G++GsGKstl++ ++ k      +v+++  t
  gi|344209953|ref|YP_004786129.1|  68 VTALIGPNGSGKSTLLKAMADKISpddgTVFVDGQT 103
                                       5679**************998766666666666655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00082      0.44       3      22 ..      70      89 ..      68     107 .. 0.84
   2 ?    2.6   0.1      0.25   1.3e+02      44      97 ..     193     250 ..     166     267 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00082
                                      EEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltge 22
                                      a++G   +GKStL++a+ ++
  gi|344209953|ref|YP_004786129.1| 70 ALIGPNGSGKSTLLKAMADK 89
                                      89***************986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.25
                                       TTEEEEEEECGGCS.S.HHHHHH.HHHHHHHHHHCTSEEEEEEETTTT.CSHHHHHHH CS
                          MMR_HSR1  44 kgkeielvDtpGli.e.gaseek.glgkaflaleeadlillvvdasee.klkpldeel 97 
                                       +++++ l+D p  + + +++ e  ++ +++++  +  ++l++ d++++  ++++   l
  gi|344209953|ref|YP_004786129.1| 193 QDTDVLLLDEPTTFlDpQHQLEVmQIVETLRDESQITVVLVLHDIAQAaRYADNIVAL 250
                                       3478899999996533234444467778888777789999999988333455554444 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.14        74      39      62 ..      70      93 ..      64     101 .. 0.85
   2 ?    9.9   0.1   0.00082      0.45     117     160 ..     192     233 ..     168     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.14
                              TniB 39 llvGdsnnGKtmivekFarlhppe 62
                                       l+G+   GK+++++  a++ +p+
  gi|344209953|ref|YP_004786129.1| 70 ALIGPNGSGKSTLLKAMADKISPD 93
                                      799************998877665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00082
                              TniB 117 elkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                       + ++ vL++DE   +l    ++q e+++++ +L +e +i++vlv
  gi|344209953|ref|YP_004786129.1| 192 AQDTDVLLLDEPTTFL--DPQHQLEVMQIVETLRDESQITVVLV 233
                                       56789***********..8999********************98 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.9e-05     0.032      27      76 ..      67     118 ..      65     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.9e-05
                                       HHHHHHS--SHHHHHHHHHHHHHHS--TTT---..----------------- CS
                              MukB  27 lvttlsGgnGaGksttmaafvtaliPdlsllhf..rntteaGatsgsrdkGl 76 
                                        vt+l G nG+Gkst + a+   + Pd   +    + + e G+++ +r  Gl
  gi|344209953|ref|YP_004786129.1|  67 EVTALIGPNGSGKSTLLKAMADKISPDDGTVFVdgQTIDEFGSKELARKLGL 118
                                       59************************98765441156668888888888777 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   7.2e-05     0.039       3      34 ..      70     107 ..      68     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.2e-05
                            AAA_28   3 vitGgestGKTtlleaLaar.....gypvv.pEaarei 34 
                                       +++G+ ++GK+tll+a+a++     g++ v   +  e+
  gi|344209953|ref|YP_004786129.1|  70 ALIGPNGSGKSTLLKAMADKispddGTVFVdGQTIDEF 107
                                       79****************76666667765544444444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   6.8e-05     0.037       2      25 ..      68      91 ..      67      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.8e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawa 25
                                      + +l G++GsGK+tLl+ +a+++ 
  gi|344209953|ref|YP_004786129.1| 68 VTALIGPNGSGKSTLLKAMADKIS 91
                                      6789***************99875 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   8.2e-05     0.044      99     123 ..      66      90 ..      57     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.2e-05
                                       TSEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpel 123
                                       d++++l+G+ G GKStL++a++ + 
  gi|344209953|ref|YP_004786129.1|  66 DEVTALIGPNGSGKSTLLKAMADKI 90 
                                       6899***************998874 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00015     0.083       3      47 ..      67     110 ..      65     127 .. 0.80
   2 ?   -1.7   0.0         5   2.7e+03      62      76 ..     193     206 ..     162     233 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla 47 
                                       ++ ++ G+  +GK+tllk ++++   +++ +++++ ++ ++  ++
  gi|344209953|ref|YP_004786129.1|  67 EVTALIGPNGSGKSTLLKAMADKIS-PDDGTVFVDGQTIDEFGSK 110
                                       57899***************98877.9999999998888876555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5
                            AAA_14  62 eekktylflDEiqev 76 
                                       + ++ +l+lDE    
  gi|344209953|ref|YP_004786129.1| 193 Q-DTDVLLLDEPTTF 206
                                       3.5677888886554 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0021       1.2      92     122 ..      71      99 ..      60     118 .. 0.82
   2 ?    3.1   0.0     0.062        34     235     259 ..     227     251 ..     216     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0021
                        Adeno_IVa2  92 iyGPtGsGksqllrnlissklisPiPetvif 122
                                       + GP GsGks ll+++   + isP   tv+ 
  gi|344209953|ref|YP_004786129.1|  71 LIGPNGSGKSTLLKAMA--DKISPDDGTVFV 99 
                                       67************985..569999999986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.062
                        Adeno_IVa2 235 gfsvlvvlhnlnPrsdiagniadlk 259
                                         +v++vlh+++  +  a+ni+ lk
  gi|344209953|ref|YP_004786129.1| 227 QITVVLVLHDIAQAARYADNIVALK 251
                                       568999*****************99 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 ?    9.1   0.0    0.0019         1       2      18 ..      72      88 ..      71      98 .. 0.87
   2 ?    2.8   0.0      0.15        82      78     134 ..     183     239 ..     174     266 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0019
                        ATP_bind_1  2 vGpaGsGKttfvgalse 18
                                      +Gp GsGK+t+ +a+++
  gi|344209953|ref|YP_004786129.1| 72 IGPNGSGKSTLLKAMAD 88
                                      8*************987 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.15
                        ATP_bind_1  78 sldwldeelekeeddyllfDtPGQielfthseslakiveeLes.efalvvvyLvDsqr 134
                                       +l w++ ++  +++d ll+D P      +h  +  +ive+L   +  +vv++L D   
  gi|344209953|ref|YP_004786129.1| 183 QLVWIAMAI-AQDTDVLLLDEPTTFLDPQHQLEVMQIVETLRDeSQITVVLVLHDIAQ 239
                                       556777777.55778888888877766778888888******9666677777777654 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   0.00025      0.14       3      23 ..      71      91 ..      69     135 .. 0.79
   2 ?   -1.2   0.0       4.8   2.6e+03      59      71 ..     195     207 ..     159     244 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00025
                                      EESSTTSSHHHHHHHHHHHHT CS
                               AAA  3 lyGppGtGKTllakavakelg 23
                                      l+Gp G GK++l ka+a +++
  gi|344209953|ref|YP_004786129.1| 71 LIGPNGSGKSTLLKAMADKIS 91
                                      89***************9985 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.8
                                       SEEEEEETGGGHH CS
                               AAA  59 psilfiDEidala 71 
                                       + +l++DE   + 
  gi|344209953|ref|YP_004786129.1| 195 TDVLLLDEPTTFL 207
                                       3666666644444 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00021      0.11      25      48 ..      65      88 ..      56      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                            AAA_27 25 eadlhliyGpNEAGKstalrAisd 48
                                       ++++ ++GpN +GKst+l+A+ d
  gi|344209953|ref|YP_004786129.1| 65 PDEVTALIGPNGSGKSTLLKAMAD 88
                                      56778899*************987 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    0.0004      0.22       3      29 ..      71      92 ..      69     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0004
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkklklk 29
                                      l Gp+g GKStl k +a++++     +
  gi|344209953|ref|YP_004786129.1| 71 LIGPNGSGKSTLLKAMADKIS-----P 92
                                      78*************999887.....4 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00028      0.15      19      54 ..      65      99 ..      59     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00028
                          ATPase_2 19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyy 54
                                      p+e+  + Gp gsGK++Llk ++ + +  d+  +++
  gi|344209953|ref|YP_004786129.1| 65 PDEVTALIGPNGSGKSTLLKAMADKISP-DDGTVFV 99
                                      67888899*************9998844.5566776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00034      0.19      21      53 ..      71     103 ..      65     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                        Zeta_toxin  21 lgGqpGAGKselaellkdelerqgnvvrldpDd 53 
                                       l G  G+GKs+l+++++d++ ++++ v +d+ +
  gi|344209953|ref|YP_004786129.1|  71 LIGPNGSGKSTLLKAMADKISPDDGTVFVDGQT 103
                                       56889**********************999865 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    0.0005      0.27       6      29 ..      70      99 ..      67     114 .. 0.77
   2 ?   -2.8   0.0       8.2   4.4e+03     110     131 ..     214     236 ..     210     253 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0005
                            AAA_24  6 liyGpsgiGKTtlakel......gpkplfi 29
                                      +++Gp+g+GK+tl+k +       + ++f+
  gi|344209953|ref|YP_004786129.1| 70 ALIGPNGSGKSTLLKAMadkispDDGTVFV 99
                                      79*************996655544445555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.2
                            AAA_24 110 efrrllkklqelrk.nvifiahe 131
                                       e+++++++l++  + +v+++ h 
  gi|344209953|ref|YP_004786129.1| 214 EVMQIVETLRDESQiTVVLVLHD 236
                                       66677777666666788888774 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 ?   11.3   0.2   0.00035      0.19       2      23 ..      68      89 ..      67     257 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00035
                                      EEEEEESTTCCHHHHHHHHHCT CS
                              cobW  2 vtvltGflGsGKTtLlnhllen 23
                                      vt l G+ GsGK+tLl+++ ++
  gi|344209953|ref|YP_004786129.1| 68 VTALIGPNGSGKSTLLKAMADK 89
                                      78999************99865 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0028       1.5       4      27 ..      71      94 ..      68     117 .. 0.80
   2 ?    1.4   0.0      0.47   2.6e+02      94     153 ..     193     256 ..     173     269 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0028
                                      EE--TTSSHHHHHHHHHHHH...G CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellkssg 27
                                      + Gp G+GK+Tl+k ++++++ ++
  gi|344209953|ref|YP_004786129.1| 71 LIGPNGSGKSTLLKAMADKISPDD 94
                                      679***************997654 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.47
                                       HHH-EEEE---ST.TGGG-HHHHHHHHHHHT..TTSEEEEE--SS-.-SHHHHHHHT-TT-EEE CS
                          NTPase_1  94 seadviviDEiGk.mElkskkfkeaveevLk..sekpvlavihrrk.dlalveeirerkdvkvf 153
                                       +++dv+++DE    +  + +    ++ e+L+  s+  v+ v+h      +  ++i   kd++++
  gi|344209953|ref|YP_004786129.1| 193 QDTDVLLLDEPTTfLDPQHQLEVMQIVETLRdeSQITVVLVLHDIAqAARYADNIVALKDGSMY 256
                                       6677777777443145555544444555554477778888888877677788888888887776 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   0.00071      0.38       4      23 ..      71      90 ..      69     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00071
                                      EE--SSSSHHHHHHHGGGGB CS
                             AAA_5  4 LvGppGtgKselaerlaaal 23
                                      L+Gp G+gKs+l + +a  +
  gi|344209953|ref|YP_004786129.1| 71 LIGPNGSGKSTLLKAMADKI 90
                                      9***************9988 PP

>> VirE  Virulence-associated protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00048      0.26      52      76 ..      66      90 ..      60     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00048
                              VirE 52 DfvlvLvGkqgsgKstfleklgeew 76
                                      D+v+ L G+ gsgKst+l++++++ 
  gi|344209953|ref|YP_004786129.1| 66 DEVTALIGPNGSGKSTLLKAMADKI 90
                                      99*******************8775 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00087      0.47       3      22 ..      71      90 ..      70     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00087
                            AAA_18  3 ltGtpGvGKttlakeLskrl 22
                                      l G+ G+GK+tl k+ +++ 
  gi|344209953|ref|YP_004786129.1| 71 LIGPNGSGKSTLLKAMADKI 90
                                      89*************99884 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00069      0.38       5      63 ..     176     238 ..     173     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00069
                                       E--SSCTCHHHHHHHHHHCTTH.....EEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCH CS
                       PAPS_reduct   5 svsgGkdslVllhLalkafkpv.....pvvfvdtghefpetiefvdeleeryglrlkvyepeee 63 
                                       s sgG   lV + +a+  + +v     p+ f+d +h+  e+++ v+ l+++ ++++ ++  ++ 
  gi|344209953|ref|YP_004786129.1| 176 SLSGGQKQLVWIAMAIAQDTDVllldePTTFLDPQHQL-EVMQIVETLRDESQITVVLVLHDIA 238
                                       78*******************889999*******9986.7889999999888777444333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 1942.33
//
Query:       gi|344209954|ref|YP_004786130.1|  [L=309]
Description: sodium-dependent transporter [Haloarcula hispanica ATCC 33960]
Scores for 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-38  130.2  10.5    9.9e-38  129.8  10.5    1.2  1  SBF             Sodium Bile acid symporter family
    6.5e-14   52.0   8.3    9.1e-14   51.5   8.3    1.3  1  SBF_like        SBF-like CPA transporter family (DUF4137)
  ------ inclusion threshold ------
      0.045   13.9   0.3       0.15   12.2   0.3    2.0  1  CBP_BcsF        Cellulose biosynthesis protein BcsF
        0.2   10.0   9.2      0.014   13.9   3.3    1.9  2  Mem_trans       Membrane transport protein
       0.22   10.8   0.9       0.47    9.8   0.9    1.5  1  Bestrophin      Bestrophin, RFP-TM, chloride channel
       0.51    9.5   4.0       0.93    8.6   4.0    1.4  1  Bac_export_2    FlhB HrpN YscU SpaS 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 !  129.8  10.5   3.3e-41   9.9e-38       2     193 ..      45     226 ..      44     228 .. 0.94

  Alignments for each domain:
  == domain 1  score: 129.8 bits;  conditional E-value: 3.3e-41
                               SBF   2 ilLilmmfpmglkveveklkellkrpkalllglvlqwvikPllmfilakillrdlklepelavGlilvglapggams 78 
                                       +lL+l+m++mgl+++  ++++l+++p  + +g v qw+++P  +++l +    +l+l+  + +Glilvg+apgg++s
  gi|344209954|ref|YP_004786130.1|  45 PLLGLIMLGMGLTLQPADFHRLIEEPVDIGIGAVTQWLVMPAAAYGLYV----LLDLPDAVGIGLILVGAAPGGTAS 117
                                       689**********************************************....8889******************** PP

                               SBF  79 nvwtylakGdlelsvvlvalstllailltPlllyllaksleqttlkvpieeivksvlivviiPliaGillryillkh 155
                                       nv++yl +Gd++lsv +++l+tl+a++++P ++ + +++     ++v+++e+++s++++viiP+++G+ +ry+l + 
  gi|344209954|ref|YP_004786130.1| 118 NVMAYLGRGDVALSVAITTLTTLAAPIVMPAWVVFTLGEQ----INVTFAEMFQSIIQIVIIPVLLGFTIRYLLDRY 190
                                       ***********************************99999....******************************994 PP

                               SBF 156 kGrewfeskllpavspisligllltivvifalkgeliv 193
                                         +    +    ++++is+++++ +++ ++  ++++i+
  gi|344209954|ref|YP_004786130.1| 191 --SPKAAEIGTDVFPVISVAAIVAIVAGVVGANVDNIL 226
                                       ..333444567889999999999999999999999886 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 !   51.5   8.3     3e-17   9.1e-14      36     267 ..      46     271 ..      12     275 .. 0.78

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 3e-17
                          SBF_like  36 gValiFllsGlslsteellanlrnwrlhllvllisflltplivlalvsllkaaldpelliGllllaalPtTvssnvv 112
                                       +  li l  Gl+l+  ++ + +++     +  ++  l++p+ +++l++ll+   ++++ iGl+l+ a+P   +snv 
  gi|344209954|ref|YP_004786130.1|  46 LLGLIMLGMGLTLQPADFHRLIEEPVDIGIGAVTQWLVMPAAAYGLYVLLDL--PDAVGIGLILVGAAPGGTASNV- 119
                                       556777788888888888888888888888889999**************85..899******************7. PP

                          SBF_like 113 mtsqAgGnealalceavignllGvfltPalvqlllsgssvsvdyaevlkklllsvllPlvvGqvlqkifpklvkrlk 189
                                       m+   +G++al++  +++  l+++++ Pa+v ++l g++++v++ae++++++  v++P+++G  +++++ ++  +  
  gi|344209954|ref|YP_004786130.1| 120 MAYLGRGDVALSVAITTLTTLAAPIVMPAWVVFTL-GEQINVTFAEMFQSIIQIVIIPVLLGFTIRYLLDRYSPKAA 195
                                       7899******************************9.89****************************99876544443 PP

                          SBF_like 190 kl....lkkvdslvlllivytsfstafaqgaftsvshiillvifnvallLllvvlvillllarllklskedeiavlf 262
                                       ++    +  ++ ++++ iv   +        ++++ + +llv+++v ++  +++l   + + r+ +++k ++ ++ f
  gi|344209954|ref|YP_004786130.1| 196 EIgtdvFPVISVAAIVAIVAGVVGAN-----VDNILTAGLLVLVAV-VAHNAIGLGSGYGVGRATGMPKDRVRTCAF 266
                                       33222277777788888876665544.....344445555555543.334667788888999999999999999999 PP

                          SBF_like 263 cgsaK 267
                                         +aK
  gi|344209954|ref|YP_004786130.1| 267 EVAAK 271
                                       88887 PP

>> CBP_BcsF  Cellulose biosynthesis protein BcsF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   5.1e-05      0.15       5      31 ..     168     194 ..     165     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.1e-05
                          CBP_BcsF   5 DivqiiilcaLiflpLgyllarllrrl 31 
                                        i+qi+i+ +L+ ++  yll r  ++ 
  gi|344209954|ref|YP_004786130.1| 168 SIIQIVIIPVLLGFTIRYLLDRYSPKA 194
                                       69********************99986 PP

>> Mem_trans  Membrane transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   3.3   4.5e-06     0.014     285     386 ..      47     149 ..      44     150 .. 0.82
   2 ?   -1.5   2.3      0.21   6.3e+02      47      84 ..     146     183 ..     133     243 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.5e-06
                         Mem_trans 285 lpmalfslGlfLalqpkkiacgnsvatfa.lavRlilgPlvmlvavlavgLrgslllvaivqaAlPqgivlfviAke 360
                                       l+++++ +Gl+L   +    ++  v   + ++   +++P++ +++ ++++L+  +  ++i++ A P g+ + v+A +
  gi|344209954|ref|YP_004786130.1|  47 LGLIMLGMGLTLQPADFHRLIEEPVDIGIgAVTQWLVMPAAAYGLYVLLDLPDAVGIGLILVGAAPGGTASNVMAYL 123
                                       7999999999998877666666555544469********************************************99 PP

                         Mem_trans 361 ynvherelstllifgmlialpitlvy 386
                                          + ++  ++ ++++l a ++++ +
  gi|344209954|ref|YP_004786130.1| 124 GRGDVALSVAITTLTTLAAPIVMPAW 149
                                       77777777777777777776666666 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.21
                         Mem_trans  47 ifhfisqnnpyemllrfiladvlvklivlillllgall 84 
                                       + + ++ +   +++++f+ +   ++ iv+i +llg+ +
  gi|344209954|ref|YP_004786130.1| 146 MPAWVVFTLGEQINVTFAEMFQSIIQIVIIPVLLGFTI 183
                                       33333333444444444444444444444444444444 PP

>> Bestrophin  Bestrophin, RFP-TM, chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.9   0.00016      0.47      18     101 ..     125     215 ..     116     242 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00016
                        Bestrophin  18 kGsvyklilrelllflllyalvvllyr..l.ee......rlfellsicelipLsfvLgFrvnavydRWweqrkllgw 85 
                                       +G v  +++ + l++l++ +++ ++    l e+      ++f+++++  ++ + ++LgF + + +dR+      +g+
  gi|344209954|ref|YP_004786130.1| 125 RGDVALSVAITTLTTLAAPIVMPAWVVftLgEQinvtfaEMFQSIIQ--IVIIPVLLGFTIRYLLDRYSPKAAEIGT 199
                                       78888888888888888888877777766665565333333766666..888899***************9999999 PP

                        Bestrophin  86 ldkaarslarqvrgls 101
                                        +  ++s+a+ v  + 
  gi|344209954|ref|YP_004786130.1| 200 DVFPVISVAAIVAIVA 215
                                       8888887777776643 PP

>> Bac_export_2  FlhB HrpN YscU SpaS Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.0   0.00031      0.93      18      93 ..     125     218 ..     120     241 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00031
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..................XXXXXXXXXXXXXXX CS
                      Bac_export_2  18 kGqvakskelssalvllaglllllllgpslveelaellrevlsa..................lelllelllalllll 76 
                                       +G+va s  ++++++l+a +++ ++++ +l e++  +++e++++                  l+ ++  + ++ + +
  gi|344209954|ref|YP_004786130.1| 125 RGDVALSVAITTLTTLAAPIVMPAWVVFTLGEQINVTFAEMFQSiiqiviipvllgftirylLDRYSPKAAEIGTDV 201
                                       79***********************9999999999999999999999899998888887666333344444444445 PP

                                       XXXXXXXXXXXXXXXXX CS
                      Bac_export_2  77 lplllvlllaallanll 93 
                                       +p++ v++++a++a ++
  gi|344209954|ref|YP_004786130.1| 202 FPVISVAAIVAIVAGVV 218
                                       56666666666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1949.95
//
Query:       gi|344209955|ref|YP_004786131.1|  [L=272]
Description: 4-hydroxybenzoate polyprenyltransferase-like prenyltransferase [Haloarcula hispanica ATCC 33960]
Scores for 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  18.9    7.7e-16   58.1  18.9    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 !   58.1  18.9   4.3e-20   7.7e-16      27     244 ..      27     251 ..       2     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 4.3e-20
                              UbiA  27 lgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnpltallgllallly 103
                                       + + l+++a+++ ++++D e+Da+    p R    +r   +  +++a++ + l+++l+ +l +p +++l+ll  ++ 
  gi|344209955|ref|YP_004786131.1|  27 IVAGLLTFAVYGNDRLADLETDAK--TSPARTAFVRRYQ-NGFYVLAAIAYGLAVALS-ALGGPISFGLSLLPGMCW 99 
                                       333488889999999*********..999**77788887.788889999999999999.9***********999888 PP

                              UbiA 104 vvYt.........g.lrlKrrtllgtvvggiafglppllgwaa.vtgslsllalllalavflltwaialan.dlrdr 168
                                       ++Y          g  rlK + ll+  +++++++l+++      v+   s+++ +++l+ f+l++ + +   ++rd+
  gi|344209955|ref|YP_004786131.1| 100 ILYAcdwiptlpsGtQRLKEVFLLNSTLVAVVWALVIVCLPLTyVGAPASPAVGVVFLF-FVLATFVNTEIpNVRDK 175
                                       9998888988999778******************9999888874666667777777777.777777777779***** PP

                              UbiA 169 egDrkagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaalallraarlvrrrdakkaak 244
                                       egD ++g++tlpvv G ++++++l+ ++ ++ ++l+++++a+   l  +++ll+ +l+l   + ++ r ++++a +
  gi|344209955|ref|YP_004786131.1| 176 EGDSEIGVRTLPVVVGVRWTKYILYGITGLTAVLLGVAFVANIINLREAVVLLVSLLFLNGVIFCLNRTENDSALA 251
                                       **********************977777777777777888888888888888888888888777777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1564.93
//
Query:       gi|344209956|ref|YP_004786132.1|  [L=557]
Description: PAS domain S-box [Haloarcula hispanica ATCC 33960]
Scores for complete 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  177.7  16.0    4.2e-52  177.4  16.0    1.1  1  HisKA_7TM    N-terminal 7TM region of histidine kinase
    4.2e-13   49.8   0.1      8e-13   48.9   0.1    1.5  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    9.5e-06   25.6   0.1      2e-05   24.6   0.1    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain
    0.00061   20.0   0.1     0.0034   17.6   0.1    2.2  1  PAS_4        PAS fold
     0.0008   19.4   0.0     0.0037   17.3   0.0    2.1  2  PAS_8        PAS domain
     0.0016   18.6   0.0     0.0058   16.9   0.0    1.9  1  PAS_9        PAS domain
     0.0038   17.2   0.1      0.013   15.5   0.1    1.9  1  PAS          PAS fold
  ------ inclusion threshold ------
      0.015   15.9   0.0      0.056   14.0   0.0    2.0  2  PAS_10       PAS domain
      0.041   13.7   0.0       0.08   12.8   0.0    1.4  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like


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 !  177.4  16.0   2.1e-55   4.2e-52       2     220 .]      10     234 ..       9     234 .. 0.95

  Alignments for each domain:
  == domain 1  score: 177.4 bits;  conditional E-value: 2.1e-55
                         HisKA_7TM   2 llisallslvlaiya.wrrrskpgaraflllllavalwslgyalellattleakllwaklqylgivfipvlwllfal 77 
                                       +l++++++ v + ++ w+ r +pga +++lll++  +ws++ ++++ a+tl+ k++w +++++g+++ip++wllf+l
  gi|344209956|ref|YP_004786132.1|  10 VLVATIAVGVTGGLLaWKERPEPGADPLILLLAGQCWWSATLIFRIDAATLSSKVFWVDVSWIGVAIIPIAWLLFSL 86 
                                       4666666666666666*9999**************************999*************************** PP

                         HisKA_7TM  78 eytgkrrwltrrrlallllvpvltlilvltnplhhlfy.....vsagsfvvlefehGplfwvhlaysyllliagvvl 149
                                       ey+g+ ++ +r++++l+++vp++t++l lt+++h+l+y     ++++++++l+ ++G++fw++++y+yll ++g++ 
  gi|344209956|ref|YP_004786132.1|  87 EYAGYTEYTARKHILLYSIVPAITVFLGLTSHSHQLLYtnsviIQEHGIATLNRTPGVWFWIIAGYTYLLGLLGALP 163
                                       ****9999999**************************999999999******************************* PP

                         HisKA_7TM 150 liralirssglyrrqalllligllvPwlanllyllglsplpgidltplafaltglllaiaifryrlldivP 220
                                       l++ + ++ + +r q+l+ll+gll+Pw++n+l+l+g  p  g+d+tp+afa++gl+++ a++r++l+   P
  gi|344209956|ref|YP_004786132.1| 164 LLKLVTSQVDPFRGQSLALLLGLLAPWVTNVLFLMGSLPSAGVDPTPIAFAVSGLAYLGALTRFQLFGANP 234
                                       ***************************************9***************************9887 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   0.1     4e-16     8e-13       9     109 ..     456     552 ..     452     555 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 4e-16
                                       HHHHHHHHHHHHHS.TTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHH CS
                         HATPase_c   9 iisnlvdNavkfat.kageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkkl 84 
                                       ++ n+++Na++++t +++ +++e++++ ++++++v+DnG+Gi+ ++l  l e+ s+    +  + g+G+Gl++v   
  gi|344209956|ref|YP_004786132.1| 456 VCLNIIQNAAQHNTsPDPVVSIEVERDGEYVQVTVQDNGPGIDSNELA-LVEHGSE----TPLKHGSGFGLALVVWG 527
                                       789*********66466677888886669*******************.4443333....46678*********999 PP

                                       HHHTTTEEEEEEETTTEEEEEEEEE CS
                         HATPase_c  85 velmgGeiwvesepgrGttftftlp 109
                                       ++  gG++ +es+++ Gtt+++++p
  gi|344209956|ref|YP_004786132.1| 528 TDIAGGTVDIESSETTGTTVILRIP 552
                                       999*******************998 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 !   24.6   0.1   9.9e-09     2e-05      40     106 ..     457     525 ..     454     551 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 9.9e-09
                       HATPase_c_2  40 ctNavehayleap.eg.pvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalik 106
                                       c N+++ a ++++  +  v++++e+d+e ++v+v+D+Gpg d  +l+  +  + +  +  +G+Glal+ 
  gi|344209956|ref|YP_004786132.1| 457 CLNIIQNAAQHNTsPDpVVSIEVERDGEYVQVTVQDNGPGIDSNELALVEHGSETPLKHGSGFGLALVV 525
                                       666666666666544405689999****************99999988888888899999******985 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   1.7e-06    0.0034       1      49 [.     245     293 ..     245     343 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.7e-06
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeeda 49 
                                       + +++++ +vld++ +++++N +a   ++ +p e+lG++l+++ p+ +a
  gi|344209956|ref|YP_004786132.1| 245 FQQMQQGALVLDTHDHIVDMNDQATTALQTRPNEALGRPLEQISPDLSA 293
                                       56899************************************99888633 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.8e-06    0.0037       5      55 ..     243     294 ..     241     305 .. 0.86
   2 ?   -2.6   0.0       3.1   6.2e+03      22      52 ..     364     392 ..     344     408 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.8e-06
                             PAS_8   5 alfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrpl 55 
                                       +lf ++++g +v+d+ d+ivd+N++a   l  + ++ +g +l q+ p+l  l
  gi|344209956|ref|YP_004786132.1| 243 SLFQQMQQGALVLDTHDHIVDMNDQATTALQTRpNEALGRPLEQISPDLSAL 294
                                       79************4456*************779999999999999888765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.1
                             PAS_8  22 rivdvNqaalellGysadlkgellgqllpvl 52 
                                       +++  N a+l       ++k+++l++   ++
  gi|344209956|ref|YP_004786132.1| 364 QVILGNAAYLATHN--SESKAATLQEHAVEI 392
                                       47777777777776..557777776444444 PP

>> PAS_9  PAS 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    0.0058       4     103 ..     253     339 ..     250     340 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.9e-06
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvll 80 
                                        ++d++d+ i+++N++a + l++ p+e lg++++++      + + l          + +   +++r+ng    +++
  gi|344209956|ref|YP_004786132.1| 253 LVLDTHDH-IVDMNDQATTALQTRPNEALGRPLEQIS----PDLSALGS--------ATQAGQTIYRPNGVSQSYDV 316
                                       34576777.****************************....44445555........55555599*****9999999 PP

                             PAS_9  81 taspvkdddgelvgiivilrDit 103
                                       + s v d +++ +g +++l+D++
  gi|344209956|ref|YP_004786132.1| 317 SESLVTDIHDRTIGRVITLHDVS 339
                                       999999999999999*****998 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   6.3e-06     0.013       5      99 ..     243     345 ..     240     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.3e-06
                                       HHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH..HHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   5 aileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda..elaelleqlleqgeesrageisf 79 
                                       ++++++  + +v+D    i+ +N+ a++ l+ +++e+lg++l  +i+++ +a     ++ ++ ++ +  s+++++s+
  gi|344209956|ref|YP_004786132.1| 243 SLFQQMQQGALVLDTHDHIVDMNDQATTALQTRPNEALGRPLE-QISPDLSAlgSATQAGQTIYRPNGVSQSYDVSE 318
                                       68899************************************98.888887768877777778888888888888888 PP

                                       EC.......TTSSEEEEEEEEEEEEET CS
                               PAS  80 kl.......rdgrpihlevraspvrda 99 
                                        l       + gr+i l+   + +rd 
  gi|344209956|ref|YP_004786132.1| 319 SLvtdihdrTIGRVITLHDVSNLLRDQ 345
                                       778787777777777777777777776 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.8e-05     0.056       2      54 ..     242     296 ..     242     338 .. 0.83
   2 ?   -2.4   0.0       3.7   7.4e+03      36      61 ..     326     353 ..     313     374 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                            PAS_10   2 nnlLnstpieltflDdnlqirrFtpaa.kklfklipadvGrpladihpk.kavkn 54 
                                       n l+++++ + + lD+ ++i   +++a + l  + ++ +Grpl++i+p+ +a+ +
  gi|344209956|ref|YP_004786132.1| 242 NSLFQQMQQGALVLDTHDHIVDMNDQAtTALQTRPNEALGRPLEQISPDlSALGS 296
                                       6799********************97625777889999*********99555555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.7
                            PAS_10  36 padvGrpla..dihpkkavknveeviea 61 
                                       +  +Gr ++  d+++  + ++  ev+++
  gi|344209956|ref|YP_004786132.1| 326 DRTIGRVITlhDVSNLLRDQQRLEVLHR 353
                                       4445553321144444333333333333 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     4e-05      0.08       6      51 ..     456     503 ..     452     525 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4e-05
                       HATPase_c_3   6 AlaelvdNsldAdaen...vkievnknrgktgeivieDdGkGmseeelk 51 
                                       + + +++N+ + +      v+iev+++ g+  +++++D+G G++ +el 
  gi|344209956|ref|YP_004786132.1| 456 VCLNIIQNAAQHNTSPdpvVSIEVERD-GEYVQVTVQDNGPGIDSNELA 503
                                       5577899988866655888******97.7899*************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3606.25
//
Query:       gi|344209957|ref|YP_004786133.1|  [L=88]
Description: hypothetical protein HAH_5015 [Haloarcula hispanica ATCC 33960]
Scores for 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-07   28.8   0.0      1e-06   28.5   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 !   28.5   0.0   5.6e-11     1e-06       5      30 ..       4      29 ..       1      47 [. 0.87

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 5.6e-11
                                      BTT-STTCCHHHHHHHHCCCGCT-EE CS
                              TusA  5 lrGlvCPePllklkkalekleegevl 30
                                      ++G+ CP+P++k+k+++++l +ge+ 
  gi|344209957|ref|YP_004786133.1|  4 VTGENCPMPVVKAKQTIDELSSGEKA 29
                                      79*********************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); 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):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 640.12
//
Query:       gi|344209958|ref|YP_004786134.1|  [L=232]
Description: hypothetical protein HAH_5016 [Haloarcula hispanica ATCC 33960]
Scores for complete 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-74  248.2   4.9    4.6e-74  248.0   4.9    1.0  1  DUF2270        Predicted integral membrane protein (DUF2270)
  ------ inclusion threshold ------
      0.025   13.6   0.2      0.025   13.6   0.2    2.0  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 !  248.0   4.9   5.2e-78   4.6e-74       1     184 []      35     213 ..      35     213 .. 0.99

  Alignments for each domain:
  == domain 1  score: 248.0 bits;  conditional E-value: 5.2e-78
                           DUF2270   1 ahlYRgeveratawreRlDrttnWavvvtaallsvalsspeashavlllgmllvlvfLliearryrfydvwrsrvrl 77 
                                       ahlYRge++r++ wreRlDrttnWav v++a+l++a+s+p+ +h++ll+g+++++vfL+iearryr yd+wrsrvr+
  gi|344209958|ref|YP_004786134.1|  35 AHLYRGEIHRMKFWRERLDRTTNWAVLVISAILTWAFSRPDIPHYILLIGTATLAVFLFIEARRYRGYDIWRSRVRT 111
                                       6**************************************************************************** PP

                           DUF2270  78 leenffaealdpeegaeeeeWreeLaedlrkPtlkislleAlgrRLrrnYlwlllvlllawllkitlfkkeeeslee 154
                                       l+ n+fa  ldp++g+ +++Wr++L++d+r+Pt+kis+ eA+++RLrr+Yl+l++vll+awl++it+f++ +     
  gi|344209958|ref|YP_004786134.1| 112 LQANVFAYGLDPAAGVADPDWRKSLSADYRQPTIKISTEEAIAHRLRRVYLPLFTVLLTAWLIRITVFSSGS----- 183
                                       **********************************************************************99..... PP

                           DUF2270 155 llerAavgplpGelvllvvalfylallvla 184
                                       ++++Aa+g+lpG++v+++v l+y+a++v+a
  gi|344209958|ref|YP_004786134.1| 184 WTDSAAIGMLPGVVVIGTVGLLYAAAIVVA 213
                                       99***********************99985 PP

>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2     0.027   2.4e+02     233     296 ..      63      90 ..      36     121 .. 0.52
   2 ?   13.6   0.2   2.8e-06     0.025      65     115 ..     143     193 ..     124     220 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.027
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 233 lalillalfgqtdggglvasvliqsaslllvslgimllllllfalpsrsafkllrylgkiSygi 296
                                       +++il ++f+                                    ++     +  +g +++++
  gi|344209958|ref|YP_004786134.1|  63 ISAILTWAFSRP--------------------------------DIPHY----ILLIGTATLAV 90 
                                       222222222222................................11111....22222222222 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.8e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3  65 lyrrrglsklikrRilrlliplliwllliillialvaghiqanasanvtlf 115
                                       ++ + ++ ++i +R++r+++pl+ +ll+ +l+   v+   +++ sa    +
  gi|344209958|ref|YP_004786134.1| 143 PTIKISTEEAIAHRLRRVYLPLFTVLLTAWLIRITVFSSGSWTDSAAIGML 193
                                       566788999*************************99999999888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1576.24
//
Query:       gi|344209959|ref|YP_004786135.1|  [L=128]
Description: hypothetical protein HAH_5017 [Haloarcula hispanica ATCC 33960]
Scores for complete 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  17.3    0.00013   22.2  17.3    1.1  1  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
     0.0014   17.7  10.1     0.0018   17.4  10.1    1.0  1  Atg14            Vacuolar sorting 38 and autophagy-related su
     0.0017   17.6   8.3     0.0019   17.4   8.3    1.0  1  Tho2             Transcription factor/nuclear export subunit 
     0.0024   17.4  14.2     0.0031   17.0  14.2    1.1  1  Golgin_A5        Golgin subfamily A member 5
     0.0083   16.0  15.4       0.01   15.6  15.4    1.1  1  ERM              Ezrin/radixin/moesin family
  ------ inclusion threshold ------
      0.019   14.5   6.3      0.026   14.1   6.3    1.3  1  PEARLI-4         Arabidopsis phospholipase-like protein (PEAR
      0.028   14.5  16.7      0.037   14.1  16.7    1.3  1  ADIP             Afadin- and alpha -actinin-Binding
      0.036   14.7  13.9       0.83   10.3  13.9    2.2  1  YabA             Initiation control protein YabA
      0.044   13.1  10.0       0.05   12.9  10.0    1.2  1  DUF3450          Protein of unknown function (DUF3450)
      0.046   13.6  15.5       0.06   13.2  15.5    1.1  1  KASH_CCD         Coiled-coil region of CCDC155 or KASH
      0.053   12.9  13.0      0.063   12.7  13.0    1.0  1  GBP_C            Guanylate-binding protein, C-terminal domain
      0.067   12.6  16.2       0.08   12.3  16.2    1.1  1  DUF3552          Domain of unknown function (DUF3552)
      0.069   13.3   5.8      0.077   13.1   5.8    1.1  1  RasGAP_C         RasGAP C-terminus
        0.1   13.1  12.5       0.12   12.8  12.5    1.1  1  Fez1             Fez1
       0.11   12.6   0.8       0.14   12.3   0.8    1.0  1  Thioesterase     Thioesterase domain
       0.11   12.6  13.7       0.14   12.2  13.7    1.1  1  DivIVA           DivIVA protein
       0.11   12.5  14.0       0.15   12.2  14.0    1.1  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.13   11.1  14.6       0.16   10.8  14.6    1.0  1  Spc7             Spc7 kinetochore protein
       0.14   12.6  12.0       0.16   12.4   2.8    2.5  2  Fungal_TACC      Fungal Transforming acidic coiled-coil (TACC
       0.17   11.7  11.3        0.2   11.4  11.3    1.1  1  MAT1             CDK-activating kinase assembly factor MAT1
        0.2   10.9   7.7       0.24   10.6   7.7    1.1  1  TMPIT            TMPIT-like protein
        0.2   12.0  10.2       0.21   11.9   9.5    1.4  1  DUF641           Plant protein of unknown function (DUF641)
       0.22   11.8  11.2       0.11   12.7   6.9    2.0  2  KxDL             Uncharacterized conserved protein
        0.3    9.5   4.7       0.35    9.3   4.7    1.0  1  FUSC             Fusaric acid resistance protein family
       0.37    8.2  13.4       0.43    8.0  13.4    1.0  1  DUF3584          Protein of unknown function (DUF3584)
       0.38   10.1   9.4       0.49    9.7   9.4    1.2  1  DUF4407          Domain of unknown function (DUF4407)
       0.39   10.2   6.6       0.45   10.0   6.6    1.1  1  Exonuc_VII_L     Exonuclease VII, large subunit
       0.48   10.8   3.7       0.99    9.7   3.7    1.6  1  Flu_NS2          Influenza non-structural protein (NS2)
       0.49   10.1   5.7       0.73    9.6   5.7    1.3  1  Lectin_N         Hepatic lectin, N-terminal domain
       0.51    9.1   9.7       0.58    8.9   9.7    1.0  1  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
       0.63   10.1  10.2        2.7    8.0   9.8    1.8  2  Laminin_II       Laminin Domain II
       0.65   10.9   7.4       0.61   11.0   5.5    2.0  1  Pup              Pup-like protein
        1.1    9.3  10.9        5.4    7.1  10.3    2.2  2  Bap31_Bap29_C    Bap31/Bap29 cytoplasmic coiled-coil domain
        1.2    9.3  15.2        2.1    8.5   8.5    2.4  2  TolA_bind_tri    TolA binding protein trimerisation
        1.2    7.6   7.3        1.4    7.5   7.3    1.1  1  FapA             Flagellar Assembly Protein A
        1.6    9.3  23.1       0.79   10.2  13.9    2.3  2  ZapB             Cell division protein ZapB
        1.8    9.5  17.7        5.8    7.9  17.7    1.9  2  PRKG1_interact   cGMP-dependent protein kinase interacting do
        2.2    7.5   6.2        2.9    7.1   6.2    1.1  1  CorA             CorA-like Mg2+ transporter protein
        2.3    8.0  16.5       0.41   10.4   5.9    2.4  2  DivIC            Septum formation initiator
        2.8    8.1  10.1       0.34   11.1   2.1    2.4  2  NYD-SP28_assoc   Sperm tail C-terminal domain
        2.9    7.7   8.8        1.8    8.4   6.9    1.5  1  DUF2570          Protein of unknown function (DUF2570)
        3.4    8.1  15.7        6.1    7.3   4.6    2.2  2  Csm1_N           Csm1 N-terminal domain
        3.5    8.2  23.5         18    5.8  23.5    1.8  1  APG6_N           Apg6 coiled-coil region
        3.7    8.1   5.6         32    5.1   4.5    2.5  3  NPV_P10          Nucleopolyhedrovirus P10 protein
        4.9    7.0  17.9        3.2    7.7  13.7    1.9  2  Ax_dynein_light  Axonemal dynein light chain
        5.5    6.6  10.9        6.3    6.4   9.1    1.7  2  Mt_ATP-synt_B    Mitochondrial ATP synthase B chain precursor
        5.5    5.4  14.1        6.5    5.2  14.1    1.0  1  Macoilin         Macoilin family
        6.7    6.3  11.1       0.62    9.7   4.2    1.9  2  MctB             Copper transport outer membrane protein, Mct
          7    7.1  18.4        1.2    9.6   9.4    2.0  2  CENP-H           Centromere protein H (CENP-H)
          8    6.7  17.3        5.7    7.2  14.8    2.0  1  Cnn_1N           Centrosomin N-terminal motif 1
          8    6.8  19.3        2.5    8.4   8.4    2.1  2  Spc24            Spc24 subunit of Ndc80


Domain annotation for each model (and alignments):
>> 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 !   22.2  17.3   3.8e-07   0.00013      45     134 ..      17     100 ..      12     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.8e-07
                     Jnk-SapK_ap_N  45 neeeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsr 121
                                        +  ++e e l +e+e+L++++++ +e+rk+++ + e++ +q+e +++++++ +++le ++++l+      a q+  
  gi|344209959|ref|YP_004786135.1|  17 AQDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLN------ASQARL 87 
                                       567899***********************************************************......444444 PP

                     Jnk-SapK_ap_N 122 leekeaelkkeys 134
                                        e++e++   + s
  gi|344209959|ref|YP_004786135.1|  88 AESRENQAGMSRS 100
                                       4444444333332 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 !   17.4  10.1   5.2e-06    0.0018      67     159 ..      15     106 ..      10     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.2e-06
                             Atg14  67 akleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqiaklqdaikri 143
                                       +++++++++ + l+++++el+++l + ++  ++ k + + l+++l +R++d + l +ele r++k ++  q  + ++
  gi|344209959|ref|YP_004786135.1|  15 DSAQDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELE-RKEKMLNASQARLAES 90 
                                       6899999***************************************99999999999986.5666777777788888 PP

                             Atg14 144 eqklsslssktlesrs 159
                                       +++++ +s++ +e+r+
  gi|344209959|ref|YP_004786135.1|  91 RENQAGMSRSEMEKRL 106
                                       8888888888888775 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 !   17.4   8.3   5.5e-06    0.0019      14     104 ..      14     104 ..       9     112 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.5e-06
                              Tho2  14 slslyDiyvpkeqYekeieklkseieelakdrsderaaakkkkkekkrlkeliekLeeEkkeqiehvekvkkrLkee 90 
                                       + s +Di++ +e+ ++e e+l+++++e+++dr++e+++a++ +k+ +  +e +++L +E++++++  ++ ++rL+e 
  gi|344209959|ref|YP_004786135.1|  14 QDSAQDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLNASQARLAES 90 
                                       66899***********************999999999999999999999***************************9 PP

                              Tho2  91 kkswfkndekkkke 104
                                       +++   +++++ ++
  gi|344209959|ref|YP_004786135.1|  91 RENQAGMSRSEMEK 104
                                       98877666655555 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 !   17.0  14.2   8.9e-06    0.0031      77     175 ..      13     109 ..       5     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.9e-06
                         Golgin_A5  77 lqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryleeelvrskatlqsrikdrekeieklrn 153
                                       +qd  +  q+e e l+ +++el+eql+e r+ +++ ++  e+l+++l++ +e++     tl s+++++ek+++  ++
  gi|344209959|ref|YP_004786135.1|  13 FQDSAQDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVD----TLLSELERKEKMLNASQA 85 
                                       4677778888999999999999999999999998888888999999999888887....888999999999999999 PP

                         Golgin_A5 154 qlttkslsss..seselesRlkqL 175
                                        l+ +  +++  s+se+e+Rl  L
  gi|344209959|ref|YP_004786135.1|  86 RLAESRENQAgmSRSEMEKRLDYL 109
                                       999886666555999999999877 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6  15.4     3e-05      0.01      39     123 ..      14     103 ..       8     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3e-05
                               ERM  39 aekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserkeeeaerLkeeleea 115
                                       + +a+  ++e e L ++++e++e+ ++ +e++++e++  e+l+++l+  ++ + +l +e erke+  +  +++l e 
  gi|344209959|ref|YP_004786135.1|  14 QDSAQDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLNASQARLAES 90 
                                       678999*********************************************************************** PP

                               ERM 116 reae.....eeak 123
                                       re++      e++
  gi|344209959|ref|YP_004786135.1|  91 RENQagmsrSEME 103
                                       *999555433333 PP

>> PEARLI-4  Arabidopsis phospholipase-like protein (PEARLI 4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   6.3   7.4e-05     0.026     186     257 ..      40     112 ..      11     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.4e-05
                          PEARLI-4 186 deqetavvEKevke...rdvllkkqEmekqekelaekEKeikevrekvtemaaklgelemkrarlekrlaflssK 257
                                       +  e+ + EK + e   +++ ++ +++++   el +kEK ++  ++++ e +    +  m r+ +ekrl++l  +
  gi|344209959|ref|YP_004786135.1|  40 ETREDRKAEKSRAEnlnKQLETRNEDVDTLLSELERKEKMLNASQARLAESRE--NQAGMSRSEMEKRLDYLCAQ 112
                                       445666666655542227899999************************99766..57789**********99765 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1  16.7   0.00011     0.037      48     115 ..      28      95 ..      14     105 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00011
                              ADIP  48 rdrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknek 115
                                       + ++ e re+lnet+++ +ae++r ++  ++l+t++e+ ++ l+ +++ke+ l++++++l +   n++
  gi|344209959|ref|YP_004786135.1|  28 HAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLNASQARLAESRENQA 95 
                                       56899******************************************************999887775 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3  13.9    0.0024      0.83      26      74 ..      12      60 ..       3     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0024
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA 26 elkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLa 74
                                      + +++ +++  en++L++ene+lre+l+e+++++k++k++ ++ +++L+
  gi|344209959|ref|YP_004786135.1| 12 AFQDSAQDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLE 60
                                      678889999******************8888888888877777777765 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9  10.0   0.00014      0.05      11      97 ..      10      93 ..       1     114 [. 0.61

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                           DUF3450 11 sgalaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqie 89
                                      +    a  d+a++ +++  a  a+ ++  ++l++ +++ +ae  ++++ +++le  ne ++ l++++e++ + l+ +++
  gi|344209959|ref|YP_004786135.1| 10 T---VAFQDSAQDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLNASQA 85
                                      3...344455555555555555666666666666666666666666666666777777777777777777777777777 PP

                           DUF3450 90 eieeiere 97
                                      ++ e +++
  gi|344209959|ref|YP_004786135.1| 86 RLAESREN 93
                                      76666554 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 ?   13.2  15.5   0.00017      0.06      54     138 ..      16     100 ..      13     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00017
                          KASH_CCD  54 stQqalqkaklleeEleelkalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlk 130
                                       s Q    + ++l+ E+eel++ ++e+ E r+  k ++++l+k  +  ++ +++L  e+++     ++++ +l+e  +
  gi|344209959|ref|YP_004786135.1|  16 SAQDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLNASQARLAESRE 92 
                                       56777888899999999999999999999999999999999999999999999999999999999999999999999 PP

                          KASH_CCD 131 ekaeLkkq 138
                                       ++a + + 
  gi|344209959|ref|YP_004786135.1|  93 NQAGMSRS 100
                                       99888654 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 ?   12.7  13.0   0.00018     0.063     192     286 ..      10     106 ..       3     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00018
                             GBP_C 192 ilqtdkaltakekeieaeqakaeaaeaekelleekqkeeeqrmeakeksle...ehvkqLkekleeereklleeqer 265
                                        ++ + ++++ + e+ea +a++e+++++ ++ +e +k e+ r e+ +k+le   e v  L + le+++++l++ q r
  gi|344209959|ref|YP_004786135.1|  10 TVAFQDSAQDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLEtrnEDVDTLLSELERKEKMLNASQAR 86 
                                       5667788889999999999********99999999998888877766665522278889999999999999999999 PP

                             GBP_C 266 llekklkeqeellkegfkeea 286
                                       l+e+++ +q+ +++ +++++ 
  gi|344209959|ref|YP_004786135.1|  87 LAESRE-NQAGMSRSEMEKRL 106
                                       888765.56677777776665 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3  16.2   0.00023      0.08      50     130 ..      22     103 ..      12     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
                           DUF3552  50 kkkealleakeeihklreelekelkerrnelqrlekRllqkeetLdrkeeslekkeesleekekelkqk.eqsleek 125
                                       +  eal   +ee++++ +e+ ++ k  ++  ++l+k+l+ ++e +d   ++le+ke+ l++ + +l++  e++    
  gi|344209959|ref|YP_004786135.1|  22 TENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLNASQARLAESrENQAGMS 98 
                                       45788999999999999999999999999999999****************************99976514444444 PP

                           DUF3552 126 eeele 130
                                       ++e+e
  gi|344209959|ref|YP_004786135.1|  99 RSEME 103
                                       45554 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   5.8   0.00022     0.077      19     105 ..       5      90 ..       1     108 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00022
                          RasGAP_C  19 gvisrennyqellneIakdirnkgrlrekrkeElesleetlktLseknnylesqlesYkayienvleqlkkkkgklp 95 
                                       g +     +q+  ++I+++   ++   e+ +e+l+ ++e  k+ +++ + l++qle+ ++ +++ l++l++k++ l+
  gi|344209959|ref|YP_004786135.1|   5 GTVGTTVAFQDSAQDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLN 81 
                                       55666667899999********************************************************9964433 PP

                          RasGAP_C  96 fskqyfkkre 105
                                        s+ +   ++
  gi|344209959|ref|YP_004786135.1|  82 ASQ-ARLAES 90 
                                       333.222222 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8  12.5   0.00035      0.12      20     101 ..      18      99 ..      12     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00035
                              Fez1  20 kdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeel 96 
                                       +d+q+e  +   e  +l+ ql e+r++ +++ +++++l+++le+++++++++ +el+rk++  +  + ++ +  e+ 
  gi|344209959|ref|YP_004786135.1|  18 QDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLNASQARLAESRENQ 94 
                                       69999999999999*********************************************877777777777666666 PP

                              Fez1  97 kelre 101
                                       +++ +
  gi|344209959|ref|YP_004786135.1|  95 AGMSR 99 
                                       66643 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.8   0.00039      0.14     101     213 ..      14     124 ..       4     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00039
                                       SCCCCCCHHCHHCCCHTTHHTHHHHHCCTTHH.HCCTTTHCCHHHHHHHHHHHHHHHHHTCCS-TTSCSEHHCEEEE CS
                      Thioesterase 101 dssapseteaqeasrraedeefveeltdlggt.epeelledeellsellpalradyraleqyslrpeaaqklratlf 176
                                         sa  ++ ++ea +++ +e ++e+l++ ++   +e++++   l ++l+++  ++ ++l     r+e++ +++ + +
  gi|344209959|ref|YP_004786135.1|  14 QDSAQDIQTENEALHAENEE-LREQLNETREDrKAEKSRAEN-LNKQLETRNEDVDTLLSEL-ERKEKMLNASQARL 87 
                                       55777788999999999999.*********995555555544.6666666666666666666.8888888899999* PP

                                       EEGSS-CTCCCCCCCHCHCHCTCESCEEEEEESSHCC CS
                      Thioesterase 177 ngsddklkdldtlelaerweqktsgevsvhvlegdhf 213
                                       ++s++ +++++  e+++r++  + ++  ++++ ++ f
  gi|344209959|ref|YP_004786135.1|  88 AESRENQAGMSRSEMEKRLDYLCAQPENIDRFGCQEF 124
                                       **************************99999999876 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2  13.7   0.00041      0.14      28     120 ..      18     110 ..      14     117 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00041
                                       HHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  28 dqvakdyeallkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakkeaeliikeAekkaekivee 104
                                       +++  + eal+ eneel+e+++e++e+ k  k++ e+L+k l +  e  + + ++ +++ +++ + +   ae+  ++
  gi|344209959|ref|YP_004786135.1|  18 QDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLNASQARLAESRENQ 94 
                                       6789999******************************************************9999999999999999 PP

                                       XXXXXXXXXXXXXXXX CS
                            DivIVA 105 aeeeakkiaeeieelk 120
                                       a  +  +++++++ l 
  gi|344209959|ref|YP_004786135.1|  95 AGMSRSEMEKRLDYLC 110
                                       9999999999888765 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 ?   12.2  14.0   0.00042      0.15      86     171 ..      19     108 ..       8     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00042
                           UPF0242  86 tkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklele...eqLaekqellqeyqetie 159
                                        ++ + e l +e+eeL+e+l++  e  +  k + ++L+++le   ed++ l+ ele   + L+  q +l e++e+  
  gi|344209959|ref|YP_004786135.1|  19 DIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELErkeKMLNASQARLAESRENQA 95 
                                       34444566778888999999999999888899999999999999999999988875221568888999988888765 PP

                           UPF0242 160 .eqrsvlekrqdq 171
                                          rs++ekr d+
  gi|344209959|ref|YP_004786135.1|  96 gMSRSEMEKRLDY 108
                                       1579999999998 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  14.6   0.00046      0.16     160     247 ..      15     103 ..       9     115 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00046
                              Spc7 160 kqeeeldellpeleeekaeleeeleklqe..aaeelesid.keeLeelreelaelkaeieekkkelaelqeqleele 233
                                       ++ + +++  ++l++e +el+e+l++ +e  +ae+  + + +++Le+  e++++l +e+e+k+k+l+  q++l+e++
  gi|344209959|ref|YP_004786135.1|  15 DSAQDIQTENEALHAENEELREQLNETREdrKAEKSRAENlNKQLETRNEDVDTLLSELERKEKMLNASQARLAESR 91 
                                       44556666666777777777777777666432222233334667888888888888888888888888888888888 PP

                              Spc7 234 ekieelkeqksele 247
                                       e+ + +  ++se+e
  gi|344209959|ref|YP_004786135.1|  92 ENQAGM--SRSEME 103
                                       877665..445554 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 ?   12.4   2.8   0.00047      0.16      36      68 ..      13      45 ..       9      51 .. 0.89
   2 ?    5.2   3.4     0.083        29      46      76 ..      44      74 ..      40      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00047
                       Fungal_TACC 36 yqkkldklelenkslkqeieqLkkqleaerkEK 68
                                      +q++ + +++en++l+ e e+L++ql+  r+++
  gi|344209959|ref|YP_004786135.1| 13 FQDSAQDIQTENEALHAENEELREQLNETREDR 45
                                      89999*********************9988865 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.083
                       Fungal_TACC 46 enkslkqeieqLkkqleaerkEKqeLlklld 76
                                      ++k+ k+  e+L+kqle+ +++ ++Ll+ l+
  gi|344209959|ref|YP_004786135.1| 44 DRKAEKSRAENLNKQLETRNEDVDTLLSELE 74
                                      5667777888999999999999888888776 PP

>> MAT1  CDK-activating kinase assembly factor MAT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4  11.3   0.00057       0.2      78     175 ..      17      99 ..      11     122 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00057
                              MAT1  78 kelIlknkeklkqeeeeleeleelekeekeekrkeekqeeeeekekkekakeelideLatsskdaeeiiekvkkkak 154
                                        + I+ ++e l++e+eel e++++ +e ++  +k  ++  +++ e+++++ + l++eL++ +k              
  gi|344209959|ref|YP_004786135.1|  17 AQDIQTENEALHAENEELREQLNETREDRKA-EKSRAENLNKQLETRNEDVDTLLSELERKEK-------------- 78 
                                       4566666666666666666666554444433.3333344444555566666666666666664.............. PP

                              MAT1 155 kkkssekekleelnkelkkka 175
                                         ++s+++ +e+ +++  +++
  gi|344209959|ref|YP_004786135.1|  79 MLNASQARLAESRENQAGMSR 99 
                                       332222222222222222222 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   7.7   0.00069      0.24       7      79 ..      13      91 ..       9     111 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00069
                             TMPIT  7 lekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeeveelkeelkerk 79
                                      +++++++++++++ ++++ eel ++ ++++++ k +k r+++l+++l++ +++v+      e++e+ ++  +++l+e +
  gi|344209959|ref|YP_004786135.1| 13 FQDSAQDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDtllselERKEKMLNASQARLAESR 91
                                      4566666666666666666666666666666666666666666666666666554443333333333333333333333 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   9.5    0.0006      0.21      70     124 ..      24      82 ..      11      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0006
                            DUF641  70 e....aeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnkk 124
                                       +    ae++el+ +++e r+  k+ + ++++l+++l++++++++ L ++Le+ ek  ++
  gi|344209959|ref|YP_004786135.1|  24 NealhAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLNA 82 
                                       12334899*******************************************99987655 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   6.9   0.00033      0.11      21      81 ..      16      76 ..       4      78 .. 0.93
   2 ?    2.3   0.4      0.59   2.1e+02      29      52 ..      77      96 ..      70     117 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00033
                              KxDL 21 tsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkaklakk 81
                                        + ++ +n+ L++ n+++ e+l+++r++ k  +  + +++k+Le+ ++ +++l ++l++k
  gi|344209959|ref|YP_004786135.1| 16 SAQDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERK 76
                                      567899**************************************************99987 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.59
                              KxDL 29 nreLlelnalsqerlaklrarfkq 52
                                      +++L    + sq+rla+ r++ + 
  gi|344209959|ref|YP_004786135.1| 77 EKML----NASQARLAESRENQAG 96
                                      4444....4466666666665444 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   4.7     0.001      0.35     256     345 ..      13      95 ..       2     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.001
                              FUSC 256 laallaelaaleaaaaaealeaalaalrarlralrraleadadtaalllarlaellaelaqllaslraleaaiaaar 332
                                       +++  +++++       eal+a+ ++lr++l+++r++++a+ ++a+ l  +l ++ +++  ll +l++ e+     +
  gi|344209959|ref|YP_004786135.1|  13 FQDSAQDIQT-----ENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLN--A 82 
                                       5555566666.....58999*************************************************99988..5 PP

                              FUSC 333 raerlarhrdhla 345
                                        ++rla +r+++a
  gi|344209959|ref|YP_004786135.1|  83 SQARLAESRENQA 95 
                                       6677777777665 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  13.4    0.0012      0.43     813     899 ..      20     105 ..       9     118 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0012
                           DUF3584 813 laeerpalkeqveelesaaeeleqeltrliedtklerkklekerkalekqldqldenlrklrdllsklaelkldada 889
                                       ++ e++al ++ eel+++++e +++ ++ ++ +++ +k+le+  +  + +l++l+ + + l++ + +lae ++++  
  gi|344209959|ref|YP_004786135.1|  20 IQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLNASQARLAESRENQAG 96 
                                       34444555555555555555555555555555555555555555555555555555554445555444444444443 PP

                           DUF3584 890 eqaegelaer 899
                                        + + e+++r
  gi|344209959|ref|YP_004786135.1|  97 MSRS-EMEKR 105
                                       3333.33333 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   9.4    0.0014      0.49     147     222 ..      18      97 ..       3     117 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                           DUF4407 147 aeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakld........atarlaal 215
                                       + i++ +++l a+++e++++l+ t+      ++ +  +a++ ++ql+++++++++l ++l+        ++arla+ 
  gi|344209959|ref|YP_004786135.1|  18 QDIQTENEALHAENEELREQLNETRE----DRKAEKSRAENLNKQLETRNEDVDTLLSELErkekmlnaSQARLAES 90 
                                       33334444444444444444443222....23344455555555555555555555555444333444444444444 PP

                           DUF4407 216 raelael 222
                                       r+++a++
  gi|344209959|ref|YP_004786135.1|  91 RENQAGM 97 
                                       4333333 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 ?   10.0   6.6    0.0013      0.45     147     240 ..      29      88 ..       8     121 .. 0.29

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0013
                      Exonuc_VII_L 147 eqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerlk. 222
                                       ++ e                      +l+++l++ +e                        k++++r e+l+++l+ 
  gi|344209959|ref|YP_004786135.1|  29 AENE----------------------ELREQLNETRED----------------------RKAEKSRAENLNKQLEt 61 
                                       1111......................111111111112......................22222222222222211 PP

                      Exonuc_VII_L 223 .........ekleekkerlkklkerle 240
                                                ++le+k++ l++ ++rl+
  gi|344209959|ref|YP_004786135.1|  62 rnedvdtllSELERKEKMLNASQARLA 88 
                                       111111111111111111111111111 PP

>> Flu_NS2  Influenza non-structural protein (NS2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.7    0.0028      0.99       2      67 ..      18      84 ..      17     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0028
                                      XXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX-CHHHHHHHHHHHHHHHHHHHHHC----TTSH CS
                           Flu_NS2  2 kdiisqfeslklrreslgelvmk.stdlhslqnrnekwreqlgqkreeirllieelrhklkiaessi 67
                                      +di++  e l    e l e +     d  + + r e+  +ql  + e++  l+ el  k k+ ++s 
  gi|344209959|ref|YP_004786135.1| 18 QDIQTENEALHAENEELREQLNEtREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLNASQ 84
                                      6999999****999999988754156899999****************************9999885 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 ?    9.6   5.7    0.0021      0.73      48     110 ..      22      87 ..      16      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0021
                          Lectin_N  48 sqnsqLqreLetLketfsnfssstlae...iqalssqggslsekvtsleaklekkqqdlkadhsel 110
                                         n  L  e e L+e+++++ ++ +ae    ++l+ q +  +e v +l ++le+k++ l+a ++ l
  gi|344209959|ref|YP_004786135.1|  22 TENEALHAENEELREQLNETREDRKAEksrAENLNKQLETRNEDVDTLLSELERKEKMLNASQARL 87 
                                       56788999999999999999998887733367899999************************9987 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 ?    8.9   9.7    0.0017      0.58     181     257 ..      18      94 ..      10     119 .. 0.50

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0017
                        Fmp27_WPPW 181 eeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseesseeeeskskelsaas 257
                                       ++++++ e l+ + eel ++ ++++e+ k+e ++ e+  k+l+++ e ++tll++l+++e+  + ++ +  e+ +++
  gi|344209959|ref|YP_004786135.1|  18 QDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLNASQARLAESRENQ 94 
                                       45555555555555555555555555555555556666666666666666666666665543221111111111111 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   9.8    0.0077       2.7      11      88 ..       9      87 ..       4      93 .. 0.84
   2 ?    5.6   1.8     0.043        15      21      78 ..      54     116 ..      52     120 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0077
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH....H CS
                        Laminin_II 11 takevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss.l 88
                                      t+++ ++  ++++++ e + ++ +e++++++et e+ k+ +   +  +++  + ++ ++ Ll+ l++ ++  +as++ l
  gi|344209959|ref|YP_004786135.1|  9 TTVAFQDSAQDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLNASQArL 87
                                      7788899999999999999999999999999999999988888888899999999999999999988888777777654 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.043
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXX--TTTTTGGGHHHH CS
                        Laminin_II  21 plsqnlentkeklseinrsveetnekvk.....dankairdArrsvkkLeklapqLldklkel 78 
                                       +l+++le  +e++ ++ +++e+ ++ ++      a    ++A+ s +++ek ++ L ++ +++
  gi|344209959|ref|YP_004786135.1|  54 NLNKQLETRNEDVDTLLSELERKEKMLNasqarLAESRENQAGMSRSEMEKRLDYLCAQPENI 116
                                       567777777777777777777777777722222344556778889999999999999886666 PP

>> Pup  Pup-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   5.5    0.0017      0.61      13      47 ..      37      73 ..       9      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0017
                               Pup 13 k..eeveeaeaeaeassevkerkeelsedvDdlLDeI 47
                                      +  e+ e+ +ae++ +++++++ e  +edvD lL e+
  gi|344209959|ref|YP_004786135.1| 37 QlnETREDRKAEKSRAENLNKQLETRNEDVDTLLSEL 73
                                      23366699999***********************996 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 ?    7.1  10.3     0.015       5.4       2      41 ..      30      69 ..      29      78 .. 0.81
   2 ?    0.4   0.2       1.9   6.7e+02       3      15 ..      66      78 ..      63      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.015
                     Bap31_Bap29_C  2 eiekLkkeLkkkkkDlealKkQaeglakEYDrLadehskl 41
                                      e+e+L+++L++++ D +a K+ ae+l+k     ++ +  l
  gi|344209959|ref|YP_004786135.1| 30 ENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTL 69
                                      99*************************9876666665555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.9
                     Bap31_Bap29_C  3 iekLkkeLkkkkk 15
                                      +  L +eL++k+k
  gi|344209959|ref|YP_004786135.1| 66 VDTLLSELERKEK 78
                                      6778889998874 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 ?    8.5   8.5    0.0061       2.1      23      73 ..      13      63 ..       8      64 .. 0.87
   2 ?    4.8   4.1     0.085        30      22      57 ..      54      89 ..      44     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0061
                     TolA_bind_tri 23 lqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrkleagg 73
                                       q   ++ q+e   L  ++Eel+ ql++++e  +      +++ ++le+++
  gi|344209959|ref|YP_004786135.1| 13 FQDSAQDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRN 63
                                      57788999***********************99999888888888888765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.085
                     TolA_bind_tri 22 elqqqlealqqelreLRGqiEelqyqleqleerQrd 57
                                      +l +qle+ ++++++L  ++E+ +  l+  + r  +
  gi|344209959|ref|YP_004786135.1| 54 NLNKQLETRNEDVDTLLSELERKEKMLNASQARLAE 89
                                      7999******************99999999988766 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   7.3    0.0039       1.4     335     411 ..      13      90 ..       2     108 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0039
                              FapA 335 lkeklkeleeeleeleeeleklkkkikklpklka.ekqlesekkeqlkklletkeklkeeleeleeelkelkeeles 410
                                       ++++ +++++e e+l++e e+l++++++ ++ ++ ek   ++  +ql+   e+   l +ele  e+ l++ +++l++
  gi|344209959|ref|YP_004786135.1|  13 FQDSAQDIQTENEALHAENEELREQLNETREDRKaEKSRAENLNKQLETRNEDVDTLLSELERKEKMLNASQARLAE 89 
                                       55666777777777777777777776666664442222222222233333333344444444444444444444444 PP

                              FapA 411 k 411
                                       +
  gi|344209959|ref|YP_004786135.1|  90 S 90 
                                       4 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  13.9    0.0022      0.79      21      69 ..      18      59 ..       4      74 .. 0.54
   2 ?   -0.3   8.6       4.4   1.6e+03      43      62 ..      68      87 ..      51     114 .. 0.43

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0022
                              ZapB 21 tlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkLLgkl 69
                                      +  q e+e+L +eneel e+ +e +       e+r+a ++r ++L ++l
  gi|344209959|ref|YP_004786135.1| 18 QDIQTENEALHAENEELREQLNETR-------EDRKAEKSRAENLNKQL 59
                                      4455555555555555555555555.......44444444444433332 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 4.4
                              ZapB 43 eleeeneqlkeereawqerl 62
                                       l +e+e+ ++  +a q+rl
  gi|344209959|ref|YP_004786135.1| 68 TLLSELERKEKMLNASQARL 87
                                      33333333333333333333 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 ?   -0.1   0.0       5.1   1.8e+03      80      93 ..      14      27 ..       8      29 .. 0.74
   2 ?    7.9  17.7     0.016       5.8       7      74 ..      25      95 ..      19     114 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 5.1
                    PRKG1_interact 80 raenqrLkdEngAL 93
                                      + + q ++ En+AL
  gi|344209959|ref|YP_004786135.1| 14 QDSAQDIQTENEAL 27
                                      56678888888887 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.016
                    PRKG1_interact  7 eeekeenerLkreLeelekelselkseleklkqqrqesvsk.rssllelekrer..rslerkiseleeelk 74
                                      e+ ++ene+L+++L+e++++ +  ks+ e+l++q ++++++  + l+ele++e+  ++ + +++e  e++ 
  gi|344209959|ref|YP_004786135.1| 25 EALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDvDTLLSELERKEKmlNASQARLAESRENQA 95
                                      56689***************************995555555145556677777622334444555544443 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   6.2    0.0083       2.9     142     234 ..      13     106 ..       5     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0083
                              CorA 142 edstkkeilrelaqlrrrlvklrralapnrevlkrlla..kaddkllddedkeylrdlldelerllemlealrerle 216
                                       ++++ ++i  e  +l+ +  +lr++l+++re  k   +   ++ ++  ++++e  ++ll+eler ++ml+a + rl 
  gi|344209959|ref|YP_004786135.1|  13 FQDSAQDIQTENEALHAENEELREQLNETREDRK-AEKsrAENLNKQLETRNEDVDTLLSELERKEKMLNASQARLA 88 
                                       677778888888899999999999*999999774.3332323333333344466*********************** PP

                              CorA 217 slqdtyssllserlNrvm 234
                                         +++ + ++  ++ + +
  gi|344209959|ref|YP_004786135.1|  89 ESRENQAGMSRSEMEKRL 106
                                       ****99999998887766 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   5.9    0.0012      0.41      18      62 ..       9      51 ..       3      53 .. 0.81
   2 ?    1.7   7.7      0.62   2.2e+02      19      58 ..      42      81 ..      40     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0012
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXX CS
                             DivIC 18 aykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieerAR 62
                                      +  + +   +++q e+++l+aeneeL +++++ +  ed+ +e+ R
  gi|344209959|ref|YP_004786135.1|  9 TTVAFQDSAQDIQTENEALHAENEELREQLNETR--EDRKAEKSR 51
                                      6677888899**********************97..666655555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.62
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXX CS
                             DivIC 19 ykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyie 58
                                      + + k+e  + ++ +++l  +ne+ +  +++L+  e ++ 
  gi|344209959|ref|YP_004786135.1| 42 REDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLN 81
                                      678899***********************99987777664 PP

>> NYD-SP28_assoc  Sperm tail C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.1   0.00096      0.34      37      58 ..      19      40 ..      17      41 .. 0.89
   2 ?    1.6   0.6      0.87   3.1e+02      36      57 ..      50      71 ..      46      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00096
                    NYD-SP28_assoc 37 klieetesLekqNeeLrnlLkq 58
                                       + +e+e+L+++NeeLr+ L++
  gi|344209959|ref|YP_004786135.1| 19 DIQTENEALHAENEELREQLNE 40
                                      5779**************9986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.87
                    NYD-SP28_assoc 36 aklieetesLekqNeeLrnlLk 57
                                      +   + +++Le  Ne   +lL 
  gi|344209959|ref|YP_004786135.1| 50 SRAENLNKQLETRNEDVDTLLS 71
                                      5556667999999*99999996 PP

>> DUF2570  Protein of unknown function (DUF2570)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   6.9    0.0051       1.8      43      86 ..      28      71 ..       9      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0051
                           DUF2570 43 qkanqrLteqLeqerqavekqqkianelkakveeekeevktilk 86
                                      ++ n++L eqL+  r   +  +  a++l++++e+ +e+v t+l 
  gi|344209959|ref|YP_004786135.1| 28 HAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLS 71
                                      35699************************************996 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   3.7     0.026       9.2      34      65 ..      22      53 ..      17      55 .. 0.80
   2 ?    7.3   4.6     0.017       6.1      32      70 .]      55      93 ..      52      93 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.026
                            Csm1_N 34 qkletkdqeiesLkeqlaeleekvkeleerrk 65
                                      +++e  + e e+L+eql+e +e++k  ++r++
  gi|344209959|ref|YP_004786135.1| 22 TENEALHAENEELREQLNETREDRKAEKSRAE 53
                                      55666778999999999999999998888765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.017
                            Csm1_N 32 LsqkletkdqeiesLkeqlaeleekvkeleerrkkqeEe 70
                                      L+++let+++ + +L  +l+  e+ ++ ++ r +++ E+
  gi|344209959|ref|YP_004786135.1| 55 LNKQLETRNEDVDTLLSELERKEKMLNASQARLAESREN 93
                                      89******************************9999997 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  23.5     0.052        18      44     125 ..      26     112 ..       9     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.052
                            APG6_N  44 k....qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreyne.lqlellel 115
                                       +    ++e +e+l+e  e+ ++e++++++  k+le+ +e+++  l++le++++ l++ ++r  +++ +   +  +e+
  gi|344209959|ref|YP_004786135.1|  26 AlhaeNEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLNASQARLAESRENqAGMSRSEM 102
                                       23333345556666667778888888888888999999999999999999999999999999888766577888888 PP

                            APG6_N 116 eeeldsleaq 125
                                       e++ld l aq
  gi|344209959|ref|YP_004786135.1| 103 EKRLDYLCAQ 112
                                       8888877666 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.3      0.74   2.6e+02      24      53 ..      14      36 ..       6      49 .. 0.53
   2 ?    5.1   4.5      0.09        32      31      67 ..      46      82 ..      18      90 .. 0.74
   3 ?   -0.9   0.0       6.5   2.3e+03      38      54 ..     100     116 ..      84     118 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.74
                           NPV_P10 24 qqqvddvqenlpdvtelnekLdaqsaqLae 53
                                      q++ +d+q+        ne L a +++L e
  gi|344209959|ref|YP_004786135.1| 14 QDSAQDIQT-------ENEALHAENEELRE 36
                                      444444444.......44444444444432 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.09
                           NPV_P10 31 qenlpdvtelnekLdaqsaqLaeletkvenIqdiLnp 67
                                      +++    ++ln++L+  ++ +++l +++e  +++Ln+
  gi|344209959|ref|YP_004786135.1| 46 KAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLNA 82
                                      33344568899*****************999999994 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 6.5
                           NPV_P10  38 telnekLdaqsaqLael 54 
                                       +e++++Ld + aq +++
  gi|344209959|ref|YP_004786135.1| 100 SEMEKRLDYLCAQPENI 116
                                       68889999988887666 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 ?    7.7  13.7    0.0091       3.2     119     175 ..      15      70 ..       9      82 .. 0.74
   2 ?    3.9   4.4      0.13        47     118     177 ..      53     112 ..      52     119 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0091
                   Ax_dynein_light 119 qgkselekkikeLeeekeelekqvaelkaklealekrekerrqeeekkheeeieflk 175
                                       +  ++++ + ++L +e+eel++q++e+++  +a+++r+++ +++ e ++e +++ l 
  gi|344209959|ref|YP_004786135.1|  15 DSAQDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNE-DVDTLL 70 
                                       56789999999***************999999888888777777766655.444443 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.13
                   Ax_dynein_light 118 eqgkselekkikeLeeekeelekqvaelkaklealekrekerrqeeekkheeeieflkks 177
                                       e+ +++le + +++++  +ele++ + l+a  + l ++ +++  + +++ e+ +++l  +
  gi|344209959|ref|YP_004786135.1|  53 ENLNKQLETRNEDVDTLLSELERKEKMLNASQARLAESRENQAGMSRSEMEKRLDYLCAQ 112
                                       455667777777777777777777777777777777777777777777777777777655 PP

>> Mt_ATP-synt_B  Mitochondrial ATP synthase B chain precursor (ATP-synt_B)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   9.1     0.018       6.3      41     110 ..      12      84 ..       3      88 .. 0.86
   2 ?    4.3   3.0     0.077        27      55     119 ..      49     110 ..      46     119 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHH CS
                     Mt_ATP-synt_B  41 fldkriekiqeelnqsrnlke...ealkerieqekklqslveltkslfevskeqvaleaeaferelqaklare 110
                                        +++ ++ iq+e ++ ++++e   e+l+e  e+ k ++s++e+ ++ +e   e v ++++  er+ ++  a++
  gi|344209959|ref|YP_004786135.1|  12 AFQDSAQDIQTENEALHAENEelrEQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSELERKEKMLNASQ 84 
                                       57889999****99999999722257888889999******************************99987766 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.077
                                       HHHHHH.HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Mt_ATP-synt_B  55 qsrnlk.eealkerieqekklqslveltkslfevskeqvaleaeaferelqaklareikkkldtlv 119
                                       +sr+++  ++l++r+e++  l s +e +++++ +s    a++ae++e +++    +e++k+ld+l 
  gi|344209959|ref|YP_004786135.1|  49 KSRAENlNKQLETRNEDVDTLLSELERKEKMLNASQ---ARLAESRE-NQAGMSRSEMEKRLDYLC 110
                                       556666568899999999999988888888888876...44555554.445556678888888875 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2  14.1     0.018       6.5     433     518 ..      17     103 ..      10     115 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.018
                          Macoilin 433 erslkselqqlkkendllqtklhelvsakqkdkqtlqqlekrLkeekearaslekqLaeekkrkkeeeetaara... 506
                                        + +++e ++l+ en++l+++l+e  + ++ +k   ++l+k+L++ +e   +l + L  e+k k  +  +a+ a   
  gi|344209959|ref|YP_004786135.1|  17 AQDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQLETRNEDVDTLLSEL--ERKEKMLNASQARLAesr 91 
                                       567899999**********************************98887765555555..344444333333222001 PP

                          Macoilin 507 valaaasrsect 518
                                         +a  srse+ 
  gi|344209959|ref|YP_004786135.1|  92 ENQAGMSRSEME 103
                                       344555555544 PP

>> MctB  Copper transport outer membrane protein, MctB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.2    0.0017      0.62      24      75 ..       7      58 ..       5      62 .. 0.84
   2 ?    1.3   2.1      0.64   2.2e+02      43      76 ..      54      87 ..      49     109 .. 0.49

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0017
                              MctB 24 lGsgvlsdnlldtlegqveelreekeelraeadaleaqleaaddfaaavapr 75
                                      +G++v  ++ +++++ ++e+l++e+eelr++ ++++++ +a+++ a+++ ++
  gi|344209959|ref|YP_004786135.1|  7 VGTTVAFQDSAQDIQTENEALHAENEELREQLNETREDRKAEKSRAENLNKQ 58
                                      6888888889999999999999999999999999999999988888877655 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.64
                              MctB 43 elreekeelraeadaleaqleaaddfaaavaprl 76
                                      +l+++ e+ ++++d l ++le+++++ +a  +rl
  gi|344209959|ref|YP_004786135.1| 54 NLNKQLETRNEDVDTLLSELERKEKMLNASQARL 87
                                      3444444444444444444444444443333333 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 ?    9.6   9.4    0.0033       1.2      25      74 ..      13      65 ..       8      69 .. 0.79
   2 ?    3.3   2.7      0.31   1.1e+02       8      46 ..      66     104 ..      59     115 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0033
                            CENP-H 25 lqeeltevekenlrlkrknrelaaellelakekesek...eklkeelekleae 74
                                       q++ ++++ en +l+++n+el ++l e++++ ++ek   e+l+++le+  ++
  gi|344209959|ref|YP_004786135.1| 13 FQDSAQDIQTENEALHAENEELREQLNETREDRKAEKsraENLNKQLETRNED 65
                                      6889999*******************888888888885666677777665555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.31
                            CENP-H   8 rdelssellklsqelrelqeeltevekenlrlkrknrel 46 
                                        d+l sel++ ++ l++ q++l+e ++++  ++r + e+
  gi|344209959|ref|YP_004786135.1|  66 VDTLLSELERKEKMLNASQARLAESRENQAGMSRSEMEK 104
                                       567777777777777777777777777777776666655 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 ?    7.2  14.8     0.016       5.7       8      71 ..      16      85 ..      12      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.016
                            Cnn_1N  8 qidkLkKENFdLKLriyfLeerleklse......eqkeellkenielkveveslqkelkekkkllreaek 71
                                      + ++++ EN  L  +  +L+e+l++++e      +  e+l k++    ++v +l  el++k+k+l+ ++ 
  gi|344209959|ref|YP_004786135.1| 16 SAQDIQTENEALHAENEELREQLNETREdrkaekSRAENLNKQLETRNEDVDTLLSELERKEKMLNASQA 85
                                      56789999999999999999999999999998877888888888888899999**********9998775 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   8.4    0.0072       2.5       8      50 ..      12      54 ..       9      61 .. 0.82
   2 ?    2.5   6.0      0.49   1.7e+02      11      44 ..      57      92 ..      52     117 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0072
                             Spc24  8 riakelsdleselesleselaelkeeleeleeeseekeserve 50
                                      +++ +++d+++e e+l +e +el+e+l+e  e +++++s++++
  gi|344209959|ref|YP_004786135.1| 12 AFQDSAQDIQTENEALHAENEELREQLNETREDRKAEKSRAEN 54
                                      567899*************************999996666544 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.49
                             Spc24 11 kelsdleselesleselaelkeeleeleeesee..k 44
                                      k+l+  +++++ l sel++++++l+  +    e  +
  gi|344209959|ref|YP_004786135.1| 57 KQLETRNEDVDTLLSELERKEKMLNASQARLAEsrE 92
                                      444444444444444444444444444444333220 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3170  (0.176809); expected 358.6 (0.02)
Passed bias filter:                     1260  (0.0702772); expected 358.6 (0.02)
Passed Vit filter:                       234  (0.0130515); 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):              51  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 878.90
//
Query:       gi|344209960|ref|YP_004786136.1|  [L=403]
Description: integrase family protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   28.0   0.0    3.4e-06   27.0   0.0    1.5  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 !   27.0   0.0   1.9e-10   3.4e-06       3     139 ..     207     347 ..     205     357 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.9e-10
                                       HHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECT...TTEEEEE..EEECSSSSEEEEECTH CS
                   Phage_integrase   3 ltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldle...ngvilvh..eregKgskeravplse 74 
                                       l+   v+rl+ a+ e   +rd+ ++  + + GlR sE++sL++ +l+l+   +++ +++    e +++   +v+l  
  gi|344209960|ref|YP_004786136.1| 207 LDRTAVQRLYGAASE---LRDRFIVVACCGWGLRPSEVASLHIRQLNLDpddDSHPYIEfgDGE-RKNGPGTVALL- 278
                                       788899*********...****************************997222567888543222.33444666665. PP

                                       HHHHHHHHHHHHHCHCCTTTSBSSBET..TSSB--HHHHHHHHHHHHHHCT-S...SC--TTHHHHHHHH CS
                   Phage_integrase  75 ealellkellskaleeaeksellfask..rgkplsrqtvrkafkraveeagie...kpltpHtlRhsfat 139
                                       + le +++ +++     e s +l++s   ++ +l+++tvr++fk+++e+a+++   + +tp t R+ + t
  gi|344209960|ref|YP_004786136.1| 279 AGLETVERRIETL-ADPEWSGYLLPSPsaATGHLTAETVRRRFKSVAEAADVTvdgDTPTPKTGRRFWYT 347
                                       3345555555555.4447899999988779**********************999999999998876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2978.51
//
Query:       gi|344209961|ref|YP_004786137.1|  [L=281]
Description: putative plasmid partitioning protein Soj [Haloarcula hispanica ATCC 33960]
Scores for 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   78.5   0.0    9.1e-22   77.8   0.0    1.2  1  AAA_31       AAA domain
    6.1e-16   58.6   0.0    1.3e-15   57.6   0.0    1.5  2  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    4.9e-08   32.7   0.0    2.3e-06   27.2   0.0    2.1  2  ParA         NUBPL iron-transfer P-loop NTPase
      5e-07   29.2   0.0    1.1e-05   24.8   0.0    2.1  2  ArsA_ATPase  Anion-transporting ATPase
    8.5e-07   28.5   0.0    0.00025   20.4   0.0    2.5  2  MipZ         ATPase MipZ
    2.9e-06   27.0   0.0    5.3e-06   26.1   0.0    1.4  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    0.00082   18.9   0.0     0.0016   18.0   0.0    1.4  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
  ------ inclusion threshold ------
      0.024   14.2   0.2       0.08   12.5   0.2    2.0  1  AAA_25       AAA domain
      0.097   12.5   0.0       0.24   11.2   0.0    1.6  1  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
       0.12   12.0   0.1       0.54   10.0   0.0    2.1  2  AAA_24       AAA domain


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.0   5.1e-25   9.1e-22       6     168 ..       6     184 ..       2     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 5.1e-25
                            AAA_31   6 ianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQa.nattglgiekne...iektlyevli..eeknikeaiikt 76 
                                       ++   GGvGKTT + nla+a a++g+ vL +D+DpQ+ ++++ +++  ++      +l++ l+   +   +++i   
  gi|344209961|ref|YP_004786137.1|   6 VYSEAGGVGKTTMAANLAVADARAGHDVLAIDMDPQEgSLSFLFDVADRRtdsEADSLVRHLVerPRGPFADLIE-- 80 
                                       67788*******************************725677777744432333335555554246677888888.. PP

                            AAA_31  77 kvenldlipssidLaeaeielvelekk..........eeilkellek..vkdeYDyiiiDcpPsLglltenaLvasd 141
                                       ++e +d++p++ +L  ++++l + e++          + +l ++l++  v +eYD +iiD p + ++ + naL a  
  gi|344209961|ref|YP_004786137.1|  81 TSEGVDVLPAHNSLEVLSKHLRRREEEaadfgenwnpNVQLLRVLKDagVPSEYDTVIIDPPATADVKLYNALHATR 157
                                       66799****************9999998888888777666888897533789************************* PP

                            AAA_31 142 sviipvqaea...yaleGleqllktieevk 168
                                        ++ip +++     ++eGl++l++ +   +
  gi|344209961|ref|YP_004786137.1| 158 NLVIPFEPSGkgqQSVEGLADLVTGL---E 184
                                       *******9761125555555555444...3 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 !   57.6   0.0     7e-19   1.3e-15       2     108 ..       5     223 ..       4     233 .. 0.90
   2 ?   -2.9   0.0       3.7   6.6e+03      55      69 ..     260     274 ..     239     277 .. 0.65

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 7e-19
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       ++ s  GGvGKTt+aanLa+a ar+g++Vl++D+Dpq  +l+ l+ ++ d+++                        
  gi|344209961|ref|YP_004786137.1|   5 TVYSEAGGVGKTTMAANLAVADARAGHDVLAIDMDPQEGSLSFLF-DVADRRTdseadslvrhlverprgpfadlie 80 
                                       578999*******************************99999543.333333358999******************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|344209961|ref|YP_004786137.1|  81 tsegvdvlpahnslevlskhlrrreeeaadfgenwnpnvqllrvlkdagvpseydtviidppatadvklynalhatr 157
                                       ***************************************************************************** PP

                                       ..............CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-E CS
                                       ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ..............dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpv 108
                                                     +++ l  l+  l  ++  ++ ++  v+nr++g n ++++ + l+ +   y +pv
  gi|344209961|ref|YP_004786137.1| 158 nlvipfepsgkgqqSVEGLADLVTGLEDTLDINVGVLAAVPNRFKGTNDQEEMLKRLRAES--YDIPV 223
                                       **********98888888888888888888888*************988777777777764..35555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.7
                                       CCHCCCHHHHHHCHC CS
                                       xxxxxxxxxxxxxxx RF
                              CbiA  55 dlkrllellealgkk 69 
                                       +l++++el+++l+++
  gi|344209961|ref|YP_004786137.1| 260 TLEQFEELAAHLRQT 274
                                       778888888888776 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 !   27.2   0.0   1.3e-09   2.3e-06       6      62 ..       4      60 ..       2      73 .. 0.90
   2 ?    3.6   0.0     0.021        37     110     129 ..     132     150 ..      78     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.3e-09
                              ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqse 62
                                      ++v S  GGVGK+t+a+nlA+a a+ g++v  +D+D    s+  l++v ++++ +++
  gi|344209961|ref|YP_004786137.1|  4 YTVYSEAGGVGKTTMAANLAVADARAGHDVLAIDMDPQEGSLSFLFDVADRRTDSEA 60
                                      57999*******************************************998777664 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.021
                              ParA 110 gelDyLiiDlPPGtgDeqlt 129
                                       +e D +iiD PP t+D++l 
  gi|344209961|ref|YP_004786137.1| 132 SEYDTVIID-PPATADVKLY 150
                                       578999**9.9******985 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   6.1e-09   1.1e-05       7      49 ..       8      51 ..       2      68 .. 0.85
   2 ?    2.6   0.0     0.036        64     121     202 ..     130     212 ..      93     249 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6.1e-09
                                      EESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTT.HHHHHHTS CS
                       ArsA_ATPase  7 gGKGGVGKttvsaatavklsekgkkvllistDPAh.slsDsfdq 49
                                      +  GGVGKtt++a +av  ++ g++vl i  DP   sls  fd 
  gi|344209961|ref|YP_004786137.1|  8 SEAGGVGKTTMAANLAVADARAGHDVLAIDMDPQEgSLSFLFDV 51
                                      557******************************75488888876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.036
                                       HCSSSSEEEEESBSCCHTCGG...GGHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSHCHHHHHHHHHHHHHHHHHHH CS
                       ArsA_ATPase 121 keeeydvvvlDtaPTGhtlrl...lslpevleklleklvklkeklsplakqlvkllglggvsieealeeleetkeei 194
                                         +eyd+v++D + T + ++l   l+  ++l   +e   k ++ ++ la  +++l ++ + ++  +l+++ ++++  
  gi|344209961|ref|YP_004786137.1| 130 VPSEYDTVIIDPPATAD-VKLynaLHATRNLVIPFEPSGKGQQSVEGLADLVTGLEDTLDINVG-VLAAVPNRFKGT 204
                                       4789*******777654.4441113334444444555566666666666666666665555555.555555555555 PP

                                       HHHHHHHT CS
                       ArsA_ATPase 195 kkveeilt 202
                                       ++ ee+l+
  gi|344209961|ref|YP_004786137.1| 205 NDQEEMLK 212
                                       55555555 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.4e-07   0.00025       7      48 ..       8      49 ..       4      70 .. 0.84
   2 !    5.3   0.0    0.0056        10      71     130 ..     104     164 ..      89     167 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.4e-07
                                      -SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHH CS
                              MipZ  7 nekGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryl 48
                                       e GG Gk+t+a  +ava +++G+ v aid+d +  +l+  +
  gi|344209961|ref|YP_004786137.1|  8 SEAGGVGKTTMAANLAVADARAGHDVLAIDMDPQEGSLSFLF 49
                                      699*****************************9887776555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0056
                                       SS-HHHHTTS-HHHHHHHHHHHHHH..HHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEE CS
                              MipZ  71 seaeeaeveeeeeaevaeleelvad..leaeldfividtPGsdsalsrlahsladtlvtPln 130
                                       +e+e+a+  e+ + +v+ l+ +++d  + +e+d ++id P + +     a      lv P+ 
  gi|344209961|ref|YP_004786137.1| 104 REEEAADFGENWNPNVQLLR-VLKDagVPSEYDTVIIDPPATADVKLYNALHATRNLVIPFE 164
                                       45556666667777755454.4444125789**********999999999999999999976 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0     3e-09   5.3e-06      11     138 ..      11     155 ..       4     166 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3e-09
                          CBP_BcsQ  11 GGvGttsllaaLawalhelgesvlviDlspdn.lLrlhFnvdieqreg....waraeldg..apwrqaaleyapgld 80 
                                       GGvG+t+++a La a  + g+ vl+iD+ p++  L + F+v+ +++++    ++r ++++   p+    +e  +g+d
  gi|344209961|ref|YP_004786137.1|  11 GGVGKTTMAANLAVADARAGHDVLAIDMDPQEgSLSFLFDVADRRTDSeadsLVRHLVERprGPFA-DLIETSEGVD 86 
                                       9****************************9874799999988665554011155544443113454.4679999999 PP

                          CBP_BcsQ  81 llPfGelnveekenlqq....laekaeallaalkelk........eqyrwillDlpagasaltrellala 138
                                       +lP  +  +   ++l+      a+  e+++ +++ l+        ++y+ +++D pa a+    ++l+ a
  gi|344209961|ref|YP_004786137.1|  87 VLPAHNSLEVLSKHLRRreeeAADFGENWNPNVQLLRvlkdagvpSEYDTVIIDPPATADVKLYNALH-A 155
                                       99965433333333333111134445778888877777768888889999999999988766655555.3 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   8.7e-07    0.0016       8      49 ..      10      51 ..       3      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8.7e-07
                         Fer4_NifH  8 kGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllgg 49
                                       GG+Gk+t ++nl+ a a+ g+ vl +  DP++ s ++l++ 
  gi|344209961|ref|YP_004786137.1| 10 AGGVGKTTMAANLAVADARAGHDVLAIDMDPQEGSLSFLFDV 51
                                      59*********************************9999875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   4.4e-05      0.08      41      74 ..      10      45 ..       5     164 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.4e-05
                            AAA_25 41 apgtGKttlaldlalava.tGkpwlg.pvapeqgkV 74
                                      a+g+GKtt+a +la+a a  G+ +l  ++ p+ g  
  gi|344209961|ref|YP_004786137.1| 10 AGGVGKTTMAANLAVADArAGHDVLAiDMDPQEGSL 45
                                      79****************999999888777766654 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 ?   11.2   0.0   0.00013      0.24       4      38 ..      12      46 ..      10      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                            CLP1_P  4 dsGKSTlarlLlNyalrkgrkpvyvDlDvGqseis 38
                                       +GK+T+a++L+   +r+g+ ++ +D+D+  +++s
  gi|344209961|ref|YP_004786137.1| 12 GVGKTTMAANLAVADARAGHDVLAIDMDPQEGSLS 46
                                      59***************************999987 PP

>> AAA_24  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      0.54      11      72 ..      11     140 ..       2     145 .. 0.68
   2 ?   -1.1   0.0      0.73   1.3e+03      40      40 ..     216     216 ..     157     278 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0003
                            AAA_24  11 sgiGKTtlakel.......gpkplfidtek..Glksldadkfpdie............swedfldevvel....... 59 
                                        g+GKTt+a++l       g ++l id++   G+ s  +d  ++ +                               
  gi|344209961|ref|YP_004786137.1|  11 GGVGKTTMAANLavadaraGHDVLAIDMDPqeGSLSFLFDVADRRTdseadslvrhlvE----------Rprgpfad 77 
                                       48**********99999999999999998655777776666665556633444444440..........34444444 PP

                            AAA_24  60 ..................................................aaeladyktlviD 72 
                                                                                         a  +++y+t++iD
  gi|344209961|ref|YP_004786137.1|  78 lietsegvdvlpahnslevlskhlrrreeeaadfgenwnpnvqllrvlkdAGVPSEYDTVIID 140
                                       444444446667777777777777777777777777777777777777777777777777777 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.73
                            AAA_24  40 a 40 
                                       a
  gi|344209961|ref|YP_004786137.1| 216 A 216
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 2195.10
//
Query:       gi|344209962|ref|YP_004786138.1|  [L=127]
Description: hypothetical protein HAH_5020 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   0.0       0.53   10.6   0.0    1.9  2  DUF2999   Protein of unknown function (DUF2999)


Domain annotation for each model (and alignments):
>> DUF2999  Protein of unknown function (DUF2999)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       0.1   1.8e+03      15      60 ..      22      38 ..      18      50 .. 0.60
   2 ?   10.6   0.0     3e-05      0.53      44      73 ..      93     122 ..      83     127 .] 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.1
                           DUF2999 15 dekiaelfealtenPlaamaliqqlGipqeklqallalvmtnPali 60
                                      de+  e++                              v t+Pa +
  gi|344209962|ref|YP_004786138.1| 22 DEQQDEVM-----------------------------DVETEPADV 38
                                      55555554.............................444555444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 3e-05
                           DUF2999  44 eklqallalvmtnPalikeaveelgldfsk 73 
                                       + l a l + m nP+l+ e + e g d+ +
  gi|344209962|ref|YP_004786138.1|  93 DALEAALVVAMDNPDLVAEKLREWGYDWEQ 122
                                       77889999******************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 888.14
//
Query:       gi|344209963|ref|YP_004786139.1|  [L=311]
Description: transcription regulator [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-36  124.3   0.1    6.4e-36  123.0   0.1    1.6  2  IclR         Bacterial transcriptional regulator
    1.6e-07   31.0   0.0    3.6e-07   29.9   0.0    1.7  1  HTH_IclR     IclR helix-turn-helix domain
    9.9e-07   28.2   0.0    1.9e-06   27.3   0.0    1.5  1  HTH_24       Winged helix-turn-helix DNA-binding
    5.5e-05   23.1   0.0    0.00034   20.5   0.0    2.2  3  HTH_45       Winged helix-turn-helix
    0.00022   21.1   0.0    0.00085   19.2   0.0    2.0  1  MarR_2       MarR family
    0.00053   19.8   0.0     0.0011   18.8   0.0    1.5  1  HTH_5        Bacterial regulatory protein, arsR family
     0.0022   17.9   0.0      0.019   14.9   0.0    2.4  2  MarR         MarR family
     0.0027   18.1   0.1      0.011   16.2   0.0    2.1  2  HTH_27       Winged helix DNA-binding domain
     0.0035   17.3   0.1      0.013   15.5   0.0    2.0  2  HTH_11       HTH domain
     0.0035   17.4   0.0       0.01   15.9   0.0    1.7  1  HTH_20       Helix-turn-helix domain
     0.0036   17.8   0.0      0.013   16.0   0.0    2.0  2  ANAPC2       Anaphase promoting complex (APC) subunit 2
  ------ inclusion threshold ------
      0.064   13.0   0.1       0.16   11.7   0.1    1.6  1  HTH_DeoR     DeoR-like helix-turn-helix domain
      0.071   13.4   0.1        5.2    7.5   0.0    2.6  2  PqqD         Coenzyme PQQ synthesis protein D (PqqD)
      0.093   12.6   0.0       0.58   10.0   0.0    2.3  2  HTH_10       HTH DNA binding domain
      0.097   12.8   0.1       0.64   10.2   0.0    2.0  2  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
       0.11   13.1   0.7        4.3    8.0   0.2    2.7  2  TAF8_C       Transcription factor TFIID complex subunit 8 C-t
       0.12   12.8   0.0        0.4   11.1   0.0    1.9  2  Rrf2         Transcriptional regulator


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 ?   -3.3   0.0         7   7.4e+03      22      46 ..     129     154 ..     116     159 .. 0.64
   2 !  123.0   0.1     6e-39   6.4e-36      12     128 ..     185     301 ..     177     302 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7
                                       HHHHHTS-HHHHHHHHHH.HT---SS CS
                              IclR  22 KalLaaldeeelealler.lelkrlt 46 
                                       ++ L++  +ee+e+l e+ +e+  lt
  gi|344209963|ref|YP_004786139.1| 129 RVDLYQIGKEEVERLAEEtSEWVHLT 154
                                       55566666677777766645665555 PP

  == domain 2  score: 123.0 bits;  conditional E-value: 6e-39
                                       EEEGGGSHHHHHHHHTS-HHHHHHHHHHHT---SSTTS--SHHHHHHHHHHHHHHTSEEEESSSSTTEEEEEEEEE- CS
                              IclR  12 rlplyataiGKalLaaldeeeleallerlelkrlterTitdpeeLleeLakvReqGyavdreEeeegvrciAapifd 88 
                                        + l++ta+GKalLa+ de++++ +l + el + te+Titdp+eL+e+La++R++Gya+++eEe  g+r+++api d
  gi|344209963|ref|YP_004786139.1| 185 PQYLHCTATGKALLAHFDEAQVTDILASEELVQQTEKTITDPDELRERLAEIRRKGYAINDEEEIRGMRSVGAPIQD 261
                                       5669************************************************************************* PP

                                       TTSSEEEEEEEEEETTTSHHHHHHHHHHHHHHHHHHHHHH CS
                              IclR  89 asgevvaAvsvsgptarlteeelkeellalvreaArkisr 128
                                         g v +A+sv++p++rl+ e+l+++l +lv+eaA+ i+ 
  gi|344209963|ref|YP_004786139.1| 262 VDGAVCGAISVTAPKMRLSGEYLNSDLPELVMEAANIIEV 301
                                       ************************************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 !   29.9   0.0   3.4e-10   3.6e-07       5      50 ..      64     108 ..      60     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 3.4e-10
                                       HHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR   5 alaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       a +iL+ + ++ + +tl++l++  +++kSt h +LqtLv +G++ +
  gi|344209963|ref|YP_004786139.1|  64 ASDILREIQSQSE-VTLADLCDDVDVAKSTLHTYLQTLVAEGFIDK 108
                                       5678888888888.8****************************976 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 !   27.3   0.0   1.8e-09   1.9e-06       7      47 ..      66     106 ..      62     107 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.8e-09
                            HTH_24   7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       +IL+++q ++  + ++L++ +++ +st++++l+ L+ eG+I
  gi|344209963|ref|YP_004786139.1|  66 DILREIQSQSEVTLADLCDDVDVAKSTLHTYLQTLVAEGFI 106
                                       7***************************************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 !   20.5   0.0   3.2e-07   0.00034       5      58 ..      61     115 ..      59     128 .. 0.91
   2 ?   -2.4   0.0       4.6   4.9e+03      57      72 ..     189     204 ..     183     208 .. 0.80
   3 ?   -1.4   0.0       2.2   2.4e+03      41      55 ..     208     222 ..     195     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.2e-07
                            HTH_45   5 leIiadILeais.egeakkTkimykanLsykllnkYLdmLvekglikkskekYvl 58 
                                       ++  +dIL+ i+ ++e +   +  +++   ++l+ YL++Lv +g+i+ks++ Y+l
  gi|344209963|ref|YP_004786139.1|  61 IQTASDILREIQsQSEVTLADLCDDVDVAKSTLHTYLQTLVAEGFIDKSDGVYRL 115
                                       56679******878888999*********************************97 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.6
                            HTH_45  57 vlTekGlelleklkel 72 
                                         T+ G+ ll +++e 
  gi|344209963|ref|YP_004786139.1| 189 HCTATGKALLAHFDEA 204
                                       5799999999999876 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.2
                            HTH_45  41 dmLvekglikkskek 55 
                                       d+L +++l+++++++
  gi|344209963|ref|YP_004786139.1| 208 DILASEELVQQTEKT 222
                                       678888899888775 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   8.1e-07   0.00085       7      56 ..      64     111 ..      62     113 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.1e-07
                                       HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2   7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                         ++L ++    +  +t ++l++  ++ ks+++  l+ Lva G++ +++g
  gi|344209963|ref|YP_004786139.1|  64 ASDILREIQSQSE--VTLADLCDDVDVAKSTLHTYLQTLVAEGFIDKSDG 111
                                       5799*******99..******************************99875 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 !   18.8   0.0     1e-06    0.0011       3      47 .]      63     108 ..      62     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1e-06
                                       HHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5   3 tRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                       t ++IL+  ++ +e +  +l++++++ +st+  +L  L  +G+++k
  gi|344209963|ref|YP_004786139.1|  63 TASDILREIQSqSEVTLADLCDDVDVAKSTLHTYLQTLVAEGFIDK 108
                                       56788888888788*****************************986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.94   9.9e+02      29      40 ..      49      60 ..      45      65 .. 0.85
   2 !   14.9   0.0   1.8e-05     0.019       7      50 ..      66     109 ..      61     111 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.94
                                      S-HHHHHHHHHH CS
                              MarR 29 vskstvtrvldr 40
                                       +++t+tr+++ 
  gi|344209963|ref|YP_004786139.1| 49 REPPTATRQIKS 60
                                      689******985 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR   7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                       +iLr + +q + ++++L + + v kst+ + l +L+ +G+i++s
  gi|344209963|ref|YP_004786139.1|  66 DILREIQSQSEVTLADLCDDVDVAKSTLHTYLQTLVAEGFIDKS 109
                                       79***************************************987 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.1e-05     0.011       8      56 ..      67     109 ..      64     117 .. 0.87
   2 ?   -2.6   0.0       7.5   7.9e+03       3      21 ..     147     164 ..     146     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                            HTH_27   8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdead 56 
                                       +L+ i+  + +++ladlc+ ++v +s+ +  l  L++ G++ +     +
  gi|344209963|ref|YP_004786139.1|  67 ILREIQ-SQSEVTLADLCDDVDVAKSTLHTYLQTLVAEGFIDK-----S 109
                                       788999.999*******************************33.....2 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.5
                            HTH_27   3 rqqalvLhlirhrrrrkkl 21 
                                       +++++ L +++ r+r+++l
  gi|344209963|ref|YP_004786139.1| 147 TSEWVHLTVAY-RNREVTL 164
                                       57899999999.8888876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.2e-05     0.013       3      44 ..      65     105 ..      63     116 .. 0.89
   2 ?   -2.9   0.0       6.6     7e+03      35      46 ..     232     243 ..     229     245 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                            HTH_11   3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44 
                                       ++il+ + ++++ ++ ++L +  +v ++t + ++++L + g+
  gi|344209963|ref|YP_004786139.1|  65 SDILREI-QSQSEVTLADLCDDVDVAKSTLHTYLQTLVAEGF 105
                                       79*****.99999************************99993 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.6
                            HTH_11  35 dIkaLeelgvpI 46 
                                       ++++++ +g+ I
  gi|344209963|ref|YP_004786139.1| 232 RLAEIRRKGYAI 243
                                       677888888777 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   9.5e-06      0.01      13      55 ..      65     107 ..      61     110 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.5e-06
                                       HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20  13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55 
                                        +ilr++ +  ++t+++l++ +d++k+tl+  L++L+  g+++
  gi|344209963|ref|YP_004786139.1|  65 SDILREIQSQSEVTLADLCDDVDVAKSTLHTYLQTLVAEGFID 107
                                       69*************************************9997 PP

>> ANAPC2  Anaphase promoting complex (APC) subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.2e-05     0.013      30      60 .]      85     115 ..      57     115 .. 0.92
   2 ?   -2.2   0.0       5.7     6e+03      30      49 ..     221     240 ..     215     241 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                            ANAPC2  30 gydisdeeLkefLdelvkegkLelsgGkYkL 60 
                                       ++d+ +++L+ +L++lv+eg ++ s+G Y+L
  gi|344209963|ref|YP_004786139.1|  85 DVDVAKSTLHTYLQTLVAEGFIDKSDGVYRL 115
                                       6789999***********************8 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.7
                            ANAPC2  30 gydisdeeLkefLdelvkeg 49 
                                       ++  + +eL+e L e  ++g
  gi|344209963|ref|YP_004786139.1| 221 KTITDPDELRERLAEIRRKG 240
                                       44567899999999887765 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 ?   11.7   0.1   0.00015      0.16       4      49 ..      66     111 ..      64     115 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                          HTH_DeoR   4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRthG 49 
                                        il  +++q  +++ +l++  +v++ T    L++L+++g + +  G
  gi|344209963|ref|YP_004786139.1|  66 DILREIQSQSEVTLADLCDDVDVAKSTLHTYLQTLVAEGFIDKSDG 111
                                       6999********************************9999988766 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 ?    7.5   0.0    0.0049       5.2      17      67 .]      62     106 ..      46     106 .. 0.77
   2 ?    3.2   0.0       0.1   1.1e+02       2      54 ..     172     233 ..     171     239 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0049
                                       CHHHHHHHH-SSSS-HHHHHHHHHHHCT--HHHHHHHHHHHHHHHHCTT-- CS
                              PqqD  17 etgafiWklldgersveeivaalaeeydvdeeeaeadvlafldqLrekgli 67 
                                       +t+++i++ ++  +s  ++++      dvd  +a+  +  +l+ L+++g+i
  gi|344209963|ref|YP_004786139.1|  62 QTASDILREIQS-QSEVTLADLCD---DVD--VAKSTLHTYLQTLVAEGFI 106
                                       689999999977.56555555443...444..499************9998 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.1
                                       EEEE-SS-.......EEE--CHHHHHHHH-SSSS-HHHHHHH..HHHHCT--...HHHHHHHH CS
                              PqqD   2 yvlldpet.....gkyisLnetgafiWklldgersveeivaa..laeeydvd...eeeaeadv 54 
                                       +v +d+ +      +y++   tg++++   d+   v +i a   l ++++ +   ++e+++++
  gi|344209963|ref|YP_004786139.1| 172 TVAMDYQRrtresPQYLHCTATGKALLAHFDE-AQVTDILASeeLVQQTEKTitdPDELRERL 233
                                       677777777777788999999*********99.777777653235555543334345566655 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.4   1.5e+03      38      49 ..      62      73 ..      60      75 .. 0.85
   2 ?   10.0   0.0   0.00055      0.58      23      45 ..      76      98 ..      72     102 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.4
                            HTH_10 38 stlsehLrkaes 49
                                      +t+s++Lr+++s
  gi|344209963|ref|YP_004786139.1| 62 QTASDILREIQS 73
                                      899******998 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00055
                            HTH_10 23 rvtlkeLAkelGIskstlsehLr 45
                                      +vtl++L ++ +++kstl+ +L+
  gi|344209963|ref|YP_004786139.1| 76 EVTLADLCDDVDVAKSTLHTYLQ 98
                                      699******************97 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 ?   10.2   0.0   0.00061      0.64      11      49 ..      56      99 ..      46     114 .. 0.67
   2 ?    0.2   0.0      0.75   7.9e+02      71     122 ..     193     246 ..     159     247 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00061
                                      HHHHHHHHH..HHHHH...--S-HHHHHHHHTS-HHHHHHHHH- CS
                       HTH_Tnp_1_2 11 kQkkaaell..vendy...ekltldeiaeevgvsrsTlykWkkk 49
                                      +Q+k ++    + ++     ++tl++++++v v++sTl+ +++ 
  gi|344209963|ref|YP_004786139.1| 56 RQIKSIQTAsdILREIqsqSEVTLADLCDDVDVAKSTLHTYLQT 99
                                      5666555443333444445689*****************99863 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.75
                                       HHHHHHHHHHSSS-.-HHHH.HHHHHHTT--EEEEEEEEE-XXXXXXXXXXXXX CS
                       HTH_Tnp_1_2  71 vykaLlrkilkgrs.svkAi.eLylkrrgeltdkkkveakledairsneeieee 122
                                       + kaLl   ++ +  ++ A  eL+ + ++ +td +++   l++  r + +i++e
  gi|344209963|ref|YP_004786139.1| 193 TGKALLAHFDEAQVtDILASeELVQQTEKTITDPDELRERLAEIRRKGYAINDE 246
                                       556666666666655555542688899999999999988888888888777765 PP

>> TAF8_C  Transcription factor TFIID complex subunit 8 C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.24   2.5e+02      13      20 ..      94     101 ..      92     107 .. 0.87
   2 ?    8.0   0.2    0.0041       4.3      21      41 ..     219     239 ..     217     241 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.24
                            TAF8_C  13 HTYkrTpv 20 
                                       HTY++T v
  gi|344209963|ref|YP_004786139.1|  94 HTYLQTLV 101
                                       ******87 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0041
                            TAF8_C  21 yneretdpkkirekaaeqsrl 41 
                                       +++++tdp ++re++ae +r+
  gi|344209963|ref|YP_004786139.1| 219 TEKTITDPDELRERLAEIRRK 239
                                       5789*************9998 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00038       0.4      16      61 ..      70     112 ..      58     117 .. 0.82
   2 ?   -2.2   0.0       5.4   5.6e+03      26      53 ..     210     240 ..     196     242 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                                       HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                              Rrf2  16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGk 61 
                                       +++++   + v+++++ + +++ +s l   l++L  +g++    G+
  gi|344209963|ref|YP_004786139.1|  70 EIQSQ---SEVTLADLCDDVDVAKSTLHTYLQTLVAEGFIDKSDGV 112
                                       34333...34******************************999987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.4
                                       B-HHHHHH...HHTS-HHHHHHHHHHHHHTT CS
                              Rrf2  26 vsseeiae...rqnispsylekilakLrkag 53 
                                       ++see+ +   ++ + p  l+  la+ r++g
  gi|344209963|ref|YP_004786139.1| 210 LASEELVQqteKTITDPDELRERLAEIRRKG 240
                                       4444444311133456666666677777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2253.51
//
Query:       gi|344209964|ref|YP_004786140.1|  [L=488]
Description: Na+/H+ antiporter [Haloarcula hispanica ATCC 33960]
Scores for complete 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-55  186.9  45.9    1.2e-50  172.5  26.0    2.1  2  Na_H_antiporter  Na+/H+ antiporter family
  ------ inclusion threshold ------
       0.12   12.3   3.9       0.32   10.9   0.0    3.0  3  Reticulon        Reticulon


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 !   28.5  11.9   9.2e-11   8.2e-07     131     264 ..      55     186 ..      21     186 .. 0.83
   2 !  172.5  26.0   1.4e-54   1.2e-50       1     303 []     172     464 ..     172     464 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 9.2e-11
                   Na_H_antiporter 131 alaglivatllelaslseidkllnrGiksmlgaililllAwgiggvlealgvteslvsslakgvvskgllplilflv 207
                                       a++gl   +   + s++e+ + ++  + + +++++il++ +++ +   + g + +l+   +  +++  +lpl+  ++
  gi|344209964|ref|YP_004786140.1|  55 AFTGLFSYYRFDI-SWDEMYSGITHTLLMGIQVVFILFIVYALISTWIQAGTIPTLMYYGLDLLHPIVFLPLTA-II 129
                                       4555555555565.77777777777777888999***********9999999*************999999865.56 PP

                   Na_H_antiporter 208 allvafatGtswgtigIilpiavplaaklgisllalvraveaggtlgdhlsPisdtt 264
                                       +++++fa+G+sw + g ++  ++ ++  lg+ ++ +++a+++g+  gd  sP+sdtt
  gi|344209964|ref|YP_004786140.1| 130 TAAITFAIGSSWTAAGTLGVAFIGIGSGLGLPEPMTAGAILTGAYTGDKQSPLSDTT 186
                                       6789****************************************************8 PP

  == domain 2  score: 172.5 bits;  conditional E-value: 1.4e-54
                   Na_H_antiporter   1 vavfgdkssplsdtvgliagilktdlieeiaalgmlvqsipanvysifallvvglvvl...llrdigamlraeaear 74 
                                       +a+ gdk+splsdt++l++++++tdl+++i+a  m   +  a+ +++++++ +g+ +      + i ++++a+++++
  gi|344209964|ref|YP_004786140.1| 172 GAYTGDKQSPLSDTTNLASAVTNTDLYDHINA--MRAGTFLAFSIAVVLYAGLGIRASgaiPVDRIAEIQTALTGSF 246
                                       6999***************************4..9999********************6654556777777777787 PP

                   Na_H_antiporter  75 eleekeltklpiavliiltlskmpytgalalvaivkafivalafqntdvatalvvgalaglivatllelaslseidk 151
                                       ++++  +   p++v+++l++ +  +++al +++++ ++i+  ++q+ +++  +   a++g+  +t+ el     +++
  gi|344209964|ref|YP_004786140.1| 247 TISPLAFF--PLLVTFGLAIYGISAIPALGAGVFA-GAITSAVLQGNSFTSVWT-VAQSGTSPETGMEL-----VNG 314
                                       88888887..*************************.7777777***98888888.**************.....*** PP

                   Na_H_antiporter 152 llnrG.iksmlgaililllAwgiggvlealgvteslvsslakgvvskgllplilflvallvafatGtswgtigIilp 227
                                       ll  G + + ++a++i ++A+++gg++e +g++++l ++l + ++s+g+l+ i++l++  +++ +++++++i++++ 
  gi|344209964|ref|YP_004786140.1| 315 LLASGgMVGGAWAVTIAIAALALGGLFECTGIIAVLAHHLGQLSDSVGSLTGITVLSSVSMNVLAAEQYISIVVPGV 391
                                       ***************************************************************************** PP

                   Na_H_antiporter 228 iavplaaklgisllalvraveaggtlgdhlsPisdttilsstglnadhidhvsytqlpyallvapitailllvfGi 303
                                       ++++l+++ g+++ +l+ra+e++gt++++l+P+++++++++ +l   ++++++y +++++ +++p+++il++v+G+
  gi|344209964|ref|YP_004786140.1| 392 TLGSLYEEKGLKTENLSRAIESSGTVTSALIPWNSGAVFMAGTL---GVSTFQYAPYYFLGFLSPLILILMGVTGW 464
                                       ********************************************...9***************************9 PP

>> Reticulon  Reticulon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.7     0.051   4.6e+02     129     144 ..      80      95 ..      57     123 .. 0.65
   2 ?   -3.1   0.0      0.75   6.7e+03      34      48 ..     366     380 ..     358     403 .. 0.56
   3 ?   10.9   0.0   3.6e-05      0.32      12      68 ..     425     480 ..     423     487 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.051
                         Reticulon 129 lyigvvlaftvPllYe 144
                                       l++g+ ++f+++++Y 
  gi|344209964|ref|YP_004786140.1|  80 LLMGIQVVFILFIVYA 95 
                                       3333334444444443 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.75
                         Reticulon  34 llslvsklllllllv 48 
                                        ++++s +++ +l++
  gi|344209964|ref|YP_004786140.1| 366 GITVLSSVSMNVLAA 380
                                       334444444444333 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 3.6e-05
                         Reticulon  12 ksgivlgglllllllfellgysllslvsklllllllvlflwaeyagllnkskppepe 68 
                                       +sg+v+++ +l    f+++ y +l ++s l+l+l++v+      ++  ++ ++++++
  gi|344209964|ref|YP_004786140.1| 425 NSGAVFMAGTLGVSTFQYAPYYFLGFLSPLILILMGVTGWQIT-YTETETDSQTPSN 480
                                       79***********************************987544.4444444555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); 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:                         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 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 3443.50
//
Query:       gi|344209965|ref|YP_004786141.1|  [L=134]
Description: hypothetical protein HAH_5023 [Haloarcula hispanica ATCC 33960]
Scores for 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-10   39.3   0.0    1.3e-09   38.6   0.0    1.3  1  DUF4864   Domain of unknown function (DUF4864)


Domain annotation for each model (and alignments):
>> DUF4864  Domain of unknown function (DUF4864)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0   7.3e-14   1.3e-09       7      95 ..      26     122 ..      22     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 7.3e-14
                           DUF4864   7 kQleAlrkdd.......aakAysfAspgirakfgtaerFlemVrq.aYpavyrprsvaflkletkeggvvqevlivd 75 
                                        Ql+Al+++d       + +Ay+fAsp  r+ +g  +rF++mV++ +Y+++    ++  + +e +e+ + q++ i++
  gi|344209965|ref|YP_004786141.1|  26 LQLNALETNDdpfenagIMTAYNFASPANRRSTGPLDRFIAMVESpQYRPMIDFGEAVRGPVERNENYAEQRITITG 102
                                       57777777664544444789***********************9768****************************** PP

                           DUF4864  76 sdgkaltaiYqlekqedgsw 95 
                                       +dg   t+++ l  q  g +
  gi|344209965|ref|YP_004786141.1| 103 PDGRTTTYEFGLSVQSVGEF 122
                                       ***********999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); 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: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 1083.38
//
Query:       gi|344209966|ref|YP_004786142.1|  [L=158]
Description: sensor histidine kinase [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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 0.21s 00:00:00.55 Elapsed: 00:00:00.39
# Mc/sec: 1222.95
//
Query:       gi|344209967|ref|YP_004786143.1|  [L=330]
Description: hypothetical protein HAH_5025 [Haloarcula hispanica ATCC 33960]
Scores for 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-26   90.7   9.6    2.8e-25   89.1   9.4    1.9  1  DUF3592   Protein of unknown function (DUF3592)
  ------ inclusion threshold ------
      0.017   15.0   0.0       0.84    9.6   0.0    2.4  2  DUF3318   Protein of unknown function (DUF3318)
      0.089   13.0   2.6      0.089   13.0   0.9    1.8  2  DUF2189   Predicted integral membrane protein (DUF2189)


Domain annotation for each model (and alignments):
>> DUF3592  Protein of unknown function (DUF3592)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   9.4   4.7e-29   2.8e-25       9     135 ..      17     221 ..       9     255 .. 0.73

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 4.7e-29
                           DUF3592   9 lifllaglallvlgglllvgkyllsgqwervpgtvlssehrhrsdgsrsstysvtvrYrysfqg.ervs..glysgs 82 
                                       +++ll++++ll +gg+ +v+++++ +++  v++t+++s+ ++r+dg+r+ +y++++rY+y++qg +++s   ++s++
  gi|344209967|ref|YP_004786143.1|  17 ALLLLLAVGLLGFGGYDYVQQSQAVDNAVPVQATITDSS-VDRMDGGRGIDYEPEIRYTYQYQGeTYTSeqVFPSTG 92 
                                       68999**********************************.************************66666**9****9 PP

                           DUF3592  83 dnvgdyaaql......yraGnavqvyynPsnPtqavldqtvsgtkagglwlmvglgav................... 134
                                       +++++ ++++      y++G++ ++y++P++P++a+l  ++++   + l ++++ g++                   
  gi|344209967|ref|YP_004786143.1|  93 VRTYSDRSRAesvvesYEPGTTARAYVSPADPDDAFLI-RERTP--WPLQAIAVGGFLsvigvlsglgaknpgqqel 166
                                       9988888888899999**********************.33333..4444444433333355555566666666666 PP

                           DUF3592 135 ......................................................l 135
                                                                                             +
  gi|344209967|ref|YP_004786143.1| 167 rpasevqpapretwvdshgetihrlskqglsvcfvgfwlslvalvfgllnttggF 221
                                       6666666666666666666666665555555555555555555555555555550 PP

>> DUF3318  Protein of unknown function (DUF3318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00014      0.84      92     126 ..       9      43 ..       2      57 .. 0.81
   2 ?    2.7   0.0     0.018   1.1e+02     101     123 ..     248     270 ..     231     279 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00014
                           DUF3318  92 vvelvqqDavgvllagglaaiaayriwrenksqka 126
                                        + l+q++a+++lla+gl ++ +y   ++ ++   
  gi|344209967|ref|YP_004786143.1|   9 TLHLSQRNALLLLLAVGLLGFGGYDYVQQSQAVDN 43 
                                       3369************************9998655 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.018
                           DUF3318 101 vgvllagglaaiaayriwrenks 123
                                       vg++l++ l +++ +  +r+ ++
  gi|344209967|ref|YP_004786143.1| 248 VGMILSVCLYGVWSFTKYRQLRQ 270
                                       8*******************998 PP

>> DUF2189  Predicted integral membrane protein (DUF2189)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.9   1.5e-05     0.089      56     116 ..     198     259 ..     179     263 .. 0.86
   2 ?   -2.2   0.0      0.79   4.7e+03      96     110 ..     310     323 ..     289     328 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                           DUF2189  56 allfllWvraaallfallfgtapleslsafledvlltpeglaflivg.llvGavlAalvFai 116
                                       + ++ +W+ ++al+f ll++t+ +e + + +++++l p gl +l+ + + vG++l+++++ +
  gi|344209967|ref|YP_004786143.1| 198 VCFVGFWLSLVALVFGLLNTTGGFEGPPQDIQAAFLGPVGLPMLAGFsFWVGMILSVCLYGV 259
                                       456679***********************************999865268999999998865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.79
                           DUF2189  96 laflivgllvGavlA 110
                                       +a +i+ + ++++lA
  gi|344209967|ref|YP_004786143.1| 310 WAWMIA-VGMTGALA 323
                                       322222.22333344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 2370.76
//
Query:       gi|344209968|ref|YP_004786144.1|  [L=542]
Description: N-methylhydantoinase B [Haloarcula hispanica ATCC 33960]
Scores for complete 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-202  673.1   2.9   2.4e-202  672.9   2.9    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 !  672.9   2.9  1.4e-206  2.4e-202       1     516 []      16     522 ..      16     522 .. 0.97

  Alignments for each domain:
  == domain 1  score: 672.9 bits;  conditional E-value: 1.4e-206
                    Hydantoinase_B   1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfege 77 
                                       Dp+tle++rn+l+s+a emg++l+r a+Spniker+D+s+alfda g++vaqa+hipvhlg+m++av  vl+   ++
  gi|344209968|ref|YP_004786144.1|  16 DPVTLEILRNQLESVATEMGHVLIRGAYSPNIKERQDCSTALFDASGRMVAQAEHIPVHLGAMPDAVDIVLQ---KD 89 
                                       9********************************************************************994...45 PP

                    Hydantoinase_B  78 lkpGDvlltNdPyaggtHlpDitvitPvfhegelvffvasraHhaDiGGitpGsmppdateifeEGlrippvklvee 154
                                        kpGDv+++NdP+aggtHlpDit+++ +  ++e+v++++sraHhaD+GG++pGsmpp a+ei+eEGlr+p v+lv++
  gi|344209968|ref|YP_004786144.1|  90 PKPGDVFIVNDPFAGGTHLPDITLVSTIAPNDEIVGYAVSRAHHADVGGSSPGSMPPGAQEIYEEGLRLPAVRLVDG 166
                                       79*************************************************************************** PP

                    Hydantoinase_B 155 geleedvlelllanvRtpednlgDlkAqiaanqvgerrlkelieeyGldtveaamdeildnaeravraalaelpdgt 231
                                       ge++e+v +l++anvRtp+++++Dl+Aq aan ++e+r+ el+ee+G +t+ +a+d+++++++++v+a+l  lpdgt
  gi|344209968|ref|YP_004786144.1| 167 GEPNEAVHDLIRANVRTPDEREADLRAQRAANVRAEERIGELLEEHG-ATLLDAFDAVIEYSRERVEAELDGLPDGT 242
                                       ***********************************************.578999*********************** PP

                    Hydantoinase_B 232 yeaedyldd.g.....ipikvtvtidgdeatvDftgtspqvkgniNaplavtlsaviyvlrclvdediplNeGclrp 302
                                       y+a+d l+  g     ipi+v+vtidg ++ vDf+gt++qv+gn+Napl+v++sav++v+r+++d++ip N+Gc++p
  gi|344209968|ref|YP_004786144.1| 243 YRAQDILEGdGvtdtdIPIEVAVTIDGASIAVDFDGTADQVAGNLNAPLSVAKSAVYFVVRAITDPEIPPNHGCYEP 319
                                       *****996645666669************************************************************ PP

                    Hydantoinase_B 303 ievklpegsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfggvderggeffgyyetia 379
                                       ++v +pegs+l+p++paavvggnvetsqrv+dv l+ala+a+p++v+A++qgtmnnl++g   +r+g+f +yyeti+
  gi|344209968|ref|YP_004786144.1| 320 VSVSVPEGSILDPKPPAAVVGGNVETSQRVMDVTLAALAEAVPDKVPAGGQGTMNNLIIG---DRTGDF-TYYETIG 392
                                       ************************************************************...666777.******* PP

                    Hydantoinase_B 380 gGaGArpgkdGasavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreieflepevtvsilse 456
                                       gG GArp+kdG+++v+v mtnt nt+vE++E++yP++ver++lrp sgG+G+yrGG+G++r+++++++ +tvs+l+e
  gi|344209968|ref|YP_004786144.1| 393 GGFGARPEKDGMDGVQVGMTNTLNTPVEAMETEYPLRVERYALRPSSGGDGRYRGGLGLERTVTVETD-ATVSLLTE 468
                                       *******************************************************************7.******** PP

                    Hydantoinase_B 457 rrvfapwGlaGGepGargrvvlnllvrgeeenlggkatvelkagdvlvietpGGGGyGdp 516
                                       rr++ap G++GGe+Ga+g+   nl+   + e +++ka+v+++ag ++ ++tpGGGG+Gdp
  gi|344209968|ref|YP_004786144.1| 469 RRRTAPAGIDGGEDGATGE---NLV---DGEPVPAKASVDVEAGTTVSVRTPGGGGHGDP 522
                                       *******************...765...4677789***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 3831.81
//
Query:       gi|344209969|ref|YP_004786145.1|  [L=664]
Description: N-methylhydaintoinase A [Haloarcula hispanica ATCC 33960]
Scores for complete 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-98  329.7  11.2    3.3e-98  328.5   5.3    2.3  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    8.4e-51  172.2   1.9      4e-50  170.0   0.2    2.3  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
     0.0026   16.4   5.7      0.026   13.1   0.4    2.6  3  MutL            MutL protein
  ------ inclusion threshold ------
       0.45   11.0   2.8        3.2    8.2   0.3    2.8  2  FtsA            Cell division protein FtsA


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 !    4.4   0.3    0.0043        19      81     100 ..       5      24 ..       2      38 .. 0.84
   2 !  328.5   5.3  7.4e-102   3.3e-98       1     288 [.     199     482 ..     199     485 .. 0.97

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0043
                    Hydantoinase_A  81 vItfDmGGTstDvslikdge 100
                                        I++D+GGT tDv l  dg+
  gi|344209969|ref|YP_004786145.1|   5 RIGVDVGGTFTDVTLSLDGT 24 
                                       69***********9877776 PP

  == domain 2  score: 328.5 bits;  conditional E-value: 7.4e-102
                    Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklag 77 
                                       rt+t++v+Ay+ p +  y++ + ++ ++ g+ ++  +mq++Gg+++ad++r++ v t+lSGPaaGvvga +++  ++
  gi|344209969|ref|YP_004786145.1| 199 RTSTTAVDAYVRPAIDHYVSHLTDRARDLGV-PQPRIMQANGGITDADTVRRNAVTTVLSGPAAGVVGAGSMAA-DE 273
                                       89***************************99.999************************************544.44 PP

                    Hydantoinase_A  78 ekkvItfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgpa 154
                                       ++ ++tfDmGGTs Dvsl++dge e+++e  i + +++ p++d++tvgagGgsi++vd gg+lr+gp+sagadpgpa
  gi|344209969|ref|YP_004786145.1| 274 QDGLVTFDMGGTSSDVSLVRDGEAERTTEGVINERPIKTPMVDVETVGAGGGSIAWVDAGGALRIGPRSAGADPGPA 350
                                       458************************************************************************** PP

                    Hydantoinase_A 155 cyrkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlk.veevAegilsvavenmanavr 230
                                       cy+kGgte+tvTDanlvLG++  +  l   +g+ +ld+++a+ a+++la+e +l+ + e+A g+++va+ nm +a+r
  gi|344209969|ref|YP_004786145.1| 351 CYGKGGTEPTVTDANLVLGYIGASTSL---GGELSLDEDAAYDALADLADEAGLGgPLEAARGVYRVANANMTRAIR 424
                                       ************************999...************************99********************* PP

                    Hydantoinase_A 231 klsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvr 288
                                       +++verg+dp+++ l++fGGaG++haa +a++l++ +v++p+++gvlsa+G+++Ad +
  gi|344209969|ref|YP_004786145.1| 425 SVTVERGYDPRKFGLAAFGGAGPMHAASIADSLDIDRVVIPRASGVLSAYGLLAADEK 482
                                       *******************************************************965 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   0.2     9e-54     4e-50       1     177 [.       5     179 ..       5     180 .. 0.97
   2 ?    1.2   0.1     0.059   2.7e+02       3      20 ..     279     296 ..     277     317 .. 0.77

  Alignments for each domain:
  == domain 1  score: 170.0 bits;  conditional E-value: 9e-54
                        Hydant_A_N   1 rigIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkge 77 
                                       rig+DvGGTfTD+ +   + ++++++K++st ++++eg++  +e++ e++ ++++ ++   ++ Tv +Nalle +g+
  gi|344209969|ref|YP_004786145.1|   5 RIGVDVGGTFTDVTLSL-D-GTLVTAKVPST-EDQSEGVIAGIEKACEAADIDPESVTEFSHAMTVSVNALLEEDGA 78 
                                       79**********99988.4.79*********.********************************************* PP

                        Hydant_A_N  78 rvaLittkgfrdlleigrqnrpdlfelrik..kplvlyeevvevderveadgevlkpldeeevrealkalkaagves 152
                                       ++aL+tt gfrd+leigrq rp l++l  +  +plv++++++ev+er++ d  + +p+de+evr+++++l++ +ves
  gi|344209969|ref|YP_004786145.1|  79 KTALVTTDGFRDVLEIGRQDRPSLYDLSAEkpTPLVPRRRRFEVSERTTTD-GIEEPVDEAEVRAIAAQLRDLDVES 154
                                       **************************999888899***************8.799********************** PP

                        Hydant_A_N 153 iavvllhSylnpehElrvaeiarei 177
                                       +av+llh+y+ pe+E+ va+i+r++
  gi|344209969|ref|YP_004786145.1| 155 VAVSLLHAYAHPENEQHVADILRDE 179
                                       **********************986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.059
                        Hydant_A_N   3 gIDvGGTfTDavaldeke 20 
                                         D+GGT  D+ +++++e
  gi|344209969|ref|YP_004786145.1| 279 TFDMGGTSSDVSLVRDGE 296
                                       56*********9999764 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.3    0.0014       6.3       4      51 ..       8      51 ..       5      73 .. 0.78
   2 !   13.1   0.4   5.8e-06     0.026     206     274 ..     233     302 ..     186     320 .. 0.74
   3 ?   -2.3   0.0      0.28   1.2e+03     428     451 ..     469     492 ..     466     493 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0014
                              MutL  4 iDiGSttTkvtlvdlekvderllgqaeapTtvee.edvleGleealeel 51
                                      +D+G t+T vtl  +       l +a+ p+t ++ e v  G+e+a e+ 
  gi|344209969|ref|YP_004786145.1|  8 VDVGGTFTDVTLSLDG-----TLVTAKVPSTEDQsEGVIAGIEKACEAA 51
                                      7999999999987663.....5788999999988889999999998765 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.8e-06
                              MutL 206 hivkakg....lskleelvsaeimpTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspekekv 274
                                       +i++a g     +++++ + +++   PaA + ++  +a +e++   +l+++D+GG+++dv  v +g+ e+++ 
  gi|344209969|ref|YP_004786145.1| 233 RIMQANGgitdADTVRRNAVTTVLSGPAAGVVGAGSMAADEQD---GLVTFDMGGTSSDVSLVRDGEAERTTE 302
                                       5666655111123344444555666799999999999997777...9****************9888776543 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.28
                              MutL 428 yilaalGllaevepeaalkllkkd 451
                                       ++l+a Glla+ e++ a++  +++
  gi|344209969|ref|YP_004786145.1| 469 GVLSAYGLLAADEKRDAVRTYQRS 492
                                       799************999998876 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.3   0.00072       3.2       1      52 [.       6      59 ..       6     144 .. 0.83
   2 ?    1.6   0.1     0.084   3.8e+02       4      21 ..     281     298 ..     278     327 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00072
                                      EEEEE-SSSEEEEEEETTEEEEEEEES-..-HHHHHHHHHHHHT--HHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                              FtsA  1 alvDiGagktdvavaedgalvhlrvigv..ggngitkdiakalrtaveeAerik 52
                                      ++vD+G++ tdv++  dg lv  +v  +  +++g+  +i+ka+  a  + e++ 
  gi|344209969|ref|YP_004786145.1|  6 IGVDVGGTFTDVTLSLDGTLVTAKVPSTedQSEGVIAGIEKACEAADIDPESVT 59
                                      58******************9999988899*********999987765555555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.084
                                       EE-SSSEEEEEEETTEEE CS
                                       xxxxxxxxxxxxxxxxxx RF
                              FtsA   4 DiGagktdvavaedgalv 21 
                                       D+G++++dv++++dg+  
  gi|344209969|ref|YP_004786145.1| 281 DMGGTSSDVSLVRDGEAE 298
                                       9************99754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (664 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 4784.02
//
Query:       gi|344209970|ref|YP_004786146.1|  [L=402]
Description: putative Mn transporter [Haloarcula hispanica ATCC 33960]
Scores for 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-97  326.4  24.4    2.5e-97  326.1  24.4    1.1  1  Nramp     Natural resistance-associated macrophage protein
  ------ inclusion threshold ------
       0.16   12.3   2.4         37    4.6   0.1    3.7  4  LPD14     Large polyvalent protein-associated domain 14


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 !  326.1  24.4  2.8e-101   2.5e-97       1     357 [.      26     373 ..      26     374 .. 0.96

  Alignments for each domain:
  == domain 1  score: 326.1 bits;  conditional E-value: 2.8e-101
                             Nramp   1 iatdlqaGaqfGykLlwvlllstllaillqelsarLGlvTgkglaelirerl.....pkkvsillwilaelaiiatd 72 
                                       ++t++  Ga+fGy+Llw++++s+ ++i+lqe+sarLGlv+g+gl e++rer+     + +  +l++ ++ ++++a++
  gi|344209970|ref|YP_004786146.1|  26 VTTASVTGAEFGYALLWTMVFSIGATIVLQEMSARLGLVSGEGLGEALRERFdnqivEYVSIFLVVGAIGIGTAAYE 102
                                       6899************************************************877766777788888999******* PP

                             Nramp  73 laeviGaAialnllfgipllvgvlitavlvllllflekggyrklEaliialvlvialsFiaelflvkpdwgevlkgl 149
                                       +++++G+A++l +++gi+ +v+++++++++ lll+  +g y+ +E+++i+lv+v+a+sF+a+++l+ pd g+++ g+
  gi|344209970|ref|YP_004786146.1| 103 AGNILGGAAGLATITGIDSTVWGVVMGLVAGLLLY--TGRYKLIEKALIGLVAVMAFSFVASAILIGPDPGSIAMGF 177
                                       ***********************************..***************************************9 PP

                             Nramp 150 vvPslpgkeslllavgilGatvmphnlflhsslvqerkitidrsekeealkyeriDtiialivaflinlailivaAa 226
                                       v P +p+ +sl+l++g++G+t++ +nlflh+s vqer+  +    ++  + ++riDt+++++++++i+++i+++aAa
  gi|344209970|ref|YP_004786146.1| 178 V-PGIPS-GSLYLITGLIGTTIVGYNLFLHASNVQERWSGP----DD--IGHSRIDTVLSIVAGGVITITIMVTAAA 246
                                       9.*****.******************************666....66..**************************** PP

                             Nramp 227 vlysggkdvesledaaeaLepllGskaasvlFaigLlaaGlsStitgtlagqyvmegflglrislwlrrlitralaf 303
                                       ++ +g++ ++++  +ae+L+p++G ++a+++F+ig++aaG+ S++t++lag+++++g+lg+++++       ++++f
  gi|344209970|ref|YP_004786146.1| 247 AFEPGTQ-ISDIGRMAEQLRPIAG-PYAELFFSIGIFAAGFTSATTAPLAGAWATTGALGWDSDM-------QSTQF 314
                                       ***7665.9***************.7***************************************.......78899 PP

                             Nramp 304 vpalivilligaele.....lvkllvlsqvllslllPfaliplllltsskklMGefkns 357
                                       ++++ +il +g  ++     +v+++v++qv++++llP+++++l++ +++ +l+Ge++n+
  gi|344209970|ref|YP_004786146.1| 315 RAVWGTILSVGVLSVllggsPVQIIVFAQVVNGILLPIVAVFLIYAMNQLDLLGEYTNG 373
                                       99999999999999999999*************************************97 PP

>> LPD14  Large polyvalent protein-associated domain 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.33     3e+03     104     115 ..      41      52 ..      34      64 .. 0.79
   2 ?    1.0   0.0     0.054   4.8e+02      90     126 ..      66     106 ..      52     112 .. 0.80
   3 ?    3.6   0.0     0.008        72      92     128 ..     252     295 ..     224     303 .. 0.77
   4 ?    4.6   0.1    0.0041        37     103     117 ..     316     330 ..     302     336 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.33
                             LPD14 104 iWgtllsvglMs 115
                                       +W++++s+g+  
  gi|344209970|ref|YP_004786146.1|  41 LWTMVFSIGATI 52 
                                       7******99855 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.054
                             LPD14  90 Gdqtledlf.qlendi..W.gtllsvglMsagfsaagaaky 126
                                       G++  e l  +++n+i  +  ++l vg+ + g  a +a++ 
  gi|344209970|ref|YP_004786146.1|  66 GEGLGEALReRFDNQIveYvSIFLVVGAIGIGTAAYEAGNI 106
                                       5555566666788888876699************9999886 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.008
                             LPD14  92 qtledlfqlendi......W.gtllsvglMsagfsaagaakyaa 128
                                        + +d+ ++ +++      + + ++s+g+  agf +a +a  a+
  gi|344209970|ref|YP_004786146.1| 252 TQISDIGRMAEQLrpiagpYaELFFSIGIFAAGFTSATTAPLAG 295
                                       55666666777777777776689**************9987776 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.0041
                             LPD14 103 diWgtllsvglMsag 117
                                       ++Wgt+lsvg++s++
  gi|344209970|ref|YP_004786146.1| 316 AVWGTILSVGVLSVL 330
                                       67**********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 2910.56
//
Query:       gi|344209971|ref|YP_004786147.1|  [L=179]
Description: CopG family ribbon-helix-helix transcription regulator [Haloarcula hispanica ATCC 33960]
Scores for 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   41.9   1.4    9.9e-11   41.2   0.2    2.0  2  RHH_1          Ribbon-helix-helix protein, copG family
    5.5e-05   23.0   0.1    0.00014   21.8   0.1    1.7  1  RHH_3          Ribbon-helix-helix domain
      0.003   18.3   0.5      0.015   16.0   0.2    2.0  2  PSK_trans_fac  Rv0623-like transcription factor
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.029   14.3   0.0    1.4  1  PUB            PUB domain
      0.027   14.5   0.3        0.1   12.7   0.1    1.9  2  TraY           TraY domain
      0.074   13.0   0.1       0.18   11.7   0.1    1.7  1  RHH_5          CopG-like RHH_1 or ribbon-helix-helix 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 !   41.2   0.2   3.3e-14   9.9e-11       1      37 [.       5      41 ..       5      42 .. 0.97
   2 ?   -2.1   0.1       1.4   4.2e+03       9      17 ..     106     114 ..     105     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 3.3e-14
                                      EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                      rv+++ldee++e+L+ l +r+g S+S+lIReA+++y 
  gi|344209971|ref|YP_004786147.1|  5 RVTVSLDEETKETLEDLTDRTGESQSQLIREAIAFYA 41
                                      9*********************************996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.4
                                       HHHHHHHHH CS
                             RHH_1   9 ellerLdel 17 
                                       e++er+d l
  gi|344209971|ref|YP_004786147.1| 106 EYAERFDSL 114
                                       889999977 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   4.6e-08   0.00014       4      37 ..       5      38 ..       4      43 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.6e-08
                             RHH_3  4 rttvsidpelaekLkaLSekTrIprSklldeAie 37
                                      r+tvs+d+e  e L++L  +T+  +S l++eAi 
  gi|344209971|ref|YP_004786147.1|  5 RVTVSLDEETKETLEDLTDRTGESQSQLIREAIA 38
                                      89******************************97 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 !   16.0   0.2   5.1e-06     0.015       7      45 ..      11      49 ..      10      90 .. 0.85
   2 ?    0.6   0.0      0.32   9.6e+02      36      57 ..      95     116 ..      75     135 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.1e-06
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     PSK_trans_fac  7 dpeverlareLarltgeskteAvrrAleerlerlrrera 45
                                      d+e+++  + L ++tges+ + +r+A++ + + +++++a
  gi|344209971|ref|YP_004786147.1| 11 DEETKETLEDLTDRTGESQSQLIREAIAFYAANFDSAHA 49
                                      89*************************999988886533 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.32
                                       XXXXXXXXXX--HHHHHHHHHH CS
                     PSK_trans_fac  36 rlerlrreraepllerllallr 57 
                                        ++++ + +a++ +er++ l +
  gi|344209971|ref|YP_004786147.1|  95 MIDQVAQYHAQEYAERFDSLED 116
                                       3333332255555555555554 PP

>> PUB  PUB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   9.7e-06     0.029      37      74 ..     107     146 ..     104     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.7e-06
                               PUB  37 fkekvlplegavelLealGFeekneeeee..flvleeesv 74 
                                       + e++++le+++e+L+++GF   + +e +   +v+++esv
  gi|344209971|ref|YP_004786147.1| 107 YAERFDSLEDVLEWLSLCGFLTVRRDEKGsfHVVFPSESV 146
                                       6799****************77666666677788888876 PP

>> TraY  TraY domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.4e-05       0.1       1      25 [.       6      30 ..       6      34 .. 0.92
   2 ?   -1.2   0.0      0.71   2.1e+03      34      40 ..      53      59 ..      52      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                              TraY  1 vtlkLdeetnklLeasaersgRSKr 25
                                      vt+ Ldeet ++Le   +r+g S +
  gi|344209971|ref|YP_004786147.1|  6 VTVSLDEETKETLEDLTDRTGESQS 30
                                      899******************8876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.71
                              TraY 34 dHLkrFp 40
                                      dHL+ + 
  gi|344209971|ref|YP_004786147.1| 53 DHLQTYY 59
                                      9**9885 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 ?   11.7   0.1   5.9e-05      0.18       2      31 ..       4      33 ..       3      38 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.9e-05
                             RHH_5  2 kRvnvtLPeelleeLeewAdeegRsvSnla 31
                                      +Rv+v+L ee +e Le + d +g s S+l+
  gi|344209971|ref|YP_004786147.1|  4 DRVTVSLDEETKETLEDLTDRTGESQSQLI 33
                                      7***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1232.96
//
Query:       gi|344209972|ref|YP_004786148.1|  [L=417]
Description: NAD(P)-specific glutamate dehydrogenase [Haloarcula hispanica ATCC 33960]
Scores for 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  241.9   0.1    9.9e-72  241.6   0.1    1.1  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    6.6e-53  178.0   0.0      1e-52  177.4   0.0    1.3  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
    0.00064   19.1   0.1     0.0013   18.2   0.1    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0016   17.3   0.0     0.0022   16.8   0.0    1.2  1  Oxidored_nitro   Nitrogenase component 1 type Oxidoreductase
  ------ inclusion threshold ------
      0.028   14.0   0.1      0.045   13.3   0.1    1.3  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.042   13.1   0.1      0.074   12.3   0.1    1.4  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain


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 !  241.6   0.1   3.3e-75   9.9e-72       1     243 []     180     414 ..     180     414 .. 0.98

  Alignments for each domain:
  == domain 1  score: 241.6 bits;  conditional E-value: 3.3e-75
                                       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++++ga+vvavsDssG+iy++  +d  
  gi|344209972|ref|YP_004786148.1| 180 GGSEGRVEATGRSTVVAAREAFEYLDKD-LEGATVAVQGYGNAGWIAAKLIHQMGANVVAVSDSSGAIYSEASFDPV 255
                                       9***********************9999.************************************************ PP

                                       HHHHHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHH CS
                     ELFV_dehydrog  78 ellelkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeA 154
                                       +++++k+e++sv  y+    ++ae ++ne ell+l+vd+l+P+A++n+ide  a+  i   ++++ E+AN+p+t++A
  gi|344209972|ref|YP_004786148.1| 256 AVKDYKRETGSVVGYP----DAAEELTNE-ELLTLDVDLLIPAALENAIDEPLAH-DIS--ADVISEAANGPITPAA 324
                                       ****************....46789***7.*************************.999..**************** PP

                                       HHHHHHTT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-T.HHHHHHHH CS
                     ELFV_dehydrog 155 keileeagvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqe.lvkgania 230
                                       +++l++++ lv+pd++aNaGGV+vS++E++qn +r++w+ee+v+e+l++i  + f ++v+++ee++ + l+++a+++
  gi|344209972|ref|YP_004786148.1| 325 DDVLSDRETLVIPDILANAGGVIVSYFEWVQNRQRFYWSEERVNEELDSIIVDQFGNLVDAYEERNLPsLRTAAYVV 401
                                       ******************************************************************999******** PP

                                       HHHHHHHHHHHCT CS
                     ELFV_dehydrog 231 gfekvaeamkaqG 243
                                       ++++v++a +++G
  gi|344209972|ref|YP_004786148.1| 402 ALQRVMNAGEQRG 414
                                       *********9998 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 !  177.4   0.0   3.4e-56     1e-52       1     129 [.      34     161 ..      34     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 177.4 bits;  conditional E-value: 3.4e-56
                                       -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES CS
                   ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvki 77 
                                       per+l+ +++v++d+G++ev+++yr+q++  +gP+kGGiR+hp+v+ devkaL+ +m+yK+a  d+p+GG+kgg+ i
  gi|344209972|ref|YP_004786148.1|  34 PERILETNLSVEMDDGSVEVFRAYRSQFNGDRGPYKGGIRYHPQVDRDEVKALSGWMVYKTATGDIPLGGGKGGIVI 110
                                       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|344209972|ref|YP_004786148.1| 111 DPSNYSESELERVTRSFAKELT-PLIGADRDVPAPDVNTGQREMNWIKDTYE 161
                                       **********************.****************************7 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 !   18.2   0.1   4.2e-07    0.0013      27      70 ..     201     244 ..     184     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.2e-07
                                       CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskk 70 
                                        ++l k+l+g tv++ G+G+ G  +ak+++++g++v+a++ s  
  gi|344209972|ref|YP_004786148.1| 201 FEYLDKDLEGATVAVQGYGNAGWIAAKLIHQMGANVVAVSDSSG 244
                                       567889********************************998754 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 !   16.8   0.0   7.3e-07    0.0022     259     309 ..     197     247 ..     176     307 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.3e-07
                                       HHHHHHHHHHHHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HH CS
                    Oxidored_nitro 259 lldaladyheylagkrvaiygdpdrvvalarllkelGmevvaagtetahrd 309
                                       + +a++ + + l+g++va+ g++   +  a+l++++G++vva++ +++   
  gi|344209972|ref|YP_004786148.1| 197 AREAFEYLDKDLEGATVAVQGYGNAGWIAAKLIHQMGANVVAVSDSSGAIY 247
                                       5677888899*******************************9986665443 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 ?   13.3   0.1   1.5e-05     0.045       2      55 ..     208     261 ..     207     279 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltva 55 
                                       l+g ++av GyG+ G   a+ +++ g +vv    ++++ +++A+ + + v++++
  gi|344209972|ref|YP_004786148.1| 208 LEGATVAVQGYGNAGWIAAKLIHQMGANVVAVSDSSGAIYSEASFDPVAVKDYK 261
                                       7899*************************9988888888888887777776654 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 ?   12.3   0.1   2.5e-05     0.074      27      58 ..     209     240 ..     205     298 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                                       ---EEEEESTSHHHHHHHHHHHHTT-EEEEEE CS
                       AlaDh_PNT_C  27 epakvlviGgGvaGlqAiatakglgakVtvlD 58 
                                       e a+v v G G aG+ A++  +++ga+V+++ 
  gi|344209972|ref|YP_004786148.1| 209 EGATVAVQGYGNAGWIAAKLIHQMGANVVAVS 240
                                       6799***********************98764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2963.53
//
Query:       gi|344209973|ref|YP_004786149.1|  [L=101]
Description: hypothetical protein HAH_5031 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       512  (0.0285571); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 728.12
//
Query:       gi|344209974|ref|YP_004786150.1|  [L=955]
Description: bacterio-opsin activator-like protein [Haloarcula hispanica ATCC 33960]
Scores for 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-37  126.6   9.3    7.8e-37  126.6   9.3    2.8  3  BAT           GAF and HTH_10 associated domain
    4.3e-26   91.8   5.0    6.1e-19   68.7   0.1    3.4  4  GAF_2         GAF domain
    4.3e-18   64.8   0.0    1.4e-17   63.2   0.0    2.0  1  HTH_10        HTH DNA binding domain
    2.2e-13   50.4   4.3    3.4e-09   36.9   0.7    3.7  3  PAS_4         PAS fold
    4.8e-13   49.6   0.2      9e-05   22.8   0.0    3.5  3  GAF_3         GAF domain
    3.5e-10   40.0   0.1    1.7e-09   37.8   0.0    2.2  2  Response_reg  Response regulator receiver domain
    5.5e-09   36.8   1.5     0.0011   19.7   0.0    3.4  3  GAF           GAF domain
      8e-09   35.7   1.7    2.7e-05   24.3   0.0    3.5  3  PAS_9         PAS domain
    8.7e-06   25.7   5.6      0.047   13.7   0.1    3.7  4  PAS           PAS fold
  ------ inclusion threshold ------
      0.062   13.3   0.4        0.9    9.6   0.1    3.1  3  PAS_8         PAS domain
       0.36   11.0   7.3       0.56   10.4   0.0    4.2  4  PAS_7         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 ?   -1.0   0.1      0.85   1.4e+03      69     105 ..     135     171 ..     120     184 .. 0.87
   2 ?   -3.9   0.1       6.7   1.1e+04     117     131 ..     200     214 ..     199     227 .. 0.78
   3 !  126.6   9.3   4.8e-40   7.8e-37       2     152 ..     731     882 ..     730     885 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.85
                               BAT  69 rvvseeddgtlleltvsgpslastlaehGgtvrsaea 105
                                       r +++++ +  + + + ++  a+++ + +g++ ++  
  gi|344209974|ref|YP_004786150.1| 135 RAITQRERARQFDAVFHDTQTATWVLDPDGSLARVNQ 171
                                       78999999999*****9********999999988765 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6.7
                               BAT 117 PpgadvRsvvealee 131
                                       ++++d+R++vea ++
  gi|344209974|ref|YP_004786150.1| 200 ATERDIRQLVEAARD 214
                                       567899999999876 PP

  == domain 3  score: 126.6 bits;  conditional E-value: 4.8e-40
                               BAT   2 avveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddg. 77 
                                       +v+++e++i+de+++l++la+ ++c++++eg +++   +  vf+tv++ad+++v++aa+d+ +++dv+ +s++d++ 
  gi|344209974|ref|YP_004786150.1| 731 SVTRVEFDIDDERFLLSRLARSAGCTLSYEGGIQHAPAGNSVFVTVEDADVQTVAAAAADMTSIDDVTQISDDDTEs 807
                                       69**********************************************************************99976 PP

                               BAT  78 tlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrtrr 152
                                        +l+l++s+p+la  la+hG+  r+a+a++++++lvv+vP+++dvR++++ +++++++veL ++ + er  ++ r
  gi|344209974|ref|YP_004786150.1| 808 GVLRLELSQPFLALELADHGAIFREATADPDGTTLVVDVPQSVDVRNIAQLVDSTFSGVELKRKETLERGIEQDR 882
                                       89******************************************************************9877655 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.7   4.4e+03      55      76 ..     162     183 ..     129     208 .. 0.66
   2 !   23.8   0.3   2.8e-08   4.5e-05       5     138 .]     403     533 ..     399     533 .. 0.80
   3 !   68.7   0.1   3.7e-22   6.1e-19       3     137 ..     577     718 ..     575     719 .. 0.90
   4 ?   -2.9   0.0       4.7   7.6e+03     105     133 ..     725     753 ..     722     755 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.7
                                       -TTHHHHHHHHTS-EEES-GGG CS
                             GAF_2  55 geglvgealrtgrpvilndlee 76 
                                        +g ++++ +tgr++i +d+++
  gi|344209974|ref|YP_004786150.1| 162 PDGSLARVNQTGRAMIDEDVDA 183
                                       5677788899999999888776 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 2.8e-08
                                       HHHHHHHHHHHHHS.S..EEEEEEE-.TTS-EEEE.EEEES-TTSTT-S-B---TT.HHHHHHHHTS-EEES-GGG- CS
                             GAF_2   5 eelldlvldelvel.gaalgyillvd.ddgglrla.awgeaeeefgaaldrplgeg.lvgealrtgrpvilndleed 77 
                                       +e++ +++d ++ + +++++ i+l+d + ++l+ +  +   +e +g  +  + ++  l  +++ + + ++++d+ + 
  gi|344209974|ref|YP_004786150.1| 403 QEIAHHIVDDVLSVfDVSASAIYLHDvETNELQPVtQSQAMTEHHGPLPAVRTNDDtLPSHSFVNDETLVFDDVHT- 478
                                       7999*********55*8888888888344557766344455555555554477666699******9****999766. PP

                                       S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  78 pdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                         +++l+ ++ +lrs +++Pl   g  +Gv++ +++  + fd+  +el ++la+++  a++
  gi|344209974|ref|YP_004786150.1| 479 --SDRLENRATDLRSVMFIPL---G-NHGVFVSGSTAVGVFDDVTQELTDLLAATAEAALD 533
                                       ..56677799***********...9.9*****87888888*****************9996 PP

  == domain 3  score: 68.7 bits;  conditional E-value: 3.7e-22
                                       HHHHHHHHHHHHHHHSS...EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B--..-TT.HHHHHHHHTS-EEES-G CS
                             GAF_2   3 dleelldlvldelvelg.aalgyillvdddgg.lrlaawgeaeeefgaaldrpl..geg.lvgealrtgrpvilndl 74 
                                       + ee+  +v+++l++++ + +++i+ vd++g+ ++++aw++ e +  ++++  +  +e  ++g+ ++tg+ +++ ++
  gi|344209974|ref|YP_004786150.1| 577 TQEEINHTVCERLTDTDrFKFAWIGSVDPGGNtVETRAWAGNEQGYLDSQPITVadSETePAGRTAATGEVTMIPNV 653
                                       679999**********77**********88774555599999999999997755778888****************9 PP

                                       GG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  75 eedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       ++d +  +++  a  +++ s l++Pl++++  +G+l++ya+ ++afde+ +++L+el+e+ia a+
  gi|344209974|ref|YP_004786150.1| 654 AADLRNAPWRsdALTRDFLSVLSIPLVYNDLRHGILTIYADTKDAFDETTRTVLRELGETIASAL 718
                                       998888888877999999999*******99**********************************8 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 4.7
                                       -EEEEES......--HHHHHH.HHHHHHHH CS
                             GAF_2 105 vGvlnlyankppafdeedlel.Leelaeqi 133
                                       ++ l+  +  + +fd +d ++ L+ la+ +
  gi|344209974|ref|YP_004786150.1| 725 HALLTT-SVTRVEFDIDDERFlLSRLARSA 753
                                       566664.66777899666666478887765 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.0   8.6e-21   1.4e-17       1      53 []     890     942 ..     890     942 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 8.6e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LT++qlev+++Ay +GYF+ PR+ + +++A  l Is++++++h+r +++kl++
  gi|344209974|ref|YP_004786150.1| 890 LTERQLEVIQTAYYSGYFESPRTKSGEDIATMLEISPPAFYQHVRTVQRKLFT 942
                                       9**************************************************85 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.7   2.1e-12   3.4e-09       4     109 ..     153     261 ..     150     262 .. 0.86
   2 !   12.6   0.0   7.7e-05      0.12       2     110 .]     279     381 ..     278     381 .. 0.80
   3 ?   -1.9   0.1       2.3   3.8e+03      22      71 ..     518     547 ..     503     562 .. 0.54

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.1e-12
                             PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktla..ellpee.daarleralrrvlegeepiefleelllpge 77 
                                       ++ a+ vldpdg   ++N+++++++  + ++++G  ++   ++ ++ + +r  r+l ++++ +++   + ++ +   
  gi|344209974|ref|YP_004786150.1| 153 TQTATWVLDPDGSLARVNQTGRAMIDEDVDAVIGDLFWtlPWWAQSaATERDIRQLVEAARDGQFGNAVVHRPTTAT 229
                                       6678899*******************************776777766667777777777777777777776666*** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +r++el+++P++++ G+v  +++ ++DiTe++
  gi|344209974|ref|YP_004786150.1| 230 DRVIELSVRPVENDFGDVTSIVIEGIDITEQV 261
                                       ******************************86 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7.7e-05
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..pg 76 
                                       +++ d +++ ++dg ++y+ ++ + +fg++++e++ + + + l        +  +r+ l+++ +++  e++++   g
  gi|344209974|ref|YP_004786150.1| 279 SNMTDTVLMTNEDGEYTYVCPNVHFIFGYTDDEIREQEPIDTLLG-----EDLFDRAELAEKGVLKNIECTVTdkAG 350
                                       67889999*******************************985553.....344444445555566666666666699 PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                        e++++++++ + + +G+   +l  +rDiT r++
  gi|344209974|ref|YP_004786150.1| 351 HEHTLLVNVREV-EIQGG--TLLYSCRDITKRKQ 381
                                       999999999999.68888..899999****9985 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.3
                             PAS_4  22 aaaaelfgappeellGktlaellpeedaarleralrrvlegeepieflee 71 
                                       ++  +l++a++e++l++ ++e                     +  e+  e
  gi|344209974|ref|YP_004786150.1| 518 QELTDLLAATAEAALDRVVRE--------------------SQLREQDRE 547
                                       444455555555555555554....................433333333 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.41   6.7e+02       6      62 ..     119     172 ..     116     191 .. 0.79
   2 !   21.5   0.1   1.4e-07   0.00023       3     127 ..     403     532 ..     402     534 .. 0.80
   3 !   22.8   0.0   5.5e-08     9e-05       2     128 ..     578     719 ..     577     720 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.41
                             GAF_3   6 lekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesldedsalarrals 62 
                                       +++l++++ ++l++ + a+ +++ + +++ ++ + ++ + +  +ld d +lar  ++
  gi|344209974|ref|YP_004786150.1| 119 IDELIQRTGNALQSARRAITQRE-RARQFDAVFHDTQTATW--VLDPDGSLARVNQT 172
                                       78999999999********8877.77899999998677766..89999999985544 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.4e-07
                             GAF_3   3 dellekllkllvkllgaevgalllldedgnklqvaagw...dgkpalsesld..edsalarralssgevvsepsfae 74 
                                       +e++ ++++ + ++++++++a++l d + n+lq++ ++   ++++ +  +++   d++ ++  ++ +  +++ +++ 
  gi|344209974|ref|YP_004786150.1| 403 QEIAHHIVDDVLSVFDVSASAIYLHDVETNELQPVTQSqamTEHHGPLPAVRtnDDTLPSHSFVNDET-LVFDDVHT 478
                                       789999*****************************888789899999999988666677777777555.55655555 PP

                             GAF_3  75 edg.....lpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                        d+     +++r+++++PL       Gv + +st  + fd++++el + lA+ +  a+
  gi|344209974|ref|YP_004786150.1| 479 SDRlenraTDLRSVMFIPLGN----HGVFVSGSTAVGVFDDVTQELTDLLAATAEAAL 532
                                       44422223667999*****99....8999****99999********999998765555 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 5.5e-08
                             GAF_3   2 ldellekllkllvkllgaevgalllldedgnklqvaagw.dgkpal.se...sldedsalarralssgevvsepsfa 73 
                                       ++e+  +++++l ++ +++++ ++ +d++gn++ ++a   +++  l s+   + d ++  a r++++gev + p +a
  gi|344209974|ref|YP_004786150.1| 578 QEEINHTVCERLTDTDRFKFAWIGSVDPGGNTVETRAWAgNEQGYLdSQpitVADSETEPAGRTAATGEVTMIPNVA 654
                                       5788889999999********************99984433333334455644458888899*******98887776 PP

                             GAF_3  74 eedg...lpd.......raalavPLvagrqviGvlalastkprafdaedlelleslArqiataie 128
                                       +  +   +++        ++l +PLv  +   G+l ++ + + afd++++  l++l+  ia+a++
  gi|344209974|ref|YP_004786150.1| 655 ADLRnapWRSdaltrdfLSVLSIPLVYNDLRHGILTIYADTKDAFDETTRTVLRELGETIASALS 719
                                       6311233333222222366799*****9999********************************96 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   1.1e-12   1.7e-09      25      98 ..      36     109 ..      22     116 .. 0.93
   2 ?   -3.9   0.1       9.2   1.5e+04      69      94 ..     766     791 ..     764     793 .. 0.70

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.1e-12
                                       EEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHHHCTESEEE CS
                      Response_reg  25 evaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahseeedavealkagaddfl 98 
                                       ++ +a ++++al+ +++++vd++++   +++ +G +l++++r+  p+lpv++ t+ ++e+ a ea++ag++d++
  gi|344209974|ref|YP_004786150.1|  36 TILTAGTPSDALDTVRQRSVDCLVTGETLDDGSGTDLVRQLRDSAPDLPVVLGTTDGSEALASEAIQAGVSDYV 109
                                       7889999******************************************************************8 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 9.2
                                       TTTSEEEEEESSTSHHHHHHHHHCTE CS
                      Response_reg  69 dpelpviiltahseeedavealkaga 94 
                                        p  + +++t ++++ ++v+a  a++
  gi|344209974|ref|YP_004786150.1| 766 APAGNSVFVTVEDADVQTVAAAAADM 791
                                       56677788998888777777777665 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.1   3.4e+03       9      65 ..     122     179 ..     118     243 .. 0.49
   2 !   14.2   0.2   3.3e-05     0.053       3     126 ..     403     525 ..     403     547 .. 0.69
   3 !   19.7   0.0   6.5e-07    0.0011      15     133 .]     588     718 ..     577     718 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.1
                                       HHHHHHHHHTESEEEEEE....EEETTEEE....CEEEEECCEEEETTSHHHHHHHHHSSSEEES CS
                               GAF   9 vveelrellgadrvalyl....pdydGlhy....dipqasrwlfmkngrgicgqvlatgqplvip 65 
                                       ++++ + +l+  r a+ +     +     +    + +q ++w+ +++g+   ++v +tg++++ +
  gi|344209974|ref|YP_004786150.1| 122 LIQRTGNALQSARRAITQreraRQ-----FdavfHDTQTATWVLDPDGSL--ARVNQTGRAMIDE 179
                                       566666666677777755333311.....123334667777744444333..2333333333322 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.3e-05
                                       HHHHHHHHHHHHHHHTESEEEEEEEEETTEEE.CEEEEECC.....EEEETTSHHHH.....HHHHHSSSEEESTGG CS
                               GAF   3 eelldtvveelrellgadrvalylpdydGlhy.dipqasrw.....lfmkngrgicg.....qvlatgqplvipdst 68 
                                       +e+++ +v+++ +++++   a+yl+d + ++  +++q+++      + + + ++  +     + + ++++lv++d+ 
  gi|344209974|ref|YP_004786150.1| 403 QEIAHHIVDDVLSVFDVSASAIYLHDVETNELqPVTQSQAMtehhgPLPAVRTN--DdtlpsHSFVNDETLVFDDVH 477
                                       689*********************655554334233333334466422222222..35555688899*******988 PP

                                       TSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHH CS
                               GAF  69 pdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvla 126
                                       +++r  +       +++  rs++ +Pl n+g    ++v  ++    f++   el   la
  gi|344209974|ref|YP_004786150.1| 478 TSDRLEN-------RATDLRSVMFIPLGNHG----VFVSGSTAVgVFDDVTQELTDLLA 525
                                       8888777.......789***********974....444444333445555555555555 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 6.5e-07
                                       HHHTESEEEE.EE..EEETTEEECEEEEECC..............EEEETTSHHHHHHHHHSSSEEESTGGTSTTHH CS
                               GAF  15 ellgadrval.yl..pdydGlhydipqasrw..............lfmkngrgicgqvlatgqplvipdstpdprfa 74 
                                       +l++ dr  + ++   d  G   ++ + ++w              + +++ ++ +g+++atg++  ip++++d r a
  gi|344209974|ref|YP_004786150.1| 588 RLTDTDRFKFaWIgsVDPGG---NTVETRAWagneqgyldsqpitVADSETEP-AGRTAATGEVTMIPNVAADLRNA 660
                                       55556664443444422333...122333333333333333223233333445.779999*********99****99 PP

                                       TTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE.SSSCSHHHHHHHHHHHHHHHHHHH CS
                               GAF  75 qynrrdllenmgirsslvvPlvndgelwGllvlhn.psppftreelellqvladqvaval 133
                                       +  +r+ +    + s+l++Plv ++   G+l+++  +++ f++  + +l++l++ +a al
  gi|344209974|ref|YP_004786150.1| 661 P--WRSDALTRDFLSVLSIPLVYNDLRHGILTIYAdTKDAFDETTRTVLRELGETIASAL 718
                                       9..99999999************9999********76669****************9987 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.7e-08   2.7e-05       3     104 .]     156     259 ..     154     259 .. 0.90
   2 !    8.7   0.1    0.0013         2       3     103 ..     284     377 ..     282     384 .. 0.74
   3 ?   -1.9   0.0       2.4     4e+03      34      73 ..     518     553 ..     505     578 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.7e-08
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       ++++ +pdg + ++N++ + ++  + ++v+g  +++l   ++++ +++++r+++e+ r+ ++   vv++  + +   
  gi|344209974|ref|YP_004786150.1| 156 ATWVLDPDGSLARVNQTGRAMIDEDVDAVIGDLFWTLPwwAQSAATERDIRQLVEAARDGQFGNAVVHRPTTATDRV 232
                                       567888***999*******************6666666999999999999999999998888888888888889999 PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       ++l+++pv +d g +++i++  +Dite
  gi|344209974|ref|YP_004786150.1| 233 IELSVRPVENDFGDVTSIVIEGIDITE 259
                                       **************************8 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0013
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgks.itdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                        +l++n+dg+ +y+ + +  ++Gy+ +e+  +  i++l+   ++  +r + a +      ++ e + ++k g +   
  gi|344209974|ref|YP_004786150.1| 284 TVLMTNEDGEYTYVCPNVHFIFGYTDDEIREQEpIDTLL--GEDLFDRAELAEKGVL---KNIECTVTDKAGHEHTL 355
                                       67899********************99987666488888..4444444444444444...66777777777766666 PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDit 103
                                       l++++ v  ++g+l      +rDit
  gi|344209974|ref|YP_004786150.1| 356 LVNVREVEIQGGTLLY---SCRDIT 377
                                       7888888777777775...888888 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.4
                             PAS_9  34 ksitdlfvtdpeanerlraaleqgrkkerevevvlirkng 73 
                                       + +tdl+  ++ a+  l++++++ +   re++ +l+r n+
  gi|344209974|ref|YP_004786150.1| 518 QELTDLL--AATAEAALDRVVRESQ--LREQDRELQRQNE 553
                                       4678888..7778888888888888..7777777777765 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   2.9e-05     0.047       2     113 .]     145     257 ..     144     257 .. 0.96
   2 !   12.5   0.0   6.8e-05      0.11       5      58 ..     276     329 ..     272     372 .. 0.85
   3 ?   -3.6   0.2       6.5   1.1e+04      46      80 ..     536     556 ..     516     580 .. 0.44
   4 ?   -0.6   0.0       0.8   1.3e+03       7      36 ..     764     794 ..     759     799 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       +++a+++++ ++++v+D dg    vN++ + +   + + v+g  +  l +  ++a + + ++ql e++++++ g+  
  gi|344209974|ref|YP_004786150.1| 145 QFDAVFHDTQTATWVLDPDGSLARVNQTGRAMIDEDVDAVIGDLFWTLPWWAQSAATERDIRQLVEAARDGQFGNAV 221
                                       7899************************************************************************9 PP

                                       EEC.TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fkl.rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       + + +  + + +e+ ++pv +  g ++ ++  + di
  gi|344209974|ref|YP_004786150.1| 222 VHRpTTATDRVIELSVRPVENDFGDVTSIVIEGIDI 257
                                       99999****************999999999888876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.8e-05
                                       HHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHH CS
                               PAS   5 aileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddael 58 
                                         l++++d +++++edg+ +yv ++   ++G++ +e+  +  +d +  ed  ++
  gi|344209974|ref|YP_004786150.1| 276 VTLSNMTDTVLMTNEDGEYTYVCPNVHFIFGYTDDEIREQEPIDTLLGEDLFDR 329
                                       56899*****************************************99874333 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 6.5
                                       GGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS  46 lldliheeddaelaelleqlleqgeesrageisfk 80 
                                       + ++   e+d+              e + ++  ++
  gi|344209974|ref|YP_004786150.1| 536 VRESQLREQDR--------------ELQRQNEQLT 556
                                       33333333333..............2222222222 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.8
                                       HHH.SSSEEEEEETTSBEEEECHHHHHHHSS CS
                               PAS   7 les.lpdpifvvDedgrilyvNaaaeellGl 36 
                                       +++ + + +fv+ ed ++  v aaa++++ +
  gi|344209974|ref|YP_004786150.1| 764 QHApAGNSVFVTVEDADVQTVAAAAADMTSI 794
                                       444677889*******************987 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00056       0.9       2      62 ..     145     208 ..     141     214 .. 0.73
   2 ?   -0.8   0.0       1.1   1.7e+03      33      56 ..     304     330 ..     274     341 .. 0.72
   3 ?   -3.1   0.0       5.4   8.8e+03       5      33 ..     415     446 ..     415     458 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00056
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellg..qllpvlrplledaeql 62 
                                       ++ a+f+  + + +v+d +g  +  vNq+   +   + + ++g+l++  +++ ++   ++d++ql
  gi|344209974|ref|YP_004786150.1| 145 QFDAVFHDTQTATWVLDpDGS-LARVNQTGRAMIDEDvDAVIGDLFWtlPWWAQSAATERDIRQL 208
                                       46679************7777.************8556666666665555555555555566665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                             PAS_8  33 llGys.adlkgellg..qllpvlrpll 56 
                                       ++Gy+ +++++++     l+++l +  
  gi|344209974|ref|YP_004786150.1| 304 IFGYTdDEIREQEPIdtLLGEDLFDRA 330
                                       799998888887765444444444444 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.4
                             PAS_8   5 alfesspdgiavvd..lgd..rivdvNqaalel 33 
                                       ++f+ s+ +i + d  + +  + v   qa+ e 
  gi|344209974|ref|YP_004786150.1| 415 SVFDVSASAIYLHDveT-NelQPVTQSQAMTEH 446
                                       68999999999977532.234555555555555 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      0.13     2e+02      57     111 ..     199     261 ..     150     265 .. 0.57
   2 ?   10.4   0.0   0.00034      0.56       1     115 []     278     384 ..     278     384 .. 0.78
   3 ?   -3.8   0.1       8.4   1.4e+04     100     110 ..     509     519 ..     505     522 .. 0.80
   4 ?   -1.1   0.1       1.2     2e+03      54      99 ..     577     621 ..     526     625 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.13
                             PAS_7  57 gdveaeverrlaaaragkphsfer...erpdgrvievrgnpl.....pdgGfVttytDiTerr 111
                                       +++e  +++ ++aar+g+  +  +   ++++ rvie+  +p+     +   +V+   DiTe++
  gi|344209974|ref|YP_004786150.1| 199 AATERDIRQLVEAARDGQFGNAVVhrpTTATDRVIELSVRPVendfgDVTSIVIEGIDITEQV 261
                                       345556666676776654444444001556789999999999422222234444556777776 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00034
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellryn.aergefgagdveaeverrlaaaragkph 76 
                                       l+nm++ +++ ++d++ + +  ++  +++++++ ++ + p+++ll     +r e++++ v + +e +++  +ag++h
  gi|344209974|ref|YP_004786150.1| 278 LSNMTDTVLMTNEDGEYTYVCPNVHFIFGYTDDEIREQEPIDTLLGEDlFDRAELAEKGVLKNIECTVT-DKAGHEH 353
                                       678999999999999998888888889999999999999999988654378888887777777776663.2233333 PP

                             PAS_7  77 sfererpdgrvievrgnplpdgGfVttytDiTerrraee 115
                                                  ++vr+ ++++g ++ ++ DiT+r++ ee
  gi|344209974|ref|YP_004786150.1| 354 --------TLLVNVREVEIQGGTLLYSCRDITKRKQREE 384
                                       ........346789*********************9986 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 8.4
                             PAS_7 100 fVttytDiTer 110
                                        V +++D+T++
  gi|344209974|ref|YP_004786150.1| 509 AVGVFDDVTQE 519
                                       6889*****97 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.2
                             PAS_7  54 fgagdveaeverrlaaaragkphsfererpdgrvievrgnplpdgG 99 
                                         +++++++v +rl+   ++k  ++    p g+++e r+ +  + G
  gi|344209974|ref|YP_004786150.1| 577 T-QEEINHTVCERLTDTDRFKFAWIGSVDPGGNTVETRAWAGNEQG 621
                                       2.46677778888888888888888888888888888776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (955 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); 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: 00:00:00.49
# Mc/sec: 5917.73
//
Query:       gi|344209975|ref|YP_004786151.1|  [L=47]
Description: hypothetical protein HAH_5033 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   0.2     0.0003   20.7   0.2    1.1  1  zf-C2HC5      Putative zinc finger motif, C2HC5-type
      0.002   18.1   1.4     0.0022   18.0   1.4    1.1  1  DZR           Double zinc ribbon
     0.0083   16.2   1.0     0.0093   16.0   1.0    1.1  1  DUF1272       Protein of unknown function (DUF1272)
  ------ inclusion threshold ------
       0.01   15.9   3.3      0.018   15.1   3.3    1.5  1  Zn-ribbon_8   Zinc ribbon domain
      0.015   14.7   1.6      0.024   14.0   1.6    1.3  1  zf-ribbon_3   zinc-ribbon domain
      0.024   14.8   0.4      0.027   14.6   0.4    1.1  1  NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
      0.069   13.2   1.0      0.071   13.1   1.0    1.1  1  HypA          Hydrogenase/urease nickel incorporation, metall
       0.11   12.8   1.0       0.16   12.3   1.0    1.4  1  RNA_pol_N     RNA polymerases N / 8 kDa subunit
       0.15   12.0   5.2        2.6    8.1   3.8    2.1  2  YhfH          YhfH-like protein


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 !   20.7   0.2   1.5e-07    0.0003      19      44 ..      15      39 ..       6      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.5e-07
                          zf-C2HC5 19 nClnCGkiiCakeglskpCsfCgspl 44
                                       C++CGk+i a  ++ ++C+ Cg ++
  gi|344209975|ref|YP_004786151.1| 15 ECFACGKVITAESQP-ENCQDCGGEM 39
                                      6**************.******9775 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.4   1.1e-06    0.0022      14      39 ..      15      40 ..       5      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.1e-06
                               DZR 14 fCseCgtklkavaaedrCpsCgekvd 39
                                       C++Cg+ + a++++++C  Cg ++ 
  gi|344209975|ref|YP_004786151.1| 15 ECFACGKVITAESQPENCQDCGGEMR 40
                                      6*********9999*******98765 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.0   4.7e-06    0.0093      14      54 ..       3      42 ..       1      45 [. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.7e-06
                           DUF1272 14 dlppdseearicsyEctFCaeCaeevl.envCPncgGelvkR 54
                                      d+++d++ea    yEc  C +  ++    + C +cgGe+ +R
  gi|344209975|ref|YP_004786151.1|  3 DVEQDHDEA--TPYECFACGKVITAESqPENCQDCGGEMRNR 42
                                      666666666..47******987654431799********998 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   3.3   9.1e-06     0.018       6      37 ..      14      40 ..      13      43 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.1e-06
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdaplta.CPeCgsevr 37
                                      Y+C +Cg++ ++        +++ C +Cg+e+r
  gi|344209975|ref|YP_004786151.1| 14 YECFACGKVITAES------QPEnCQDCGGEMR 40
                                      9******9998554......5555******988 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.6   1.2e-05     0.024       4      25 ..      15      38 ..      14      39 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                       zf-ribbon_3  4 rCPnCGa.p.lssddnvCpyCGtk 25
                                      +C +CG+ + ++s+  +C  CG++
  gi|344209975|ref|YP_004786151.1| 15 ECFACGKvItAESQPENCQDCGGE 38
                                      7999***999999999******86 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 ?   14.6   0.4   1.4e-05     0.027       9      36 ..      14      42 ..      10      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                      NOB1_Zn_bind  9 lrChaCfkvt.kdmtkkFCpkCGnktLkr 36
                                      ++C aC kv+  +++ + C+ CG ++ +r
  gi|344209975|ref|YP_004786151.1| 14 YECFACGKVItAESQPENCQDCGGEMRNR 42
                                      58******87256899*******987666 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   1.0   3.6e-05     0.071      69      96 ..      12      39 ..       4      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.6e-05
                                      -EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA 69 vkvrCreCgkefeleekalrCpkCgsad 96
                                        ++C  Cgk ++ e++ ++C++Cg++ 
  gi|344209975|ref|YP_004786151.1| 12 TPYECFACGKVITAESQPENCQDCGGEM 39
                                      5689******9998877678*****975 PP

>> 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 ?   12.3   1.0   8.1e-05      0.16       4      16 ..      13      25 ..      12      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.1e-05
                                      -SS-TTT--B-ST CS
                         RNA_pol_N  4 PVrCFtCGkvige 16
                                      P  CF CGkvi  
  gi|344209975|ref|YP_004786151.1| 13 PYECFACGKVITA 25
                                      678********86 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.8    0.0013       2.6      15      37 .]      15      35 ..      12      35 .. 0.90
   2 ?    6.4   1.5    0.0045       8.9      15      24 ..      31      40 ..      26      43 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0013
                              YhfH 15 kCteCGkeieEqaecYgneCekC 37
                                      +C  CGk+i   ae+  ++C++C
  gi|344209975|ref|YP_004786151.1| 15 ECFACGKVIT--AESQPENCQDC 35
                                      7********6..89999999999 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0045
                              YhfH 15 kCteCGkeie 24
                                       C++CG e+ 
  gi|344209975|ref|YP_004786151.1| 31 NCQDCGGEMR 40
                                      6*****9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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: 0.32u 0.27s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 343.19
//
Query:       gi|344209976|ref|YP_004786152.1|  [L=431]
Description: NAD(P)-specific glutamate dehydrogenase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-71  239.6   0.1    4.8e-71  239.3   0.1    1.1  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    1.5e-56  189.9   0.0    2.4e-56  189.2   0.0    1.4  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
     0.0065   15.9   0.0      0.011   15.1   0.0    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.017   14.7   0.0      0.031   13.8   0.0    1.4  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
       0.13   12.4   0.0       0.24   11.5   0.0    1.5  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
       0.18   12.2   0.0       0.51   10.7   0.0    1.9  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 !  239.3   0.1   1.6e-74   4.8e-71       1     243 []     197     428 ..     197     428 .. 0.98

  Alignments for each domain:
  == domain 1  score: 239.3 bits;  conditional E-value: 1.6e-74
                                       T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HH CS
                     ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldie 77 
                                       GGs++r++a g++v+++++ +++++++  l++++va++G+G vg +aa+ll e+ga+vva+sD +G++ydp G+d++
  gi|344209976|ref|YP_004786152.1| 197 GGSKGREDAPGRSVAIITQLVCEYYDQP-LSETTVAVQGYGSVGANAARLLDEQGATVVAISDVNGAMYDPAGIDTA 272
                                       9***********************7777.************************************************ PP

                                       HHHHHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHH CS
                     ELFV_dehydrog  78 ellelkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeA 154
                                       ++ ++ ee ++v+ey+    +  ++i+n+ ell+l+vd+l+P+A+ n+i+e+na+  i+  +++vvEgAN+ptt+ A
  gi|344209976|ref|YP_004786152.1| 273 TVPSHDEEPEAVTEYA----D--TVISND-ELLTLDVDVLIPAALGNVITEANAD-DIA--ADFVVEGANGPTTSTA 339
                                       ****************....3..689997.*************************.999..**************** PP

                                       HHHHHHTT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-THHHHHHHHH CS
                     ELFV_dehydrog 155 keileeagvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqelvkganiag 231
                                       ++il +++v+v+pd++aNaGGVtvS++E+lq+++r sw+ e+v+++l+++m+++++av +e e+++ +++++a+i++
  gi|344209976|ref|YP_004786152.1| 340 DSILADRDVMVIPDILANAGGVTVSYFEWLQDINRRSWSLERVNDELDEEMRAAWDAVRTEFENRDITWRDAAYIVA 416
                                       ***************************************************************************** PP

                                       HHHHHHHHHHCT CS
                     ELFV_dehydrog 232 fekvaeamkaqG 243
                                       + ++aea++a+G
  gi|344209976|ref|YP_004786152.1| 417 LSRIAEAHEARG 428
                                       **********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 !  189.2   0.0   8.1e-60   2.4e-56       1     130 []      51     179 ..      51     179 .. 0.99

  Alignments for each domain:
  == domain 1  score: 189.2 bits;  conditional E-value: 8.1e-60
                                       -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES CS
                   ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvki 77 
                                       p++v +vtvp++rd+G++ev++gyraqh+s++gP+kGG+R+hp+v+ de+  L+ +mt+K+a++dlpfGGakgg+ +
  gi|344209976|ref|YP_004786152.1|  51 PRNVHEVTVPIERDDGTVEVFTGYRAQHDSVRGPYKGGLRYHPDVTRDECVGLGIWMTWKCAVMDLPFGGAKGGIAV 127
                                       67899************************************************************************ PP

                                       -GGGS-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHHH CS
                   ELFV_dehydrog_N  78 dpkklseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeykk 130
                                       +pk+ls++e er+trrf++el+ k+iGp+ D+pApD+gt++++mawl+d y++
  gi|344209976|ref|YP_004786152.1| 128 NPKTLSRDEKERLTRRFAQELR-KVIGPNLDIPAPDMGTDPQTMAWLMDAYSM 179
                                       **********************.****************************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 !   15.1   0.0   3.7e-06     0.011      32      69 ..     223     260 ..     215     297 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-06
                                       S-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSH CS
                      2-Hacid_dh_C  32 kelsgktvGiiGlGrIGqavakrlkafgmkviaydrsk 69 
                                       + ls+ tv++ G+G++G ++a++l + g+ v+a++  +
  gi|344209976|ref|YP_004786152.1| 223 QPLSETTVAVQGYGSVGANAARLLDEQGATVVAISDVN 260
                                       67999***************************998764 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 ?   13.8   0.0     1e-05     0.031       2      56 ..     225     279 ..     224     297 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1e-05
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvae 56 
                                       l++ ++av GyGs G + a+ l ++g  vv     +++ ++ A  +  +v + +e
  gi|344209976|ref|YP_004786152.1| 225 LSETTVAVQGYGSVGANAARLLDEQGATVVAISDVNGAMYDPAGIDTATVPSHDE 279
                                       6789***********************9988777777788888877777766554 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 ?   11.5   0.0     8e-05      0.24      21      55 ..     225     260 ..     217     322 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8e-05
                                       -TTSEEEEE--SHHHHHHHHHHHHCT-EEE.EE-S- CS
                     AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvi.vtevd 55 
                                       l+  ++ v GyG vG  +a+ l ++Ga v+ +++v+
  gi|344209976|ref|YP_004786152.1| 225 LSETTVAVQGYGSVGANAARLLDEQGATVVaISDVN 260
                                       5667899********************875255654 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 ?   -3.4   0.0       4.3   1.3e+04      41      55 ..      74      88 ..      66      93 .. 0.81
   2 ?   10.7   0.0   0.00017      0.51       2      38 ..     229     264 ..     228     331 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.3
                                      HHHHEETTTEC-SS- CS
                           Gp_dh_N 41 yllkyDsvhgrfkge 55
                                      y  ++Dsv g +kg 
  gi|344209976|ref|YP_004786152.1| 74 YRAQHDSVRGPYKGG 88
                                      567899999999875 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00017
                                       EEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS-HHH CS
                           Gp_dh_N   2 kvainGfGRIGrlvlralleekelevvaindltdlet 38 
                                        va+ G+G +G +++r l  e+  +vvai d+  + +
  gi|344209976|ref|YP_004786152.1| 229 TVAVQGYGSVGANAARLLD-EQGATVVAISDVNGAMY 264
                                       69************99875.66999****99866655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3100.95
//
Query:       gi|344209977|ref|YP_004786153.1|  [L=1274]
Description: light and oxygen sensing histidine kinase [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-52  176.5  15.5    3.9e-14   52.8   0.0    7.0  6  PAS_4         PAS fold
    8.5e-37  125.6   4.6    5.3e-17   61.9   0.0    5.6  5  PAS           PAS fold
    2.2e-31  108.2   3.7      2e-12   47.3   0.0    6.0  6  PAS_9         PAS domain
    3.9e-20   71.4   1.8    1.6e-06   28.0   0.0    5.8  5  PAS_8         PAS domain
    1.1e-19   70.4   0.4    2.3e-09   37.4   0.1    3.9  4  PAS_3         PAS fold
      1e-17   64.7  12.2      7e-10   39.3   0.8    5.3  6  GAF_2         GAF domain
    3.2e-17   63.1   0.1    1.5e-09   38.3   0.0    4.3  4  GAF_3         GAF domain
    1.1e-14   54.9   0.0    2.4e-14   53.8   0.0    1.7  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    5.1e-13   48.9   6.4    5.2e-13   48.8   0.4    4.0  4  HisKA         His Kinase A (phospho-acceptor) domain
    1.1e-12   48.2   0.1    4.1e-12   46.3   0.0    2.0  2  Response_reg  Response regulator receiver domain
    6.2e-09   36.6   0.1    9.5e-07   29.5   0.0    3.6  3  GAF           GAF domain
  ------ inclusion threshold ------
      0.063   13.9   0.0        1.3    9.6   0.0    3.1  3  PAS_10        PAS domain
       0.54   10.3   2.1        1.6    8.8   0.7    2.6  2  MCU           Mitochondrial calcium uniporter
        7.5    7.4   8.1         28    5.5   0.1    4.4  4  TetR_C_15     Tetracyclin repressor-like, C-terminal 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 ?   -0.5   0.0       1.1   1.5e+03      28      59 ..      91     130 ..      90     133 .. 0.59
   2 !   49.4   0.1   3.5e-16   4.5e-13       1     110 []     127     229 ..     127     229 .. 0.95
   3 !   31.7   0.0   1.1e-10   1.5e-07       1     109 [.     241     361 ..     241     362 .. 0.86
   4 !    8.0   0.9    0.0026       3.3      42     109 ..     585     653 ..     580     654 .. 0.89
   5 !   39.2   0.2   5.2e-13   6.6e-10      13     109 ..     689     784 ..     670     785 .. 0.88
   6 !   52.8   0.0     3e-17   3.9e-14       2     109 ..     802     909 ..     801     910 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                             PAS_4  28 fgappeellGktla...ellpee.....daarleralrrv 59 
                                       +g   +ellG++ +   e + ++     + +r++r l+r+
  gi|344209977|ref|YP_004786153.1|  91 AGENSFELLGRRIQtlvEAARKQavaerLSDRFQRTLERA 130
                                       5777889999999966655555573333555555555554 PP

  == domain 2  score: 49.4 bits;  conditional E-value: 3.5e-16
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       l++  d++++++++ r++y+N+ +a+ + + p++++G + +e +p  ++++le+ +r ++e++ep++f+++l   + 
  gi|344209977|ref|YP_004786153.1| 127 LERATDGIYAVNDEWRIEYINEKMARRVDRNPDDIIGASIWEEFPSIVGTELEDKYRTAMETGEPVSFEQYLGE-PF 202
                                       67889************************************99***************************8888.** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       + ++e+r++P +d      g+ ++sr++T++r+
  gi|344209977|ref|YP_004786153.1| 203 DYWVEVRVFPDDD------GLTIFSRETTAERE 229
                                       **********655......99********9885 PP

  == domain 3  score: 31.7 bits;  conditional E-value: 1.1e-10
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaae.lfgappeellGktlaellpee....daarleralrrvl...egeepiefl 69 
                                       l+++ da++vld++g++++aNaa+ + ++g +  ++ G+ l+ ++  +    d +++ +a+r  l   eg+  ++ l
  gi|344209977|ref|YP_004786153.1| 241 LENIHDAVFVLDDEGTIEFANAASKRlIAGDQSTQIAGQQLETVVGNRistsDTEQFTSAVRSTLndiEGDGGVTGL 317
                                       7999**********************9***************99999999999********9998333444445555 PP

                             PAS_4  70 eelll......pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                          +l      +g+ r++++r++P+   s +   +lv++rDiTe++
  gi|344209977|ref|YP_004786153.1| 318 YDADLqlditaEGDKRTFDVRVTPF--QSNKSNQALVVARDITEQS 361
                                       55444666999**************..678889***********85 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0026
                             PAS_4  42 ellpeedaarleralrrvlegeepiefleelll.pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       e++ ++d++ + +a++r+++ +ep++     ++ +g+ r +     ++++++ +   + ++++DiTer+
  gi|344209977|ref|YP_004786153.1| 585 EFYHPDDRETITTAVERAIADREPYDLDLRIVRtGGDVRDVRAWGERVDEPQDDEPVIRGVFQDITERK 653
                                       677788***********************999998888888888888888888899999********98 PP

  == domain 5  score: 39.2 bits;  conditional E-value: 5.2e-13
                             PAS_4  13 pdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhyelrllPlr 89 
                                       + + + ++++ +++  g++ +e++G+t++e++ +e +a+l+++++r++e+++pi+ +eel+  ++ r+++++l P+ 
  gi|344209977|ref|YP_004786153.1| 689 RAFEFARLSPGYESQTGLTTDEVRGQTPREVFGAERGAELAANYTRCVEQRAPISYQEELDIAPDARFWDTSLAPV- 764
                                       44667788899*****************************************************************. PP

                             PAS_4  90 desGe.vigvlvisrDiTerr 109
                                        + G+ ++ +++i+r +Te++
  gi|344209977|ref|YP_004786153.1| 765 -MLGDeIVRIVGIARNVTEQV 784
                                       .778889************86 PP

  == domain 6  score: 52.8 bits;  conditional E-value: 3e-17
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..pg 76 
                                       +++p  +  +d+dg+v+++N  a+ +fg+++ee+lG+    ++p+e++a++e++ +r+l+ge pi+  e+++   +g
  gi|344209977|ref|YP_004786153.1| 802 EATPLTVMEIDTDGTVIRWNDGAENMFGWSREEVLGEFNP-MVPDEQQAEFESHRQRALSGE-PIRGKEIRREtkDG 876
                                       5678888899**************************9877.9*******************5.88888877776888 PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       e   ++l++ P+ +++Ge+  +l+++ DiT+++
  gi|344209977|ref|YP_004786153.1| 877 EVLDLLLSVAPITAPDGEITSILAVLEDITDQK 909
                                       888888888*********************997 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   6.5e-08   8.3e-05       2      76 ..     122     196 ..     121     212 .. 0.93
   2 !   25.0   0.1   1.1e-08   1.4e-05       4     113 .]     238     357 ..     235     357 .. 0.82
   3 ?   -0.7   0.0       1.1   1.4e+03      46     113 .]     583     649 ..     541     649 .. 0.71
   4 !   12.9   0.0   6.7e-05     0.085       1      99 [.     664     767 ..     664     780 .. 0.73
   5 !   61.9   0.0   4.1e-20   5.3e-17       2     113 .]     796     905 ..     795     905 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6.5e-08
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCC CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrage 76 
                                       ++++ le ++d+i +v+   ri y+N+++++    ++++++g s+ ++++     el +++++++e+ge+ + ++
  gi|344209977|ref|YP_004786153.1| 122 RFQRTLERATDGIYAVNDEWRIEYINEKMARRVDRNPDDIIGASIWEEFPSIVGTELEDKYRTAMETGEPVSFEQ 196
                                       7899**********************************************98777**************998776 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.1e-08
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHH.SSTHHHCTTSBGGGGBSTTHHH....HHHHHHHHHHHHTT-ECCC CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeell.Glsreevlgkslldliheedda....elaelleqlleqgeesrag 75 
                                       ++ile+++d++fv+D  g i ++Naa  +l  G +  ++ g+ l  ++ +  +     ++ ++++  l++ e   ++
  gi|344209977|ref|YP_004786153.1| 238 ETILENIHDAVFVLDDEGTIEFANAASKRLIaGDQSTQIAGQQLETVVGNRISTsdteQFTSAVRSTLNDIEGDGGV 314
                                       79************************9997516666*******9988766555533346666666666666666666 PP

                                       CEEEEC.......TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  76 eisfkl.......rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                           +          g ++ ++vr++p+ + +++  ++l+v+rdi
  gi|344209977|ref|YP_004786153.1| 315 TGLYDAdlqlditAEGDKRTFDVRVTPFQSNKSN--QALVVARDI 357
                                       66666699**************************..********8 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.1
                                       GGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  46 lldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        ++++h++d+++   ++e++++++e+     + ++ + g ++ ++ +   v ++++    + gv++di
  gi|344209977|ref|YP_004786153.1| 583 AIEFYHPDDRETITTAVERAIADREPYDLDLRIVR-TGGDVRDVRAWGERVDEPQDDEPVIRGVFQDI 649
                                       57889998877777777777776666655444444.48888888887777777777766777777776 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 6.7e-05
                                       HHHHHHHHHSSSEEEEEE....TTS...BEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT CS
                               PAS   1 edlraileslpdpifvvD....edg...rilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqge 70 
                                       e+++a+l+++ d+if++D     d    ++   ++ +e+++Gl+ +ev g++  +++  e  aela+ ++++ eq+ 
  gi|344209977|ref|YP_004786153.1| 664 EEYEALLDTSGDAIFMLDvdtaGDErafEFARLSPGYESQTGLTTDEVRGQTPREVFGAERGAELAANYTRCVEQRA 740
                                       689***************6643333223355679********************99988777799999999999999 PP

                                       -ECCCCEEEECTTSSEEEEEEEEEEEEET CS
                               PAS  71 esrageisfklrdgrpihlevraspvrda 99 
                                       + + +e     +d r   +++  +pv+ +
  gi|344209977|ref|YP_004786153.1| 741 PISYQEELDIAPDAR--FWDTSLAPVMLG 767
                                       988877766665544..344444444444 PP

  == domain 5  score: 61.9 bits;  conditional E-value: 4.1e-20
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       +l++++e++p  ++ +D dg ++ +N+ ae ++G+sreevlg+  +  +++++++   e  +q++++ge+ r++ei+
  gi|344209977|ref|YP_004786153.1| 796 RLESLIEATPLTVMEIDTDGTVIRWNDGAENMFGWSREEVLGE--FNPMVPDEQQAEFESHRQRALSGEPIRGKEIR 870
                                       7899**************************************8..556777777889******************** PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       ++++dg++  l++ ++p++ ++gei+ +l vl di
  gi|344209977|ref|YP_004786153.1| 871 RETKDGEVLDLLLSVAPITAPDGEITSILAVLEDI 905
                                       *********************************98 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.1     4e+03      30      55 ..      97     120 ..      92     129 .. 0.64
   2 !   18.0   0.0     2e-06    0.0026       2      90 ..     132     216 ..     131     225 .. 0.81
   3 !   24.3   0.1   2.2e-08   2.9e-05       2     104 .]     246     359 ..     245     359 .. 0.72
   4 ?    3.5   0.0     0.066        84      37     104 .]     585     651 ..     549     651 .. 0.66
   5 !   10.6   0.0    0.0004      0.51      18     104 .]     698     782 ..     675     782 .. 0.78
   6 !   47.3   0.0   1.6e-15     2e-12       6     104 .]     809     907 ..     805     907 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.1
                             PAS_9  30 evlgksitdlfvtdpeanerlraale 55 
                                       e+lg++i +l+  ++ +++ +++ l 
  gi|344209977|ref|YP_004786153.1|  97 ELLGRRIQTLV--EAARKQAVAERLS 120
                                       89*********..4444444444443 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2e-06
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       dgi  +n++ ri+y+Ne+++r    +p++++g si++ f  ++    +l++ +++    e  ++v +    ge+f +
  gi|344209977|ref|YP_004786153.1| 132 DGIYAVNDEWRIEYINEKMARRVDRNPDDIIGASIWEEF--PSIVGTELEDKYRTAM--ETGEPVSFEQYLGEPFDY 204
                                       67787889999****************************..7777777777777777..777788888888888877 PP

                             PAS_9  79 lltaspvkdddg 90 
                                        + ++ + dddg
  gi|344209977|ref|YP_004786153.1| 205 WVEVRVFPDDDG 216
                                       777777777654 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 2.2e-08
                             PAS_9   2 dgilidnpdgrilyaNeaalrllG.yspeevlgksitdlf......vtdpeanerlraaleqgrk..........ke 61 
                                       d++++ +++g+i++aN a +rl+   ++ ++ g+++++++      ++ ++  + +r  l+   +            
  gi|344209977|ref|YP_004786153.1| 246 DAVFVLDDEGTIEFANAASKRLIAgDQSTQIAGQQLETVVgnristSDTEQFTSAVRSTLN---DiegdggvtglYD 319
                                       7899988***************66488*************888555444444444444444...2555999996644 PP

                             PAS_9  62 revevvlirkngetfwvlltaspvkdddgelvgiivilrDite 104
                                        + +++++ + g +  ++++++p++++  +   ++v+ rDite
  gi|344209977|ref|YP_004786153.1| 320 ADLQLDITAE-GDKRTFDVRVTPFQSN--KSNQALVVARDITE 359
                                       5555555444.5566679******755..455567*******8 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.066
                             PAS_9  37 tdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwvlltaspv..kdddgelvgiivilrDite 104
                                       +     +++++    a+ +++ + ++++ ++ ++r  g    v++   +v   +dd+ +++  ++++Dite
  gi|344209977|ref|YP_004786153.1| 585 EFYH--PDDRETITTAVERAIADrEPYDLDLRIVRTGGDVRDVRAWGERVdePQDDEPVIR--GVFQDITE 651
                                       4444..4444444444444444466*****************99999***65555555555..*******8 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.0004
                             PAS_9  18 eaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwvlltaspvkdddgelv 93 
                                       ++ +  +G + +ev g+  +++f ++++++e  +++ +  ++  + +++ +l    + +fw + +++pv+  ++e+v
  gi|344209977|ref|YP_004786153.1| 698 PGYESQTGLTTDEVRGQTPREVF-GAERGAELAANYTRCVEQrAPISYQEELDIAPDARFW-DTSLAPVML-GDEIV 771
                                       5556679999*************.66666666666666666663666666666677788**.*******75.67999 PP

                             PAS_9  94 giivilrDite 104
                                       +i++i r++te
  gi|344209977|ref|YP_004786153.1| 772 RIVGIARNVTE 782
                                       9*********8 PP

  == domain 6  score: 47.3 bits;  conditional E-value: 1.6e-15
                             PAS_9   6 i.dnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwvll 80 
                                       + +++dg+++++N++a++++G s+eevlg   ++ +v+d++ +e++++  ++++  + r +e+   +k+ge +  ll
  gi|344209977|ref|YP_004786153.1| 809 MeIDTDGTVIRWNDGAENMFGWSREEVLG--EFNPMVPDEQQAEFESHRQRALSGePIRGKEIRRETKDGEVLDLLL 883
                                       3367*************************..66666456666666555555555567******************** PP

                             PAS_9  81 taspvkdddgelvgiivilrDite 104
                                       +++p+   dge+++i+++l+Dit+
  gi|344209977|ref|YP_004786153.1| 884 SVAPITAPDGEITSILAVLEDITD 907
                                       *****999***************6 PP

>> PAS_8  PAS 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     0.049       2      52 ..     122     173 ..     121     189 .. 0.84
   2 !   16.5   0.0   5.1e-06    0.0065       1      34 [.     235     268 ..     235     300 .. 0.80
   3 !    7.1   0.0    0.0045       5.7       3      46 ..     666     717 ..     664     735 .. 0.77
   4 !   28.0   0.0   1.2e-09   1.6e-06       1      43 [.     795     838 ..     795     862 .. 0.75
   5 ?   -2.2   0.0       3.6   4.6e+03      10      21 ..    1207    1218 ..    1186    1228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-05
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvl 52 
                                       r++  +e + dgi  v++ +ri ++N+++++    + +d++g+ +++ +p +
  gi|344209977|ref|YP_004786153.1| 122 RFQRTLERATDGIYAVNDEWRIEYINEKMARRVDRNpDDIIGASIWEEFPSI 173
                                       88999999********9777*************9789****99999666655 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 5.1e-06
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalell 34 
                                       er ++++e+++d+++v+d +g+ i ++N a  +l 
  gi|344209977|ref|YP_004786153.1| 235 ERSETILENIHDAVFVLDdEGT-IEFANAASKRLI 268
                                       67899***********995666.*****9988876 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0045
                             PAS_8   3 lralfesspdgiavvd...lgd....rivdvNqaalellGys.adlkgellg 46 
                                       ++al+++s d+i+++d   +gd     +    + ++  +G++ ++++g++ +
  gi|344209977|ref|YP_004786153.1| 666 YEALLDTSGDAIFMLDvdtAGDerafEFARLSPGYESQTGLTtDEVRGQTPR 717
                                       99************66547555755448889999999999888888887664 PP

  == domain 4  score: 28.0 bits;  conditional E-value: 1.2e-09
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkge 43 
                                       +rl++l+e+ p  ++ +d +g +++ +N+ a+ ++G+s ++++ge
  gi|344209977|ref|YP_004786153.1| 795 QRLESLIEATPLTVMEIDtDG-TVIRWNDGAENMFGWSrEEVLGE 838
                                       79****************555.5*************995555554 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 3.6
                             PAS_8   10 spdgiavvdlgd 21  
                                        spdg  v+d+gd
  gi|344209977|ref|YP_004786153.1| 1207 SPDGFYVADDGD 1218
                                        899999998555 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.9   6.2e+03       3      34 ..     145     178 ..     143     197 .. 0.60
   2 !   37.4   0.1   1.8e-12   2.3e-09       2      75 ..     560     632 ..     559     645 .. 0.87
   3 ?   -1.3   0.0       2.2   2.8e+03       4      52 ..     696     742 ..     693     747 .. 0.81
   4 !   28.2   0.0   1.3e-09   1.7e-06       2      88 ..     818     901 ..     817     902 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.9
                             PAS_3   3 yvserveeilGyspeellgk..veswldlvhpeD 34 
                                       y++e++ + ++  p++++g   +e++ ++v  e 
  gi|344209977|ref|YP_004786153.1| 145 YINEKMARRVDRNPDDIIGAsiWEEFPSIVGTEL 178
                                       7888888888888888888744444444444444 PP

  == domain 2  score: 37.4 bits;  conditional E-value: 1.8e-12
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvi 75 
                                       + +s+ v++i G++++     +++ +++ hp+Dre + +a+++a++++epy+ + Ri+r  G++r v+a ++ +
  gi|344209977|ref|YP_004786153.1| 560 LDWSDGVRRIHGVDDD-YDPVLDDAIEFYHPDDRETITTAVERAIADREPYDLDLRIVRTGGDVRDVRAWGERV 632
                                       67***********865.555567********************************************9988777 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.2
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepy 52 
                                       +s+ +e  +G++ +e++g+  + +++   e  +++ +++ +++++++p+
  gi|344209977|ref|YP_004786153.1| 696 LSPGYESQTGLTTDEVRGQ--TPREVFGAERGAELAANYTRCVEQRAPI 742
                                       78999999*********99..8888888888888888888888777766 PP

  == domain 4  score: 28.2 bits;  conditional E-value: 1.3e-09
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepy.egeyRirrkdGeyrwveararvird 77 
                                       i +++  e+++G+s+ee+lg      + + p++++  +e++ + + +gep+   e+R+ +kdGe+  +  ++ +i  
  gi|344209977|ref|YP_004786153.1| 818 IRWNDGAENMFGWSREEVLGE----FNPMVPDEQQAEFESHRQRALSGEPIrGKEIRRETKDGEVLDLLLSVAPITA 890
                                       89*******************....77788888888888888888899*997888********************** PP

                             PAS_3  78 engkpvrvigv 88 
                                        +g+++ +++v
  gi|344209977|ref|YP_004786153.1| 891 PDGEITSILAV 901
                                       ****9998876 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.8   2.4e+03       6      75 ..     114     198 ..     109     203 .. 0.54
   2 !   27.8   0.0     2e-09   2.6e-06       5     134 ..     389     520 ..     385     524 .. 0.79
   3 ?   -2.2   0.0       3.7   4.8e+03      61     110 ..     734     776 ..     656     791 .. 0.50
   4 !   39.3   0.8   5.5e-13     7e-10       2     136 ..     929    1059 ..     928    1061 .. 0.81
   5 ?    1.0   0.1      0.38   4.9e+02       3      38 ..    1075    1114 ..    1073    1149 .. 0.79
   6 ?   -1.7   0.0       2.6   3.3e+03      11      46 ..    1198    1231 ..    1179    1252 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHH.S.S..EEEEEEE-TTS-EEEE.......EEEES-TTSTT-S-B--........-TTHHHHHHHH CS
                             GAF_2   6 elldlvldelve.l.gaalgyillvdddgglrla.......awgeaeeefgaaldrpl........geglvgealrt 65 
                                        +++++ d+ ++ l  a+ g++++ d+ + +++        + +++++  ga++   +        ++    +a++t
  gi|344209977|ref|YP_004786153.1| 114 AVAERLSDRFQRtLeRATDGIYAVNDEWR-IEYInekmarrVDRNPDDIIGASIWEEFpsivgtelED-KYRTAMET 188
                                       56666666666645447777777766332.22223333344666777777776666333344443222.23478888 PP

                                       TS-EEES-GG CS
                             GAF_2  66 grpvilndle 75 
                                       g+pv ++++ 
  gi|344209977|ref|YP_004786153.1| 189 GEPVSFEQYL 198
                                       8888877765 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 2e-09
                                       HHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-.GGG-S- CS
                             GAF_2   5 eelldlvldelvel.gaalgyillvdddgglrlaawgeaeeefgaaldrplgeglvgealrtgrpvilnd.leedpd 79 
                                       e+ l+++l+  +++ + ++g++  v++d++ ++ a   +e e  +  + +l++  ++ ++ t   + ++d +++ + 
  gi|344209977|ref|YP_004786153.1| 389 ETRLQELLELGCRMlDLEIGIVSRVQGDDY-TVKAVHAPESEIESGDQFDLESTYCEAVIGTDSVCSFADaVADGRE 464
                                       666899999999955999********9887.344555555555555544888889*******99999***7777555 PP

                                       HHHHHHHHHTT--EEEEEE-TTS---EEEEE..S......--HHHHHHHHHHHHHHH CS
                             GAF_2  80 kkglpaghaglrsflavPlisegrvvGvlnl..yankppafdeedlelLeelaeqia 134
                                        +++  ++  l s ++vPl+ +g  +G +n+   +++ ++f + +++++++l+e+++
  gi|344209977|ref|YP_004786153.1| 465 THPAY-REFELESYIGVPLVVDGTRYGTVNFssPTTRVDSFGALERTFVKLLSELVS 520
                                       55555.99999999*******9*********543777777*************9987 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.7
                                       HHHHHTS-EEES-GGG-S-HHHHHHHHHTT--E...EEEEE-TTS---EEEEE CS
                             GAF_2  61 ealrtgrpvilndleedpdkkglpaghaglrsf...lavPlisegrvvGvlnl 110
                                       ++++++ p+  +           +++ a+ ++f      P++ ++++v ++++
  gi|344209977|ref|YP_004786153.1| 734 RCVEQRAPISYQE----------ELDIAPDARFwdtSLAPVMLGDEIVRIVGI 776
                                       3333333333222..........222222222233345577666666666666 PP

  == domain 4  score: 39.3 bits;  conditional E-value: 5.5e-13
                                        HHHHHHHHHHHHHHHHS.S...EEEEEEE-TTS-EEEE.EEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES- CS
                             GAF_2    2 adleelldlvldelvel.gaa.lgyillvdddgglrla.awgeaeeefgaaldrplgeglvgealrtgrpvilnd 73  
                                        ++  e+ d++++++v++ g++  g+    +++++l+ + a++ ++e +g+ ++   ge+l++ea++  +   l  
  gi|344209977|ref|YP_004786153.1|  929 QSSAEIGDIAVEAAVDIlGFElTGIWESANQADELVPLtASAATRELLGELPRLESGEALAWEAFEASE---LRK 1000
                                        6778999*********66***455555566667766664666666666666644779999*******88...455 PP

                                        GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHH CS
                             GAF_2   74 leedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaia 136 
                                        +++  +   l  ++a+lrs+l+vPl   g  +G ++++++++++f+++d++l++ l++++  a
  gi|344209977|ref|YP_004786153.1| 1001 YDDLQSEVTLGKADAQLRSGLFVPL---G-EFGLIGVGTTQEQTFSDTDVDLFQILGATVEAA 1059
                                        666777899999*************...8.9***************************99877 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.38
                                        HHHHHHHHHHHHHHH.SS..EEEEEEE-TTS-EEEE...E CS
                             GAF_2    3 dleelldlvldelve.lgaalgyillvdddgglrla...a 38  
                                         l+e+++ v   l++ l +a+g++ +v++ g+l ++    
  gi|344209977|ref|YP_004786153.1| 1075 RLDEFASVVAHDLRNpLSIAIGFLDIVEETGDLSYLeriE 1114
                                        689**********9999************99955444331 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 2.6
                                        HHHHHHHSS..EEEEEEE-TTS-EEEEEEEES-TTS CS
                             GAF_2   11 vldelvelgaalgyillvdddgglrlaawgeaeeef 46  
                                        v+ ++ +l++  g+++ +d+dg     a +e+  e+
  gi|344209977|ref|YP_004786153.1| 1198 VTVTVGQLDSPDGFYVADDGDGI--PPAKREEVLEH 1231
                                        44445556666777777776665..44444444444 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.4   1.8e+03      52      76 ..     177     201 ..     159     205 .. 0.78
   2 !   38.3   0.0   1.2e-12   1.5e-09       3     129 .]     389     525 ..     387     525 .. 0.86
   3 ?    1.2   0.0      0.34   4.4e+02      61     126 ..     858     928 ..     790     928 .. 0.77
   4 !   17.5   0.1   3.1e-06    0.0039       4     121 ..     933    1054 ..     930    1056 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.4
                             GAF_3  52 edsalarralssgevvsepsfaeed 76 
                                       e +  +r+a+++ge+vs+ ++ +e+
  gi|344209977|ref|YP_004786153.1| 177 ELEDKYRTAMETGEPVSFEQYLGEP 201
                                       5566689**********99987775 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 1.2e-12
                             GAF_3   3 dellekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesldedsalarralssgevvsepsf..aeedg 77 
                                       +  l++ll+l++++l++e+g++  +++d  +++++++ + +      +d +s  + ++++++ v s++++  +++++
  gi|344209977|ref|YP_004786153.1| 389 ETRLQELLELGCRMLDLEIGIVSRVQGDDYTVKAVHAPESEIESGDQFDLESTYCEAVIGTDSVCSFADAvaDGRET 465
                                       5679**********************************99999999******************9995542222222 PP

                             GAF_3  78 ......lpdraalavPLvagr.qviGvlalastkpra..fdaedlelleslArqiataier 129
                                              ++++++ vPLv+ + + +G++ + s+ +r   f+a ++ +++ l+ +++ +i+r
  gi|344209977|ref|YP_004786153.1| 466 hpayreFELESYIGVPLVV-DgTRYGTVNFSSPTTRVdsFGALERTFVKLLSELVSAEISR 525
                                       333444788**********.66***********999557***************9999976 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.34
                             GAF_3  61 lssgevvsepsfaeedglpdraa.....lavPLvagr.qviGvlal.astkprafdaedlelleslArqiata 126
                                       + sge++ +++ ++e+   d+ +      ++P++a++ +   +la+ +   +++ +++ l+ l++ A++++ a
  gi|344209977|ref|YP_004786153.1| 858 ALSGEPIRGKEIRRETK--DGEVldlllSVAPITAPDgEITSILAVlEDITDQKQLESKLRSLQATAQRLSGA 928
                                       44577777777766533..444334444579******9999999965999999999*********99999875 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 3.1e-06
                             GAF_3    4 ellekllkllvkllgaevgalllldedgnklqvaagwdgkpalse...sldedsalarralssgevvsepsfaee 75  
                                        e+ +++++++v++lg+e   +++  ++ ++l++  ++ +   l      l+ ++ala++a++  e     +   e
  gi|344209977|ref|YP_004786153.1|  933 EIGDIAVEAAVDILGFELTGIWESANQADELVPLTASAATRELLGelpRLESGEALAWEAFEASELRKYDDLQSE 1007
                                        777999*****************999999**99977734443333256667*************98666554444 PP

                             GAF_3   76 dg.....lpdraalavPLvagrqviGvlalastkprafdaedlelleslAr 121 
                                         +      ++r+ l+vPL      +G++++++t+++ f+++d++l++ l++
  gi|344209977|ref|YP_004786153.1| 1008 VTlgkadAQLRSGLFVPLGE----FGLIGVGTTQEQTFSDTDVDLFQILGA 1054
                                        34111116667778888888....***********************9986 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 !   53.8   0.0   1.9e-17   2.4e-14       1     107 [.    1174    1273 ..    1174    1274 .] 0.90

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 1.9e-17
                                        EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSS CS
                         HATPase_c    1 gdekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtG 75  
                                        gd  rL+q++ nl  Na+++   ++ ++v++ + +    + v D+G Gip+++++++ e+ ++     +++ggtG
  gi|344209977|ref|YP_004786153.1| 1174 GDAGRLTQLFENLFRNAIEH--GGDAVTVTVGQLDSPDGFYVADDGDGIPPAKREEVLEHGVT-----STKGGTG 1241
                                        7999***************9..68889999997345788999*****************6666.....578**** PP

                                        HHHHHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c   76 lGlsivkklvelmgGeiwvesepgrGttftft 107 
                                        +Glsiv  +++ +g +++v+++  +G +f f+
  gi|344209977|ref|YP_004786153.1| 1242 FGLSIVADIAKAHGWTVRVTESTAGGAQFEFR 1273
                                        *******************99999****9985 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 ?   -0.8   0.1       1.3   1.6e+03      20      48 ..     103     134 ..      95     152 .. 0.76
   2 ?   -1.1   0.2       1.5     2e+03      17      52 ..     895     926 ..     895     927 .. 0.80
   3 !   48.8   0.4   4.1e-16   5.2e-13       2      66 ..    1076    1135 ..    1075    1136 .. 0.94
   4 ?   -1.9   0.0       2.7   3.5e+03      36      58 ..    1164    1186 ..    1154    1191 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.3
                                       HHHHHHHHHC.....T-HSSCHHHHHHHHHHH CS
                             HisKA  20 ilgnaeaLkre...gklteelkeyletiesea 48 
                                       i+  +ea +++   ++l+++ ++ le++ +++
  gi|344209977|ref|YP_004786153.1| 103 IQTLVEAARKQavaERLSDRFQRTLERATDGI 134
                                       66677777666777788888998999888776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHH CS
                             HisKA  17 LsailgnaeaLkregklteelkeyletiesearrld 52 
                                       +++il+ +e + ++     +l+  l++++  a+rl+
  gi|344209977|ref|YP_004786153.1| 895 ITSILAVLEDITDQ----KQLESKLRSLQATAQRLS 926
                                       68888888888883....788889999999999985 PP

  == domain 3  score: 48.8 bits;  conditional E-value: 4.1e-16
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA    2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66  
                                        l +f++ vaH+Lr+PLs  +g++++ ++          yle+ie   +r+++l++dlL+l+r e+
  gi|344209977|ref|YP_004786153.1| 1076 LDEFASVVAHDLRNPLSIAIGFLDIVEE-----TGDLSYLERIEAAHDRMEQLIDDLLTLARGET 1135
                                        689***********************99.....67789************************986 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 2.7
                                        SCHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA   36 elkeyletiesearrldhlvedl 58  
                                         ++e++ t+   a rl++l e+l
  gi|344209977|ref|YP_004786153.1| 1164 TVAEAVPTVAGDAGRLTQLFENL 1186
                                        57888999999999******998 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   3.2e-15   4.1e-12      18      98 ..       7      87 ..       2      93 .. 0.95
   2 ?   -2.7   0.1       5.1   6.5e+03       5      26 ..     637     658 ..     637     679 .. 0.64

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 3.2e-15
                                      HH.HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHHHCTES CS
                      Response_reg 18 le.eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltahseeedavealkagad 95
                                      ++ ++g+ ev+++   ++al+ll +++vd++++  ++p+ +G++ll+++++e++e+p i++t++++e  a ea +ag++
  gi|344209977|ref|YP_004786153.1|  7 VNiSSGF-EVTAVGAVEAALDLLVTSTVDCVVTSYSLPDGTGIDLLDRLQAEQYEIPTILFTGRGSERIASEATQAGVS 84
                                      5557899.9********************************************************************** PP

                                      EEE CS
                      Response_reg 96 dfl 98
                                      d++
  gi|344209977|ref|YP_004786153.1| 85 DYI 87
                                      **9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.1
                                       SSSHHHHHHHHHHHHHTTEEEE CS
                      Response_reg   5 dDdplvrellrqlleeegyeev 26 
                                       dD+p++r +++++ e++  e+ 
  gi|344209977|ref|YP_004786153.1| 637 DDEPVIRGVFQDITERKAEERA 658
                                       99******99999994433332 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.2   4.1e+03      34      66 ..     152     196 ..     110     206 .. 0.59
   2 !   29.5   0.0   7.4e-10   9.5e-07       3     133 .]     389     523 ..     387     523 .. 0.79
   3 ?    2.5   0.0      0.17   2.2e+02      88     132 ..    1018    1059 ..     933    1060 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.2
                                       E.......CEEEEECCEEEETTSHHHH..........HHHHHSSSEEEST CS
                               GAF  34 y.......dipqasrwlfmkngrgicg..........qvlatgqplvipd 66 
                                               di  as w + +                 ++++tg+p++++ 
  gi|344209977|ref|YP_004786153.1| 152 RrvdrnpdDIIGASIWEEFPS-----IvgteledkyrTAMETGEPVSFEQ 196
                                       033333344555555533333.....022445568889999999999885 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 7.4e-10
                                       HHHHHHHHHHHHHHHTESEEEEEEEEETTEEE..........CEEEEECCEEEETTSHHHHHHHHHSSSEEESTGGT CS
                               GAF   3 eelldtvveelrellgadrvalylpdydGlhy..........dipqasrwlfmkngrgicgqvlatgqplvipdstp 69 
                                       e+ l++++e  +++l+++ +++ +   +G +y          +i+ ++++  + + +  c +v+ t+ +++++d+ +
  gi|344209977|ref|YP_004786153.1| 389 ETRLQELLELGCRMLDLEIGIVSR--VQGDDYtvkavhapesEIESGDQF--DLESTY-CEAVIGTDSVCSFADAVA 460
                                       8999******************87..666555555544454444444444..555555.7788889*******9777 PP

                                       STTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS...CSHHHHHHHHHHHHHHHHHHH CS
                               GAF  70 dprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp...pftreelellqvladqvaval 133
                                       d+r  +       ++++  s+++vPlv+dg  +G++ + +p++   +f   e+ +++ l+++v+ ++
  gi|344209977|ref|YP_004786153.1| 461 DGRETH----PAYREFELESYIGVPLVVDGTRYGTVNFSSPTTrvdSFGALERTFVKLLSELVSAEI 523
                                       777444....33457*************************777789**************9999876 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.17
                                        SEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHHH CS
                               GAF   88 rsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvava 132 
                                        rs l vPl      +Gl+ +  +++  f++ +++l+q l++ v+ a
  gi|344209977|ref|YP_004786153.1| 1018 RSGLFVPLGE----FGLIGVGTTQEqTFSDTDVDLFQILGATVEAA 1059
                                        5555555553....7888888866668*************999877 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.5   3.2e+03      11      33 ..     133     155 ..      98     167 .. 0.50
   2 ?   -0.8   0.1       1.8   2.3e+03       4      66 ..     240     305 ..     238     309 .. 0.72
   3 ?    9.6   0.0     0.001       1.3       1     106 []     797     906 ..     797     906 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.5
                            PAS_10  11 eltflDdnlqirrFtpaakklfk 33 
                                       ++  ++d+ +i + +++ ++ ++
  gi|344209977|ref|YP_004786153.1| 133 GIYAVNDEWRIEYINEKMARRVD 155
                                       23334445555555555555555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.8
                            PAS_10   4 lLnstpieltflDdnlqirrFtpaakklfklip..advGrpladihpk.kavknveeviealrtge 66 
                                       +L+++  ++  lDd+  i + + a+k+l+   +  +  G +l++++ +  + +++e+++ a+r++ 
  gi|344209977|ref|YP_004786153.1| 240 ILENIHDAVFVLDDEGTIEFANAASKRLIAGDQstQIAGQQLETVVGNrISTSDTEQFTSAVRSTL 305
                                       567777777888999999988888888876544114579999999855477888888888888775 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.001
                            PAS_10   1 lnnlLnstpieltflDdnlqirrFtpaakklfklipadvGrpladihpkkavknveeviealrtgek.devevvvp. 75 
                                       l+ l+++tp+ ++ +D++  ++r+++ a+++f   +++v  + + ++p++++ ++e+  ++  +ge    +e+ ++ 
  gi|344209977|ref|YP_004786153.1| 797 LESLIEATPLTVMEIDTDGTVIRWNDGAENMFGWSREEVLGEFNPMVPDEQQAEFESHRQRALSGEPiRGKEIRREt 873
                                       678999*********************************999************************94444444446 PP

                            PAS_10  76 kngkw..vlvrylpyrdedgeiaGvvetfvDit 106
                                       k+g++   l+ + p+   dgei  ++ ++ Dit
  gi|344209977|ref|YP_004786153.1| 874 KDGEVldLLLSVAPITAPDGEITSILAVLEDIT 906
                                       88888567899******************9997 PP

>> MCU  Mitochondrial calcium uniporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.7    0.0012       1.6      46     109 ..     351     413 ..     206     419 .. 0.86
   2 ?   -3.5   0.0       7.6   9.8e+03      50      71 ..     781     802 ..     764     814 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0012
                                       SSSSSTSSSSSHHHHHHHHHHHHH-SHHHHHHHHTCCCGGGCHHHHGGGHHHHHHHHTHHHHHH CS
                               MCU  46 lnveeeqlkkereleekleelreelepleekkeeidekAerrtrrllwagLallavqlgilarL 109
                                       l v   +  ++++++++le+ r+ l++l+++ ++ d +Ae+r + ll +g  +l + +gi++r 
  gi|344209977|ref|YP_004786153.1| 351 L-VVARDITEQSDVKRQLERERDALRELQTVMAKSDVSAETRLQELLELGCRMLDLEIGIVSRV 413
                                       3.3335667788899999999***************************************9996 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.6
                                       STSSSSSHHHHHHHHHHHHH-S CS
                               MCU  50 eeqlkkereleekleelreele 71 
                                        eq k+erele+  ++l++ +e
  gi|344209977|ref|YP_004786153.1| 781 TEQVKRERELETTNQRLESLIE 802
                                       3566677776666666655444 PP

>> TetR_C_15  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   0.1       1.8   2.3e+03      14      61 ..      87     133 ..      76     141 .. 0.69
   2 ?    5.5   0.1     0.022        28      26      70 ..     641     685 ..     634     686 .. 0.88
   3 ?   -2.9   0.1         9   1.1e+04      73      93 ..    1051    1072 ..    1048    1085 .. 0.58
   4 ?    3.1   0.0      0.12   1.6e+02      34      68 ..    1107    1141 ..    1096    1150 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.8
                         TetR_C_15  14 laahrenpalrrvlleeapslgelelvealeqriaealaalLarrrpe 61 
                                       +  h+ +  +  + ++ + +l e+++ +a+ +r+ +++++ L+r+ + 
  gi|344209977|ref|YP_004786153.1|  87 IPIHAGENSFELLGRRIQ-TLVEAARKQAVAERLSDRFQRTLERATDG 133
                                       555566666666666666.56666788888888999999888888765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.022
                         TetR_C_15  26 vlleeapslgelelvealeqriaealaalLarrrpelppedlela 70 
                                       v+++++ +++e ++ e++++++ae+ +alL++  ++++  d+++a
  gi|344209977|ref|YP_004786153.1| 641 VIRGVFQDITERKAEERAHRELAEEYEALLDTSGDAIFMLDVDTA 685
                                       56777788889999**********************998777766 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 9
                         TetR_C_15   73 vaveaveallhlaleedp.adr 93  
                                        ++ ++vea + +a +e + +++
  gi|344209977|ref|YP_004786153.1| 1051 ILGATVEAAFTRASRETElQRQ 1072
                                        4556666666666666664333 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.12
                         TetR_C_15   34 lgelelvealeqriaealaalLarrrpelppedle 68  
                                        l  le+ ea+++r+++++ +lL+ +r e++ +d++
  gi|344209977|ref|YP_004786153.1| 1107 LSYLERIEAAHDRMEQLIDDLLTLARGETTITDTK 1141
                                        5556999******************9999877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); 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):              14  [number of targets reported over threshold]
# CPU time: 0.74u 0.28s 00:00:01.02 Elapsed: 00:00:00.44
# Mc/sec: 8671.69
//
Query:       gi|344209978|ref|YP_004786154.1|  [L=648]
Description: HTR-like protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   81.8   0.0    9.4e-23   80.5   0.0    1.7  1  Response_reg  Response regulator receiver domain
    1.8e-18   67.1   1.4      4e-18   65.9   0.1    2.2  3  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    3.4e-18   66.3   1.7    1.3e-17   64.4   0.1    2.7  3  GAF_2         GAF domain
    4.2e-16   59.2   0.0    8.8e-16   58.1   0.0    1.6  1  PAS_4         PAS fold
    2.8e-14   52.9   1.2    2.8e-14   52.9   1.2    3.4  4  HisKA         His Kinase A (phospho-acceptor) domain
    1.1e-10   41.7   0.0    3.1e-10   40.2   0.0    1.8  1  PAS_9         PAS domain
    3.3e-10   40.0   0.0      1e-09   38.4   0.0    1.9  1  PAS           PAS fold
    1.5e-09   38.6   0.0    2.1e-08   34.8   0.0    2.6  2  GAF           GAF domain
    1.5e-07   31.8   0.0    5.6e-07   30.0   0.0    2.0  2  GAF_3         GAF domain
    1.5e-06   28.4   0.0    4.8e-06   26.8   0.0    1.9  1  PAS_3         PAS fold
    6.7e-05   22.8   0.0    0.00028   20.8   0.0    2.1  1  PAS_8         PAS domain
  ------ inclusion threshold ------
      0.023   14.6   0.1      0.023   14.6   0.1    2.7  3  HATPase_c_2   Histidine kinase-like ATPase domain
      0.026   14.4   0.0      0.062   13.1   0.0    1.6  1  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
      0.094   13.1   0.3       0.33   11.3   0.3    1.9  1  TBCA          Tubulin binding cofactor A


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 !   80.5   0.0   7.3e-26   9.4e-23       1     104 [.       6     110 ..       6     118 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 7.3e-26
                                       EEEESSSHHHHHHHHHHHH..HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlle..eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpvi 75 
                                       vl vdD+p+++++ +++le  ++++ +v +a++++eal+ l + +vd+++ D +mpg dG+ellk++ree p+lp i
  gi|344209978|ref|YP_004786154.1|   6 VLHVDDEPDFLDVATEILEqqSSKL-NVITAASATEALDCLATTRVDCLISDYRMPGKDGIELLKTVREEYPDLPFI 81 
                                       789****************866778.999************************************************ PP

                                       EEESSTSHHHHHHHHHCTESEEEESSG-H CS
                      Response_reg  76 iltahseeedavealkagaddflsKpfdp 104
                                       ++t++++e++a +a+ aga d+l K   +
  gi|344209978|ref|YP_004786154.1|  82 LFTGEGSEAVASDAIAAGATDYLRKGHGM 110
                                       *************************7655 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 ?   -2.0   0.0         4   5.2e+03       8      20 ..     114     126 ..     111     168 .. 0.74
   2 ?   -3.2   0.0       9.2   1.2e+04      17      34 ..     372     393 ..     367     436 .. 0.49
   3 !   65.9   0.1   3.1e-21     4e-18       2     107 ..     543     642 ..     542     645 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4
                                       HHHHHHHHHHHHH CS
                         HATPase_c   8 qiisnlvdNavkf 20 
                                       +++ n v+Nav+ 
  gi|344209978|ref|YP_004786154.1| 114 ELLANRVENAVEQ 126
                                       7899999999996 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.2
                                       HHHHHSTTTEEEEEEEE....E CS
                         HATPase_c  17 avkfatkageieveika....s 34 
                                       a+++a ++g+ ++e +      
  gi|344209978|ref|YP_004786154.1| 372 AIEEALTTGHSTIEAEFltgaG 393
                                       5555445555555544333220 PP

  == domain 3  score: 65.9 bits;  conditional E-value: 3.1e-21
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE...TEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSS CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikase...ddlvisveDnGiGipkedlkklfe.kfsqddstkrggggt 74 
                                       d +++r+++ nl  N +++a+   +++v +       d++ + +eD+G+Gip+ed++k+fe  +s+      + +gt
  gi|344209978|ref|YP_004786154.1| 543 DTDQFRHLLENLFRNTIDHAG--LDVTVVVG--GifdDTNGFYIEDDGPGIPVEDREKVFEaGYST------SESGT 609
                                       7899**************944..34444444..23346***********************88888......889** PP

                                       SHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  75 GlGlsivkklvelmgGeiwvesepgrGttftft 107
                                       GlGl ivk++++ +g +i+v++++ +Gt+f +t
  gi|344209978|ref|YP_004786154.1| 610 GLGLNIVKRVADAHGWDIRVTESSMGGTRFEIT 642
                                       ********************9999******985 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.7   7.3e+03     105     130 ..       4      27 ..       3      40 .. 0.72
   2 !   64.4   0.1   9.8e-21   1.3e-17       2     137 ..     154     298 ..     153     299 .. 0.85
   3 ?   -0.4   0.1         1   1.3e+03      86     110 ..     393     418 ..     308     449 .. 0.43

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.7
                                       -EEEEES......--HHHHHHHHHHH CS
                             GAF_2 105 vGvlnlyankppafdeedlelLeela 130
                                       ++vl++  +++p+f +   e+Le+ +
  gi|344209978|ref|YP_004786154.1|   4 IAVLHV--DDEPDFLDVATEILEQQS 27 
                                       567776..677777777777777654 PP

  == domain 2  score: 64.4 bits;  conditional E-value: 9.8e-21
                                       HHHHHHHHHHHHHHHHSS...EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B....--.-TTHHHHHHHHTS-EEE CS
                             GAF_2   2 adleelldlvldelvelg.aalgyillvdddgg.lrlaawgeaeeefgaaldr....pl.geglvgealrtgrpvil 71 
                                       ++l+e+  +v++ + +     +++i++ ++d++ ++  aw++ e+e  + +      ++ g+g++g+a+r++r    
  gi|344209978|ref|YP_004786154.1| 154 SSLSEIKTRVCEIISDSEpYLFAWIGEQEPDTDrIEPQAWAGVEDEYLDTIVVtaddSPtGRGPAGTAVRERRIATS 230
                                       678888888999998853377******997766477779998888886666554433336***********999999 PP

                                       S-GGG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  72 ndleedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       +++++dp+   ++  a ++g+rs++avPl ++  ++G l++y+++  af+e+++elL+el++ i+ a+
  gi|344209978|ref|YP_004786154.1| 231 QNIQDDPAFEVWReeALDRGYRSTAAVPLEYNSTLYGLLCVYSSRSFAFSEDEQELLDELGDSISHAM 298
                                       99***********99**************77678************99*****************997 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1
                                       HHHTT--EEEEEE-T.TS---EEEEE CS
                             GAF_2  86 ghaglrsflavPlis.egrvvGvlnl 110
                                       g++ ++ f +  l++ +g+++G ++ 
  gi|344209978|ref|YP_004786154.1| 393 GKRIPHEFTGDRLTDqDGNLIGLVGT 418
                                       33333333333344545556666665 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0   6.8e-19   8.8e-16       1     109 [.     318     426 ..     318     427 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 6.8e-19
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ldsl d+++vld++g+v+++N+++++l+g+++ee+      +l+pee ++++++a++++l+++++ +++e+l+  g+
  gi|344209978|ref|YP_004786154.1| 318 LDSLADIFYVLDSEGNVQRCNEQFERLAGYADEEISEFDALSLFPEEEREGVSEAIEEALTTGHSTIEAEFLTGAGK 394
                                       799************************************************************************** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                       + ++e++  +l d +G  ig+++++r i+er 
  gi|344209978|ref|YP_004786154.1| 395 RIPHEFTGDRLTDQDGNLIGLVGTGRNISERT 426
                                       ******************************95 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   0.0       3.7   4.7e+03      38      63 ..      29      62 ..      16      64 .. 0.57
   2 ?   -0.6   0.2       1.1   1.4e+03      46      58 ..     125     146 ..     103     156 .. 0.56
   3 !   52.9   1.2   2.2e-17   2.8e-14       2      65 ..     439     497 ..     438     499 .. 0.95
   4 ?   -2.8   0.0       5.4   6.9e+03      44      58 ..     540     554 ..     538     558 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.7
                                      HHHHHHHHHHHH........HHHHHHHHHHHHCC CS
                             HisKA 38 keyletiesear........rldhlvedlLdlsr 63
                                      k ++ t+ s ++        r+d l++d ++ ++
  gi|344209978|ref|YP_004786154.1| 29 KLNVITAASATEaldclattRVDCLISDYRMPGK 62
                                      3333333333335556667788888888887776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.1
                                       HHHH.........HHHHHHHHH CS
                             HisKA  46 sear.........rldhlvedl 58 
                                       ++ r         r+++lv+ +
  gi|344209978|ref|YP_004786154.1| 125 EQYRtnqraaeleRVRDLVSSI 146
                                       3333333344466888888776 PP

  == domain 3  score: 52.9 bits;  conditional E-value: 2.2e-17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrie 65 
                                       l++f+a+v+H+Lr+PL++i+g +++ ++         + l++ie  ++r++++vedlL l+r++
  gi|344209978|ref|YP_004786154.1| 439 LEQFAATVSHDLRNPLNVIRGRLDLVQE-----THSSDHLAVIETATERMERIVEDLLWLAREQ 497
                                       79**************************.....899************************9987 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 5.4
                                       HHHHHHHHHHHHHHH CS
                             HisKA  44 iesearrldhlvedl 58 
                                       i+  +++ +hl+e+l
  gi|344209978|ref|YP_004786154.1| 540 IKADTDQFRHLLENL 554
                                       677889999999998 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   2.4e-13   3.1e-10       3     104 .]     324     424 ..     322     424 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.4e-13
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvl 79 
                                        + + +++g++ ++Ne+++rl Gy  ee+   +   lf +++e++   +a+ e++++   + e ++ +  g++++ +
  gi|344209978|ref|YP_004786154.1| 324 IFYVLDSEGNVQRCNEQFERLAGYADEEISEFDALSLF-PEEEREGVSEAIEEALTTGHSTIEAEFLTGAGKRIPHE 399
                                       566778********************************.444444444444444444779***************** PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDite 104
                                       +t  ++ d+dg+l+g++++ r+i+e
  gi|344209978|ref|YP_004786154.1| 400 FTGDRLTDQDGNLIGLVGTGRNISE 424
                                       ***********************98 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   7.8e-13     1e-09       3     113 .]     314     422 ..     312     422 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 7.8e-13
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                       +++ l+sl+d   v+D  g++  +N+ +e+l G++ ee++    l l++ee+++ + e++e++l +g++    e   
  gi|344209978|ref|YP_004786154.1| 314 IDQALDSLADIFYVLDSEGNVQRCNEQFERLAGYADEEISEFDALSLFPEEEREGVSEAIEEALTTGHSTIEAEFLT 390
                                       6789********************************************************************99977 PP

                                       ECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  80 klrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                           g+ i+ e +   ++d +g+++g++g++r i
  gi|344209978|ref|YP_004786154.1| 391 GA--GKRIPHEFTGDRLTDQDGNLIGLVGTGRNI 422
                                       77..**************************9965 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   1.7e-11   2.1e-08      45     132 ..     211     297 ..     161     298 .. 0.87
   2 ?    0.3   0.0      0.77   9.9e+02      98     130 ..     409     447 ..     400     450 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.7e-11
                                       EETTSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHH CS
                               GAF  45 mkngrgicgqvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreele 120
                                        ++grg +g++++++++ + +++++dp f    +r+ +   g+rs ++vPl  +  l+Gll++++ +   f+++e e
  gi|344209978|ref|YP_004786154.1| 211 SPTGRGPAGTAVRERRIATSQNIQDDPAFEV--WREEALDRGYRSTAAVPLEYNSTLYGLLCVYSSRSfAFSEDEQE 285
                                       455899999**********************..999*****************************988888****** PP

                                       HHHHHHHHHHHH CS
                               GAF 121 llqvladqvava 132
                                       ll +l+d ++ a
  gi|344209978|ref|YP_004786154.1| 286 LLDELGDSISHA 297
                                       ******999876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.77
                                       TTEEEEEEEEEE.....SSS..CSHHHHHHHHHHHHHHHH CS
                               GAF  98 dgelwGllvlhn.....psp..pftreelellqvladqva 130
                                       dg+l+Gl+   +     + +  + ++++ e l+++a+ v+
  gi|344209978|ref|YP_004786154.1| 409 DGNLIGLVGTGRniserT-KreRELQDQKEQLEQFAATVS 447
                                       899*********998652.144558888999999999886 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   4.3e-10   5.6e-07      69     127 ..     239     298 ..     197     299 .. 0.78
   2 ?   -3.1   0.0       7.4   9.5e+03     102     125 ..     425     448 ..     415     452 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 4.3e-10
                             GAF_3  69 epsfaeedglpdraala.vPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                       +  ++ee   +++  +a vPL   ++++G+l+++s++ +af+++++ell++l++ i+ a+
  gi|344209978|ref|YP_004786154.1| 239 FEVWREEALDRGYRSTAaVPLEYNSTLYGLLCVYSSRSFAFSEDEQELLDELGDSISHAM 298
                                       455677777776555444*****99*****************************999875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.4
                             GAF_3 102 stkprafdaedlelleslArqiat 125
                                       +tk +  +++++e le +A+ ++ 
  gi|344209978|ref|YP_004786154.1| 425 RTKRERELQDQKEQLEQFAATVSH 448
                                       455566788999999999987775 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   3.7e-09   4.8e-06       3      88 ..     336     418 ..     334     419 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.7e-09
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirden 79 
                                        ++e++e++ Gy +ee+ +   + l+l   e+re v ea++eal++g+  ++e  +++  G+ +  e ++  + d++
  gi|344209978|ref|YP_004786154.1| 336 RCNEQFERLAGYADEEISEF--DALSLFPEEEREGVSEAIEEALTTGH-STIEAEFLTGAGKRIPHEFTGDRLTDQD 409
                                       59******************..**********************9999.4788888999999999999999999999 PP

                             PAS_3  80 gkpvrvigv 88 
                                       g+ + ++g+
  gi|344209978|ref|YP_004786154.1| 410 GNLIGLVGT 418
                                       999999887 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.2e-07   0.00028       3      56 ..     314     368 ..     311     381 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.2e-07
                             PAS_8   3 lralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrpll 56 
                                       + ++++s++d   v+d +g+ +  +N+++++l Gy  +++++ +   l+p+ + + 
  gi|344209978|ref|YP_004786154.1| 314 IDQALDSLADIFYVLDsEGN-VQRCNEQFERLAGYAdEEISEFDALSLFPEEEREG 368
                                       55778899999999**7777.***************99988877776666665554 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 ?    0.5   0.1      0.43   5.5e+02       4      40 ..     132     167 ..     129     169 .. 0.86
   2 ?   -3.0   0.1       5.2   6.7e+03      20      41 ..     357     378 ..     346     378 .. 0.79
   3 ?   14.6   0.1   1.8e-05     0.023      26     114 ..     541     625 ..     525     638 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.43
                       HATPase_c_2   4 dpehvrtvrevaeavlrraglseelldeirlaveEac 40 
                                       ++++++ vr+ + ++  +a + ++ l ei+  v E++
  gi|344209978|ref|YP_004786154.1| 132 RAAELERVRDLVSSI-DQALIRASSLSEIKTRVCEII 167
                                       567889999999999.7999**********9999987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.2
                       HATPase_c_2  20 rraglseelldeirlaveEact 41 
                                       + + ++ee+++ +  a+eEa+t
  gi|344209978|ref|YP_004786154.1| 357 ALSLFPEEEREGVSEAIEEALT 378
                                       4467889999999999999986 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 1.8e-05
                       HATPase_c_2  26 eelldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGl 102
                                       ++++d+ r  +e ++ N + ha l+ +   v v   + +++  + ++D+Gpg ++e++++  e ++++s+   G+Gl
  gi|344209978|ref|YP_004786154.1| 541 KADTDQFRHLLENLFRNTIDHAGLDVT---VVVG-GIFDDTNGFYIEDDGPGIPVEDREKVFEAGYSTSESGTGLGL 613
                                       566677777777888899999998544...6666.66777777899******************************* PP

                       HATPase_c_2 103 alikglvDevey 114
                                        ++k+++D   +
  gi|344209978|ref|YP_004786154.1| 614 NIVKRVADAHGW 625
                                       ********8754 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 ?   13.1   0.0   4.9e-05     0.062       9      63 ..     553     607 ..     546     618 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.9e-05
                       HATPase_c_3   9 elvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskea 63 
                                        l +N +d     v+++v     +t+ + ieDdG G++ e+ +++++ + s+ e+
  gi|344209978|ref|YP_004786154.1| 553 NLFRNTIDHAGLDVTVVVGGIFDDTNGFYIEDDGPGIPVEDREKVFEAGYSTSES 607
                                       5778999999999******99999**********************999998874 PP

>> TBCA  Tubulin binding cofactor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00026      0.33      10      74 ..     420     493 ..     417     505 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                              TBCA  10 RlvKEeasYekEleeqearleklkadgdedeydlkkq............eevleetkamipdlkkrlekavekLeel 74 
                                       R + E +  e+El++q+++le++ a      +dl++             e+   ++ a+i+++ +r+e  ve+L  l
  gi|344209978|ref|YP_004786154.1| 420 RNISERTKRERELQDQKEQLEQFAATV---SHDLRNPlnvirgrldlvqETHSSDHLAVIETATERMERIVEDLLWL 493
                                       778899999****************55...34444444444445555556667777899*********999999655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (648 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 4773.47
//
Query:       gi|344209979|ref|YP_004786155.1|  [L=238]
Description: putative esterase [Haloarcula hispanica ATCC 33960]
Scores for 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-20   72.4   4.1    9.4e-20   72.2   4.1    1.0  1  Abhydrolase_6  Alpha/beta hydrolase family
    1.3e-09   38.1   0.0    2.7e-09   37.0   0.0    1.5  2  Abhydrolase_1  alpha/beta hydrolase fold
     0.0013   18.0   0.0     0.0018   17.6   0.0    1.1  1  Hydrolase_4    Serine aminopeptidase, S33
     0.0045   16.8   0.0     0.0087   15.8   0.0    1.5  1  Abhydrolase_5  Alpha/beta hydrolase family
  ------ inclusion threshold ------
       0.15   11.7   0.0       0.21   11.3   0.0    1.2  1  PGAP1          PGAP1-like protein


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 !   72.2   4.1   2.6e-23   9.4e-20       1     212 [.       5     225 ..       5     232 .. 0.74

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 2.6e-23
                                       EEEE--GC.....GCHHHHHHHHCCT.CEEEEE--TTSTS-GGCS--HHHCHHHHHHHCCTT.......TTSEEEEE CS
                     Abhydrolase_6   1 vlllHGagssassWlvapLaallaag.vhvlapDlpGhGrsdpppldledladlaalldelaa.....gggpvvlvG 71 
                                       ++l++Ga++++++W    L++ll++  ++v++p l G G  ++ +l++++ +dl+ +++++++     +  +vvl+G
  gi|344209979|ref|YP_004786155.1|   5 FVLVPGAWLGGWCWK--YLHPLLREEgHEVYTPTLTGLG--EREHLSHCE-VDLETHITDIVNvleynDLTDVVLLG 76 
                                       69************7..7777777777777*********..*********.99999999999999999********* PP

                                       ETCHHHHHHHHHHCC.......EE.EEES-..----TTT...S----TTHHHHHHTT-C.....CCCHCCHS-HS.C CS
                     Abhydrolase_6  72 HSlGGalalaaapla.....lvvg.vlldppptalpagl...laaalelllallallrl.....lawlsreplpr.l 133
                                       HS+ G++++    +a     ++   v+ld+     p+ +    aa + +l+ + + +++      +w+   p+++ +
  gi|344209979|ref|YP_004786155.1|  77 HSYAGLVVTG---VAervpeRLKHmVYLDA---LIPMNDdpvSAAEFYPLDEWKTMEAAaedhaGGWPL--PDDHsG 145
                                       ******9999...555547643447*****...666666543444444444444433332234568886..344479 PP

                                       CCCHHHCCCCHCHCCCGHHHHCCHHC.HTTCCHHTT-TTGCEEECTT-CHHHHCHHCCCH...STTEEETCE...SS CS
                     Abhydrolase_6 134 fladedadaawrarlarlaallaglg.llpaaawadlpvpllvlggeDplvprllerlla...qagarlpvvlpgaG 206
                                       +++  d+d++w +  a + +l++++   +  ++   lp+++ +l+++  +   +l+ + +   q+ ++l+    ++G
  gi|344209979|ref|YP_004786155.1| 146 WVGISDEDTEWMREKAVPHPLDTFRQqVNVGTPDVSLPTSY-ILCTQSGMDGSTLDMIRQlceQREWQLG--ELDTG 219
                                       99977788***************999444555666666666.8898888777666655555467777776..889** PP

                                       S-HHHH CS
                     Abhydrolase_6 207 Hlphle 212
                                       H+p+ +
  gi|344209979|ref|YP_004786155.1| 220 HWPMVS 225
                                       ***985 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   7.6e-13   2.7e-09       4     120 ..       6     118 ..       4     154 .. 0.84
   2 ?   -1.8   0.0      0.54     2e+03     213     251 ..     183     221 ..     140     224 .. 0.63

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 7.6e-13
                                       EEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEE CS
                     Abhydrolase_1   4 vilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGh 80 
                                       v+++G   +++ w    l p L ++g++v+++ l G g+ +  + c   +  + ++  d+  +l+  ++  ++l+Gh
  gi|344209979|ref|YP_004786155.1|   6 VLVPGAWLGGWCWKY--LHPLLREEGHEVYTPTLTGLGEREHLSHC---EVDLETHITDIVNVLEYNDLTDVVLLGH 77 
                                       667776666766777..99999999********************9...567888********************** PP

                                       THHHHHHHHHHHHHGGGEEEEEEESE.CSSCCHHHHHHHHH CS
                     Abhydrolase_1  81 SmGGmialayaaeyperVkalvllga.idpaaslieaqrqq 120
                                       S+ G++++ +a++ per k++v l+a i+ + ++ +a++++
  gi|344209979|ref|YP_004786155.1|  78 SYAGLVVTGVAERVPERLKHMVYLDAlIPMNDDPVSAAEFY 118
                                       **************************877777777776665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.54
                                       EEEEEEETTCSSSCHHHHHHHHHCHTS.EEEEEEETCSSS CS
                     Abhydrolase_1 213 ptlvisgtsDplvppkaledlaqllpk.krlvvisdagHl 251
                                       pt +i  t+ +++  + l+ ++ql+ + +  + + d+gH+
  gi|344209979|ref|YP_004786155.1| 183 PTSYILCTQSGMDG-STLDMIRQLCEQrEWQLGELDTGHW 221
                                       44444445555554.5666667777774445556777777 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.9e-07    0.0018      20     110 ..      18     104 ..       2     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.9e-07
                       Hydrolase_4  20 yaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllr 96 
                                        + l   L ++G +vy+    G G+ e       +++++++D+  ++e     +  + ++llGhS  Gl+++ +++r
  gi|344209979|ref|YP_004786155.1|  18 WKYLHPLLREEGHEVYTPTLTGLGEREHLSHCEVDLETHITDIVNVLE----YNDLTDVVLLGHSYAGLVVTGVAER 90 
                                       555666789999999999999999997666666688888888877763....444669******************* PP

                       Hydrolase_4  97 ypdkvaglilsaPa 110
                                        p++++ ++   ++
  gi|344209979|ref|YP_004786155.1|  91 VPERLKHMVYLDAL 104
                                       ******99976555 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.4e-06    0.0087      49      95 ..      63     110 ..       4     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.4e-06
                     Abhydrolase_5  49 iikeapklekfvvgGhslGGvvasrfaaee.ekiegvvflas.YPekde 95 
                                       ++ e+++l + v+ Ghs  G v++ +a++  e+++ +v+l +  P++d+
  gi|344209979|ref|YP_004786155.1|  63 VL-EYNDLTDVVLLGHSYAGLVVTGVAERVpERLKHMVYLDAlIPMNDD 110
                                       33.5999*********************9868********662688665 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.9e-05      0.21      73     105 ..      54      84 ..      44     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.9e-05
                             PGAP1  73 ndaIkyIlslysssekeptsviliGHSmGGiva 105
                                       +  I  I ++   + ++ t+v+l+GHS+ G+v 
  gi|344209979|ref|YP_004786155.1|  54 ETHITDIVNVL--EYNDLTDVVLLGHSYAGLVV 84 
                                       56677777777..67899*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 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:                        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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 1853.04
//
Query:       gi|344209980|ref|YP_004786156.1|  [L=414]
Description: ferrichrome-binding protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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-12   45.9   0.0    8.5e-12   45.1   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 !   45.1   0.0   4.8e-16   8.5e-12      10     236 ..      81     355 ..      79     357 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 4.8e-16
                                       HHHHHTT-GGGEEEB-GGG--GGGGGGT...........TS-BSBESSSB-HHHHHHH--SEEEE-GGG........ CS
                      Peripla_BP_2  10 eillalGatdkvvgvdtttsdpldadklee.........aivevgadgeidvEklaalkPDlvilskgl......gl 71 
                                       +il alG++dk+ + ++   + +  ++++             +   d+++ +E+l +l+PDl   +++       ++
  gi|344209980|ref|YP_004786156.1|  81 DILTALGEADKLIAAEGNQFWFTGFYDQLPgvdvpdpesLELVRTDDWSLRTEMLYELDPDLFATDPNRfisyygAD 157
                                       799****************999999998877866655432377777888888************999988999999* PP

                                       .GGGHHHHHHHS-EEE----TTS...............HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS- CS
                      Peripla_BP_2  72 tdedeellksgiptvivessntg...............eslkeqiralgellgledeaeklvaeidsklaaaksaid 133
                                         +++e+ +s+ p++   s+                  +++ e +  +g llg+++ a ++ + ++++l++ +s+++
  gi|344209980|ref|YP_004786156.1| 158 EGDISEITDSIGPFFGNASRRKRgddwptwpsgesypyYDIPEFVSRYGALLGKPETAAAINTLYEQALQEMRSRVP 234
                                       ********************988************99999999********************************** PP

                                       TT..-EEEEEEEETTE............EEEE-TTSTTTHHHHTS--EESTTT--.STT-EEE-HHHHHHH--SEEE CS
                      Peripla_BP_2 134 se.kpkpvlvfggade..........ggyvvagsnsyigdlldalgieniaaesk.kseyeeisaEqilasdpdvif 198
                                        e +++ v  + +a+           + +    ++ y+++  ++lg+ ++++ +  ++++++++ E++l  dpdv++
  gi|344209980|ref|YP_004786156.1| 235 PEsDRPSV-GLLNAQInpdnegffraYNPRTEIDKAYGKKQYRDLGVVDAFEGEYgGQSGIQVDYEALLDIDPDVLV 310
                                       **533333.3333332579999998888899999****************998778********************* PP

                                       EEEH.......HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-H CS
                      Peripla_BP_2 199 vsgr.......aeadnktgleflkenpllaelpAvkngrVyalds 236
                                       ++          e+   + +e++  + l +el+Av++   y  +s
  gi|344209980|ref|YP_004786156.1| 311 FHFGvnyrdwnGEDALRKTVEGMRDSSLGQELTAVQEDELYVGGS 355
                                       *9999999998777778889******************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 3084.50
//
Query:       gi|344209981|ref|YP_004786157.1|  [L=362]
Description: inosine-5'-monophosphate dehydrogenase [Haloarcula hispanica ATCC 33960]
Scores for 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-117  391.1   7.3   4.6e-117  390.9   7.3    1.0  1  IMPDH         IMP dehydrogenase / GMP reductase domain
    9.6e-09   35.1  13.6    0.00026   20.5   0.3    2.4  2  NMO           Nitronate monooxygenase
    7.6e-07   28.5  10.1    1.6e-06   27.4  10.1    1.6  1  FMN_dh        FMN-dependent dehydrogenase
    5.5e-06   26.0   1.8    0.00019   21.0   0.1    2.4  2  His_biosynth  Histidine biosynthesis protein
     0.0016   17.7   8.2     0.0016   17.6   3.9    2.7  3  Glu_synthase  Conserved region in glutamate synthase
      0.009   15.4   5.7      0.018   14.4   5.3    1.7  2  TMP-TENI      Thiamine monophosphate synthase
  ------ inclusion threshold ------
      0.011   14.9   0.7      0.011   14.9   0.7    1.7  3  DHO_dh        Dihydroorotate dehydrogenase
      0.062   12.7   3.1       0.14   11.5   1.0    2.2  2  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 !  390.9   7.3  2.1e-120  4.6e-117       3     345 .]       2     332 ..       1     332 [. 0.96

  Alignments for each domain:
  == domain 1  score: 390.9 bits;  conditional E-value: 2.1e-120
                                       -GGGEEEE---B-S-GG.GSB--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH   3 tfddvllvpaksevlpk.evdlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqaeevkk 78 
                                       ++ dvllvp++s v ++ ++dl+t lt  ++l +Plvsaamdtvte+++A++lar+Gg gv+h+ l++eeqae+vk+
  gi|344209981|ref|YP_004786157.1|   2 SYGDVLLVPKRSPVDSRsDIDLSTPLTPAVELDTPLVSAAMDTVTEADLATELARSGGFGVLHRFLTPEEQAEQVKQ 78 
                                       79*************998*********************************************************** PP

                                       HHTSTTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  79 vkrspnaakdekgrllvgaavgvkedalervkalveagvdvlvvdsahghsekvleavkeikkkveeveviaGnvat 155
                                       vk       de     vgaavg++ed+ +r + +++agvd+lvvd+ahgh +++l+av+++ +++++ ++iaGnvat
  gi|344209981|ref|YP_004786157.1|  79 VKA-----ADE----QVGAAVGINEDYVARSASVIAAGVDALVVDVAHGHLDRTLNAVETLADEFPDTNIIAGNVAT 146
                                       **3.....343....59************************************************************ PP

                                       HHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 156 aegakaLieagadavkvGiGpGsiCttrvvagvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGada 232
                                        +g+++L++agad+vkvGiGpGs Cttr vag+GvpqltAv ++a+aa++ +v+++aDGGi++sgd vkAl aGad+
  gi|344209981|ref|YP_004786157.1| 147 PAGVEDLAAAGADCVKVGIGPGSHCTTRKVAGAGVPQLTAVDDCATAAEDLDVTICADGGIRTSGDAVKALMAGADT 223
                                       ***************************************************************************** PP

                                       EEESCCCTTBTTSSSEEEEETTEEEEEEEETTSHHHHHH-SS-TTS-..--SS-SBEEEEEE--B-HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 233 vmlGsllagteEspgeviliegrkyKeyrGmgslgamkkgskdryfqkkeklvpeGvegrvpykgsvkevveqlvgg 309
                                       vmlGsl+agteE+pg v+ ++g++yK  rGm++++a +    dr  ++++    eGve+ +pykgsv+ v e++++g
  gi|344209981|ref|YP_004786157.1| 224 VMLGSLFAGTEEAPGAVVEVDGTRYKRSRGMATTAAAE----DRDDKQNNVSADEGVEALTPYKGSVAVVAEEFCAG 296
                                       **********************************9993....33322356899************************ PP

                                       HHHHHHHHT-SSHHHHHHH-EEEEE-HHHHHHHS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 310 lrsgmgylGaktieelkekakfvritaaglkeshvH 345
                                       +rsg++y+G +ti++ ++ka+f+r+++++ +  + H
  gi|344209981|ref|YP_004786157.1| 297 IRSGLSYCGGHTIAAARDKAEFIRVAQSAKEREGFH 332
                                       ***************************998776665 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.3   1.2e-07   0.00026       3      60 ..      26      82 ..      24     147 .. 0.83
   2 !   17.1   8.5   1.2e-06    0.0028     142     235 ..     143     240 ..     121     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.2e-07
                               NMO  3 lltellkikppvvqpgmggiskarLaaavsnaGgLGvlasgyltaDrlakeirkvkal 60
                                      +lt  ++   p+v + m  +++a+La   +  Gg Gvl    lt+ + a+++++vka+
  gi|344209981|ref|YP_004786157.1| 26 PLTPAVELDTPLVSAAMDTVTEADLATELARSGGFGVLH-RFLTPEEQAEQVKQVKAA 82
                                      5666777889*****************************.9**************986 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.2e-06
                               NMO 142 tissvkearkvearGaDalivqGpeaGGhqGtpevgd..kglfaLvpqvldavd...iPviAaGGiidrrgvaaaLa 213
                                        +++   +  ++a+GaD + v G   G h  t++v++  + +++ v+  + a +   + + A GGi +  +   aL 
  gi|344209981|ref|YP_004786157.1| 143 NVATPAGVEDLAAAGADCVKV-GIGPGSHCTTRKVAGagVPQLTAVDDCATAAEdldVTICADGGIRTSGDAVKALM 218
                                       5566666778999****8655.9999*****99999955444444555555555677**************999*** PP

                               NMO 214 lGAsgvqigtrfLltkesdakd 235
                                       +GA  v +g+ f +t+e++  +
  gi|344209981|ref|YP_004786157.1| 219 AGADTVMLGSLFAGTEEAPGAV 240
                                       *****************98654 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4  10.1   7.3e-10   1.6e-06     193     303 ..     114     230 ..      15     241 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 7.3e-10
                                       HHCCCHB-TC--HHHHHHHHHHHS.SEEEEEEE-SHHHHHHHHHTTESEEEE--GGG.....TSSTT-.--HHHCHH CS
                            FMN_dh 193 efvgkqldpsltwddikwlreqtk.lplvvKGvltaedakraveaGvdgivvSNHGG.....Rqldga.patidvLp 262
                                       ++++ +ld+  t + +++l ++ +  +++   v t++ ++ +++aG+d + v    G     R++ ga ++ + +  
  gi|344209981|ref|YP_004786157.1| 114 DVAHGHLDR--TLNAVETLADEFPdTNIIAGNVATPAGVEDLAAAGADCVKVGIGPGshcttRKVAGAgVPQLTAVD 188
                                       333333333..56678888888874667777799*****************96555545545766665245577777 PP

                                       HHHHHH...SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                            FMN_dh 263 eiveavgg.rievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                       +++ a+++ ++++ +DgGir+  D++kAl  GAd v+lG  f
  gi|344209981|ref|YP_004786157.1| 189 DCATAAEDlDVTICADGGIRTSGDAVKALMAGADTVMLGSLF 230
                                       7788888779*****************************876 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.012        28      31     102 ..      96     164 ..      72     168 .. 0.80
   2 !   21.0   0.1   8.4e-08   0.00019      64     105 ..     189     230 ..     176     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEES CS
                      His_biosynth  31 pvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviig 102
                                        v+   +  ++g+d l vvD+  a+ + ++ l++ve++a+e+  +  + G + +   ve+l  agad v +g
  gi|344209981|ref|YP_004786157.1|  96 YVARSASVIAAGVDAL-VVDV--AHGHLDRTLNAVETLADEFPDTNIIAGNVATPAGVEDLAAAGADCVKVG 164
                                       4555555556666666.5788..888999999*********9999999999***************977665 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 8.4e-08
                                       HHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHH CS
                      His_biosynth  64 lveeiaeevfipvqvGGGIrsledveelleagadkviigtaa 105
                                         ++ ae ++++++ +GGIr+  d+ ++l agad v++g+  
  gi|344209981|ref|YP_004786157.1| 189 DCATAAEDLDVTICADGGIRTSGDAVKALMAGADTVMLGSLF 230
                                       456789999******************************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 ?   -1.4   0.1      0.43   9.6e+02     184     236 ..      66     116 ..      55     119 .. 0.61
   2 !   17.6   3.9   7.2e-07    0.0016     223     304 ..     153     228 ..     136     231 .. 0.74
   3 ?    0.1   0.0      0.16   3.5e+02     140     155 ..     319     334 ..     307     360 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.43
                                       -SSHHHHHHHHHHHHHH-TTSEEEEEEE-STTHHHHHHHHHHTT-SEEEEE-T CS
                      Glu_synthase 184 iysiedlaqliedLkevnkeakvsvKlvaeagvetiaagvakanadiilidGl 236
                                       +  +e+ a+ +++ k + +  +v+  ++ ++ + +  a v  a++d++++d  
  gi|344209981|ref|YP_004786157.1|  66 FLTPEEQAEQVKQVKAADE--QVGAAVGINEDYVARSASVIAAGVDALVVDVA 116
                                       5556666666666666664..44444444444444445577788888877755 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 7.2e-07
                                       HHHTT-SEEEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SE CS
                      Glu_synthase 223 vakanadiilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAda 299
                                       +a a+ad++++ G+  G   +    +  aG+P ++a+    ++    +l   v++ adGg++t+ d vkal+ GAd+
  gi|344209981|ref|YP_004786157.1| 153 LAAAGADCVKV-GIGPGSHCTTR-KVAGAGVPQLTAVDDCATAAE--DL--DVTICADGGIRTSGDAVKALMAGADT 223
                                       46677777777.55444444333.345688999888887766544..44..699*********************** PP

                                       EE-SH CS
                      Glu_synthase 300 vgigt 304
                                       v +g+
  gi|344209981|ref|YP_004786157.1| 224 VMLGS 228
                                       *9997 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.16
                                       EE---TTSTTS--EE- CS
                      Glu_synthase 140 ikiaQGakpgeGgqlp 155
                                       i++aQ ak +eG + +
  gi|344209981|ref|YP_004786157.1| 319 IRVAQSAKEREGFHTD 334
                                       99**********8865 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   5.3   7.8e-06     0.018      38     177 ..      68     226 ..      39     230 .. 0.78
   2 ?    1.6   0.0     0.067   1.5e+02     107     131 ..     211     235 ..     207     250 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.8e-06
                          TMP-TENI  38 darellelaeklaalcrkygvpliindrvdlala...........vgadgvHlgqddlpvaearellgpdliiGlSv 103
                                       +++e +e++++++a+ ++ g+++ in++     a           v++   Hl  +  +v++++  +++  ii   v
  gi|344209981|ref|YP_004786157.1|  68 TPEEQAEQVKQVKAADEQVGAAVGINEDYVARSAsviaagvdalvVDVAHGHLDRTLNAVETLADEFPDTNIIAGNV 144
                                       578999********************97665555566677777777778889999999******************* PP

                          TMP-TENI 104 hsleeaeeaealgadYi..gvGpifpTdtKkdaeplgleglkelaeale......iPvvaiGGitle.nvaevleag 171
                                        +++ +e ++a+gad +  g+Gp  + +t+k a  +g+ +l+++ + ++      + ++a GGi+++ ++ ++l ag
  gi|344209981|ref|YP_004786157.1| 145 ATPAGVEDLAAAGADCVkvGIGPGSHCTTRKVA-GAGVPQLTAVDDCATaaedldVTICADGGIRTSgDAVKALMAG 220
                                       **************9972255666666665555.4555555544444444447779********8753788888899 PP

                          TMP-TENI 172 adgvav 177
                                       ad v +
  gi|344209981|ref|YP_004786157.1| 221 ADTVML 226
                                       988865 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.067
                          TMP-TENI 107 eeaeeaealgadYigvGpifpTdtK 131
                                        +a +a ++gad +++G++f+ +  
  gi|344209981|ref|YP_004786157.1| 211 GDAVKALMAGADTVMLGSLFAGTEE 235
                                       5689999************987654 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         2   4.5e+03     103     132 ..      85     115 ..      62     119 .. 0.54
   2 ?   -3.2   0.1       1.7   3.8e+03     232     273 ..     125     164 ..     120     166 .. 0.66
   3 ?   14.9   0.7   5.1e-06     0.011     244     276 ..     198     230 ..     176     241 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2
                                       E-TTSS.HHHHHHH.HHHHHGGGESEEEEES CS
                            DHO_dh 103 kakktenavddyve.vvrkigpfadilelNv 132
                                         ++ + + +dyv+ ++  i+  +d+l++ v
  gi|344209981|ref|YP_004786157.1|  85 QVGAAVGINEDYVArSASVIAAGVDALVVDV 115
                                       3344445556665513444456666666655 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.7
                                       HHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEES CS
                            DHO_dh 232 kvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvy 273
                                       + + +l++++  +  iI+ G + +   + + + aGA  v+v+
  gi|344209981|ref|YP_004786157.1| 125 NAVETLADEFP-DTNIIA-GNVATPAGVEDLAAAGADCVKVG 164
                                       55555555555.555664.77777777778888888888876 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 5.1e-06
                                       .S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
                            DHO_dh 244 eipiIgvGGiesgeDalekieaGAslvqvytal 276
                                       ++ i + GGi ++ Da+  ++aGA  v +++ +
  gi|344209981|ref|YP_004786157.1| 198 DVTICADGGIRTSGDAVKALMAGADTVMLGSLF 230
                                       599************************999865 PP

>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.0   6.4e-05      0.14      20      84 ..      94     161 ..      84     195 .. 0.80
   2 ?    0.6   0.0      0.14   3.2e+02      43      76 ..     200     233 ..     181     244 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.4e-05
                                       GGHHHHHHHHHHTT--EEEEETTS...TTHHHHHHHHHHH-TTSEEEEES--SHHHHHHHHHCT-SEE CS
                          Aldolase  20 edalplaeaLvagGlrvlevtlrt...eaaldairvlrkerpdllvgaGtvlnaeqlaeakeaGaqfv 84 
                                       ed +    +++a G+ +l v +     + +l+a++ l+ e pd  + aG v ++  +++ ++aGa+ v
  gi|344209981|ref|YP_004786157.1|  94 EDYVARSASVIAAGVDALVVDVAHghlDRTLNAVETLADEFPDTNIIAGNVATPAGVEDLAAAGADCV 161
                                       5666677788999999877666541126799**********************************976 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.14
                                       STTHHHHHHHHHHH-TTSEEEEES--SHHHHHHH CS
                          Aldolase  43 teaaldairvlrkerpdllvgaGtvlnaeqlaea 76 
                                       t +a   ir +   ++ l+ ga tv+  + +a  
  gi|344209981|ref|YP_004786157.1| 200 TICADGGIRTSGDAVKALMAGADTVMLGSLFAGT 233
                                       2344444555555555555555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2617.98
//
Query:       gi|344209982|ref|YP_004786158.1|  [L=92]
Description: hypothetical protein HAH_5040 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   0.0      0.017   15.0   0.0    1.2  1  DUF934    Bacterial protein of unknown function (DUF934)
      0.026   14.0   0.1      0.028   13.8   0.1    1.2  1  DUF969    Protein of unknown function (DUF969)


Domain annotation for each model (and alignments):
>> DUF934  Bacterial protein of unknown function (DUF934)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.9e-06     0.017      20      57 ..      25      62 ..       9      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-06
                            DUF934 20 lalialefpkFtDGRgySqarlLRerlgykgelravGd 57
                                      ++ i+++f k + G+ +  a+ L  +  y+ +lravG 
  gi|344209982|ref|YP_004786158.1| 25 FPQISVKFIKAMIGKNFDNASELQVKPAYRRQLRAVGV 62
                                      6889********************************95 PP

>> DUF969  Protein of unknown function (DUF969)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   3.2e-06     0.028      20      55 ..      11      46 ..       7      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-06
                            DUF969 20 tllvvvvaglvtglvaglslveiletlGkaFvknrl 55
                                      + +vv++ g+vt+l+ ++s++ i +++Gk+F +   
  gi|344209982|ref|YP_004786158.1| 11 SAAVVLLQGVVTALFPQISVKFIKAMIGKNFDNASE 46
                                      579****************************88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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 0.22s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 752.83
//
Query:       gi|344209983|ref|YP_004786159.1|  [L=683]
Description: formate dehydrogenase alpha subunit [Haloarcula hispanica ATCC 33960]
Scores for complete 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-80  271.2   0.0    1.9e-80  270.9   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    3.6e-32  110.7   0.0    7.6e-32  109.6   0.0    1.6  1  Molydop_binding  Molydopterin dinucleotide binding domain
    1.1e-05   25.3   4.8    1.4e-05   25.0   3.1    2.0  2  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
  ------ inclusion threshold ------
      0.028   14.2   0.3          5    6.9   0.0    2.9  3  TPP_enzyme_M     Thiamine pyrophosphate enzyme, central domai
      0.043   13.2   0.3       0.15   11.6   0.2    2.0  2  zf-ribbon_3      zinc-ribbon 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 !  270.9   0.0   5.4e-84   1.9e-80       1     430 [.      62     482 ..      62     484 .. 0.92

  Alignments for each domain:
  == domain 1  score: 270.9 bits;  conditional E-value: 5.4e-84
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       Rl+ P+vR   +  G Fv + W++Al  +a++l ++i+++gpd+v +f+s++ + +e+ ++++k ++ lg    +++
  gi|344209983|ref|YP_004786159.1|  62 RLTEPLVR---E-SGHFVTAPWETALSRVANRLGEIIDQHGPDAVEFFASSNCT-NEENYVFQKIARMLGT---NNV 130
                                       9*******...6.9********************************99998888.999999*****99999...899 PP

                                       ECCGGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHH.HHHHHHHHHTTC-EEEEECSSB-H CS
                     Molybdopterin  78 dwyadlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreerpil.narirkaalkkkakvivigpryae 153
                                       d++a+l+++s++ ++ s+   + +++n+l dl+++d  ++ G+N++e +p+   ++++ a ++ +a +i i+pr ++
  gi|344209983|ref|YP_004786159.1| 131 DNCARLCHSSTVAAM-SERLGAGAMTNTLDDLAETDCLLVTGANPAEQHPVIfRSYFLPAIRN-GATLIHIDPRETD 205
                                       9*******9997666.55566888999************************956666666666.499********** PP

                                       CGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHHH CS
                     Molybdopterin 154 llkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarelarn 230
                                       ++  ad +l ++pg d +l+++m++v+++e++vd++f++ +t+ +  ++ +l+    e  +   +v  +++re ar 
  gi|344209983|ref|YP_004786159.1| 206 TTDAADIHLDVRPGYDIQLLNSMAKVVVEEGLVDESFIEDRTTSYTDLTAHLDDADIESGADAAGVAPETVREAARA 282
                                       99********************************************************6666666666666666666 PP

                                       HHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTT. CS
                     Molybdopterin 231 aaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslke. 306
                                       +a+++ +++i+ G+g+ ++++g++++ a++nLall+gnvg+pg+g++ l+Gq++++g a +vgalp  l+ ++ ++ 
  gi|344209983|ref|YP_004786159.1| 283 YAEAD-RAAIVTGMGMSQHTSGTDNVHALLNLALLTGNVGRPGTGVNPLRGQNNVQG-AGDVGALPNVLPGYEPVTd 357
                                       66555.599999*********************************************.99******99999999999 PP

                                       ..HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHH CS
                     Molybdopterin 307 ..ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrltstal 381
                                          + ++a+e+  + +n p+ + + + +  ++  k ++ + g+np v+ ++++ v   ++ ld+ vv+d + t t++
  gi|344209983|ref|YP_004786159.1| 358 adARQRLADEWGVEPPNEPGLTETTATHQFGDAVKAAV-VFGENPAVTEPNASSVRAGFGELDFCVVIDLFETATVE 433
                                       9999********************999***97555555.************************************** PP

                                       TSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHH CS
                     Molybdopterin 382 yaDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaLa 430
                                       +aD++LP+++w Ek +++tn+++r++++++  + pg+a+ d +Il +L 
  gi|344209983|ref|YP_004786159.1| 434 HADVVLPGSSWAEKAGTVTNTDRRVMRMRPNADLPGNARRDLDILTDLG 482
                                       *********************************************9996 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   0.0   2.1e-35   7.6e-32       1     110 [.     570     675 ..     570     676 .. 0.98

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 2.1e-35
                                       EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEE CS
                   Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfm 76 
                                       l+L+tgr l++++s++ tr+++ l + ++ +v+ei+p+dAaa++i+dGd+V+ves+rG+v+v a+vt ++rpGvvf 
  gi|344209983|ref|YP_004786159.1| 570 LVLTTGRALQHFNSGALTRRSETLMRMRGeDVLEIHPDDAAARNIEDGDTVVVESERGRVTVSAAVTAAIRPGVVFC 646
                                       79*************************************************************************** PP

                                       ESSHCC.....S-GHCTS--SCSTTT--CSTT-E CS
                   Molydop_binding  77 pfgwweagekggnaNaltddatdplsgtpefksv 110
                                       +f++ +       aNalt da+dp++ +pe+k+ 
  gi|344209983|ref|YP_004786159.1| 647 TFHYLD-----PLANALTGDALDPVAEIPEYKHS 675
                                       ****99.....********************985 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   3.1   3.8e-09   1.4e-05       5      54 ..      13      58 ..      10      59 .. 0.80
   2 ?   -3.4   0.0       2.7   9.8e+03      19      37 ..     451     469 ..     450     471 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.8e-09
                                      EEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTT.T---HHHHTCHHCCC CS
                    Molybdop_Fe4S4  5 ktaCpyCgvgCglevhvkdgkivkvegdpdhpvne.grlCvKGrtllervy 54
                                      +t+CpyCgvgC +e   +++ +      + +pvn  g +C+KG ++ + v 
  gi|344209983|ref|YP_004786159.1| 13 QTVCPYCGVGCTIEYAGNGKAT-----GTAGPVNTkGEICPKGGAAFDVVE 58
                                      8************976555444.....556777766*******99998876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.7
                                       EEEETTEEEEEEE-TTSTT CS
                    Molybdop_Fe4S4  19 vhvkdgkivkvegdpdhpv 37 
                                       v+  d ++++++++ d p 
  gi|344209983|ref|YP_004786159.1| 451 VTNTDRRVMRMRPNADLPG 469
                                       566799999***9998775 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 ?    6.9   0.0    0.0014         5      63     119 ..     149     209 ..     138     219 .. 0.68
   2 ?    3.8   0.0     0.012        44       1      35 [.     276     311 ..     276     318 .. 0.83
   3 ?   -1.8   0.0      0.67   2.4e+03      72     118 ..     562     613 ..     555     623 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0014
                                       SGGGSCHHHHHHHHH-SEEEEES-SSSTCCCTT...TTTTTTTT-.EEEEEESSCCCCTTC CS
                      TPP_enzyme_M  63 lglhgskaanealeeaDlvlalGarfddirttg...sepefapea.kiihididpaeigkn 119
                                       lg  + +++ + l+e+D++l+ Ga+  +   +    ++ +  +++ ++ihid+ +++   +
  gi|344209983|ref|YP_004786159.1| 149 LGAGAMTNTLDDLAETDCLLVTGANPAEQHPVIfrsYFLPAIRNGaTLIHIDPRETDTTDA 209
                                       56666677778889*********996663322233344444555559****9887766555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.012
                                       HHHHHHHHHH-SSEEEEE-CHHCHT.TGHHHHHHHH CS
                      TPP_enzyme_M   1 iekaaellkaakrpvilvGggvars.gaseelrela 35 
                                       +++aa + ++a r +i+ G g++++   ++ +++l+
  gi|344209983|ref|YP_004786159.1| 276 VREAARAYAEADRAAIVTGMGMSQHtSGTDNVHALL 311
                                       5799******************98855677777665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.67
                                       HHHHHH-SEEEEES-SSSTCCCTT....TTTTTTTT-.EEEEEESSCCCCTT CS
                      TPP_enzyme_M  72 nealeeaDlvlalGarfddirttg....sepefapea.kiihididpaeigk 118
                                        +a++e  lvl  G  ++ +++++    se+ +  ++  +++i++d a + +
  gi|344209983|ref|YP_004786159.1| 562 ADAVAEEQLVLTTGRALQHFNSGAltrrSETLMRMRGeDVLEIHPDDAAARN 613
                                       5677888888888888777666555442222333334467777777666554 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2     4e-05      0.15      12      23 ..       9      20 ..       6      22 .. 0.83
   2 ?   -2.8   0.0       1.4   4.9e+03      12      20 ..     639     647 ..     638     648 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4e-05
                       zf-ribbon_3 12 lssddnvCpyCG 23
                                      ++++++vCpyCG
  gi|344209983|ref|YP_004786159.1|  9 PRAEQTVCPYCG 20
                                      4899******** PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.4
                       zf-ribbon_3  12 lssddnvCp 20 
                                       +++++++C+
  gi|344209983|ref|YP_004786159.1| 639 IRPGVVFCT 647
                                       4899****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (683 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 4737.09
//
Query:       gi|344209984|ref|YP_004786160.1|  [L=637]
Description: copper-binding protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   82.2   4.7    1.3e-22   80.3   1.3    2.1  2  NosD        Periplasmic copper-binding protein (NosD)
    1.4e-14   54.3  12.7    7.7e-11   42.1   2.6    3.0  2  Beta_helix  Right handed beta helix region
    1.7e-13   51.1   0.0      3e-13   50.2   0.0    1.4  1  NosL        NosL
    0.00043   19.7  13.6      0.076   12.3  13.6    2.4  1  DUF1565     Protein of unknown function (DUF1565)


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 ?    2.9   0.1     0.012        54      20      80 ..     304     364 ..     278     374 .. 0.69
   2 !   80.3   1.3   2.8e-26   1.3e-22      28     209 ..     383     550 ..     373     578 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.012
                              NosD  20 qlensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlss 80 
                                       q + s  +    ++  ns ++++  n+s+  + + t+e  ++G++l  + + ++e+ t+++
  gi|344209984|ref|YP_004786160.1| 304 QSNDSAWDATVTTAYGNSDAAVTGRNASGLYVANITVETPASGVVLRRTPGAVVENVTVNG 364
                                       4444444444556666677777778888888888888888888888888887777766655 PP

  == domain 2  score: 80.3 bits;  conditional E-value: 2.8e-26
                              NosD  28 eisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssne.sGialmsss.nntlenNtisn 102
                                       ++++   + +rdg++l  +++  +++nt++++r G+hl++++++ + dn+++++e +G+++m +  +n + +N +++
  gi|344209984|ref|YP_004786160.1| 383 VVQDSVFNGGRDGVYLHRADGTAVRNNTFRDNRFGVHLMYTSRSLVADNVARGQEyAGVVVMTNPvANAIVGNDVRH 459
                                       468888999**************************************************999888688999****** PP

                              NosD 103 nenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinnsenvkyd 179
                                       +   G++l +s+ + i++N++++++++ + ++ +++ +++N +++n +iG+   +   +n +++N+Fi n  ++   
  gi|344209984|ref|YP_004786160.1| 460 SGS-GVMLAGSR-SYIAHNVVVDTDQAMSTNA-DRSLYEHNVLYGN-DIGVRASTVVPSNIVTENDFIANDRHAVSG 532
                                       *99.*******9.68************99877.9************.*****8888899*****************9 PP

                              NosD 180 gsnnneWnttktsgtniiggpylgGNyWsd 209
                                        +    +++++            +GNyWs 
  gi|344209984|ref|YP_004786160.1| 533 PGPLRVYTHDG------------RGNYWSG 550
                                       999********............*****85 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 !   42.1   2.6   1.7e-14   7.7e-11      12     146 ..     311     445 ..     251     447 .. 0.72
   2 !   17.1   2.7   8.2e-07    0.0037       3      93 ..     443     528 ..     441     555 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.7e-14
                                       EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---..SEEE-TT.--S--EEES- CS
                        Beta_helix  12 tiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnn..gggialf.gasnnlienn 85 
                                         +  t +++++++++ r++s+  + n +++    sG+ ++++++++++n t+++    ++g++   g ++ ++   
  gi|344209984|ref|YP_004786160.1| 311 DATVTTAYGNSDAAVTGRNASGLYVANITVET-PASGVVLRRTPGAVVENVTVNGTAdwQDGFMGViGMHGPIVVQD 386
                                       44444555666666666666666666666666.77777777777777777777655566444444436666666666 PP

                                       EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT CS
                        Beta_helix  86 eitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvg 146
                                        +++ g++G+yl+ ++ + ++nN++++n+  G++++++s +  v +N++ +   aG+ v++
  gi|344209984|ref|YP_004786160.1| 387 SVFNGGRDGVYLHRADGTAVRNNTFRDNR-FGVHLMYTS-RSLVADNVARGQEYAGVVVMT 445
                                       66666777999999999999999999999.999999999.888999999999999987765 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 8.2e-07
                                       EEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT.--S CS
                        Beta_helix   3 isingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialf.gas 78 
                                       ++ n++ n  i +n++++ +g+G++l gs++  i  n++ + ++  ++++ ++++  ++n+ ++n   g+ ++    
  gi|344209984|ref|YP_004786160.1| 443 VMTNPVAN-AIVGNDVRH-SGSGVMLAGSRS-YIAHNVVVD-TDQAMSTN-ADRSLYEHNVLYGND-IGVRAStVVP 513
                                       45666777.99*******.7**********9.888899999.66666665.6***********999.9999998999 PP

                                       --EEES-EEES-SS- CS
                        Beta_helix  79 nnlienneitdnggs 93 
                                        n++  n+++ n+++
  gi|344209984|ref|YP_004786160.1| 514 SNIVTENDFIANDRH 528
                                       999999999999775 PP

>> NosL  NosL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   6.8e-17     3e-13      23     127 ..      65     180 ..      61     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 6.8e-17
                              NosL  23 pkgqifyededepakFcstrdlfafllepeerk...eikaiyvtDmsavdw........espdaeafidakkalyVv 88 
                                       p +q+fy++   ++ + +  ++++ l ep +++    + ++yv+D+s            ++++   +++a++a+yVv
  gi|344209984|ref|YP_004786160.1|  65 PRAQVFYSQYRYVVGYVGLSQAVTALTEPGHEQqfgYPLVVYVSDYSDRPVrcgddgslRTATPPDWVEANQAHYVV 141
                                       899******999999999999999999986654234789********877789999987556889************ PP

                              NosL  89 gsdveGaMGpelvpFsdeadAeaFaaehgGkvlrfedvt 127
                                       +  ++ + Gp +vpF+d++dA+aFa++ gG+++++e ++
  gi|344209984|ref|YP_004786160.1| 142 DGPARVPSGPAVVPFADRDDAAAFAETCGGRIIDWETLK 180
                                       *********************************998776 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3  13.6   1.7e-05     0.076      17     199 ..     228     512 ..     223     531 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.7e-05
                           DUF1565  17 tiTkAlllakageviqlapGtYseatgEtFPlvip.egvnlvGneagKGlskslyagk..kvgplisggg....... 83 
                                       t+  A+ +a++++++ + +GtY+e+     Pl++  +g++l G  +  G   ++ a++   +g  i g g       
  gi|344209984|ref|YP_004786160.1| 228 TVQAAVDAAPPNTTVVVPAGTYDEQVTIDKPLTLSgPGATLDGGGS--GTVVTVTADRvgVTGFEITGIGnttvgdp 302
                                       7778999***************************646888888655..55446666666633445555554455554 PP

                           DUF1565  84 ....ddls..gvqnvtivlaneatiaGvtitNp............................................ 110
                                           d  s  +    t  +++ a ++G    N                                             
  gi|344209984|ref|YP_004786160.1| 303 tqsnD--SawDATVTTAYGNSDAAVTGR---NAsglyvanitvetpasgvvlrrtpgavvenvtvngtadwqdgfmg 374
                                       43331..033333333334444444432...222224444455566******************************* PP

                           DUF1565 111 ..............nilkgtgvliesa.sakianNtitgniadGievsiyeaktgaggni................. 155
                                                     +     gv+++ a ++ ++nNt+ +n + G++  ++ ++  +++n+                 
  gi|344209984|ref|YP_004786160.1| 375 vigmhgpivvqdsvFNGGRDGVYLHRAdGTAVRNNTFRDN-RFGVHLMYT-SRSLVADNVargqeyagvvvmtnpva 449
                                       ********9998763345568****999***********7.99**99888.48888887755555566666666666 PP

                           DUF1565 156 ..isGnsilfeknGiaisgasaave.nkien................NiivkNliGvvanala 199
                                         i+Gn ++   +G++  g++  +  n + +                N+++ N iGv a+++ 
  gi|344209984|ref|YP_004786160.1| 450 naIVGNDVRHSGSGVMLAGSRSYIAhNVVVDtdqamstnadrslyehNVLYGNDIGVRASTVV 512
                                       668888888777777766666653313222245666666666677779********9987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 4898.78
//
Query:       gi|344209985|ref|YP_004786161.1|  [L=241]
Description: ABC transporter ATP-binding protein [Haloarcula hispanica ATCC 33960]
Scores for 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-28   97.9   0.0      9e-28   97.5   0.0    1.2  1  ABC_tran     ABC transporter
    1.6e-17   64.3   0.1    4.4e-09   36.6   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.5e-05   23.8   0.0      0.046   13.1   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    7.7e-05   22.6   0.0     0.0029   17.4   0.0    2.0  2  AAA_15       AAA ATPase domain
    0.00053   19.7   0.0     0.0011   18.6   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00094   19.7   0.0     0.0013   19.3   0.0    1.1  1  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.012   15.5   0.1      0.026   14.4   0.1    1.5  2  RsgA_GTPase  RsgA GTPase
      0.013   15.6   0.0      0.019   15.1   0.0    1.5  1  AAA_33       AAA domain
      0.015   15.7   0.0      0.026   14.9   0.0    1.5  1  AAA_16       AAA ATPase domain
      0.033   13.0   0.0      0.045   12.5   0.0    1.2  1  Adeno_IVa2   Adenovirus IVa2 protein
      0.046   12.4   0.0        2.7    6.5   0.0    2.0  2  AAA_13       AAA domain
       0.19   11.8   0.1       0.37   10.9   0.1    1.5  1  MMR_HSR1     50S ribosome-binding GTPase
       0.23   11.0   0.3       0.42   10.2   0.3    1.4  1  cobW         CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.5   0.0   6.5e-31     9e-28       2     136 ..      23     151 ..      22     152 .. 0.95

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 6.5e-31
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++vsl++  + +++++G+nG+GKStLl++l+g ++pt+G++ +          +++++++g+lpq p++ p+ +vre
  gi|344209985|ref|YP_004786161.1|  23 SEVSLDVPSDAVTGFIGPNGSGKSTLLRVLLGVERPTSGTVSYS--------GPEAERQLGYLPQRPTFRPGFSVRE 91 
                                       689**************************************555........578899******************* PP

                                       H......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +        d++++++l+++gl+e++ ++v    s LSgG+ + + +a+al+ +p++++lDEp 
  gi|344209985|ref|YP_004786161.1|  92 TaafyadLVDDDPDRLLERVGLEEVAGRPV----SGLSGGMTRLLGIAQALAGDPPIVMLDEPA 151
                                       ****99888899******************....*****************************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 !   25.8   0.1   6.2e-09   8.5e-06       1      23 [.      34      56 ..      34      92 .. 0.75
   2 !   36.6   0.0   3.2e-12   4.4e-09     231     298 ..     118     182 ..      93     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 6.2e-09
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      ++++iGpNgsGKS+LL+ l ++ 
  gi|344209985|ref|YP_004786161.1| 34 VTGFIGPNGSGKSTLLRVLLGVE 56
                                      699****************6653 PP

  == domain 2  score: 36.6 bits;  conditional E-value: 3.2e-12
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                        +p++ lS G+ rll+++ al+ ++   +++ +DEp +gL+P++ r +++++++ ++ g  v+l +H 
  gi|344209985|ref|YP_004786161.1| 118 GRPVSGLSGGMTRLLGIAQALAGDP---PIVMLDEPASGLDPAMSRLIFDIVESIADAGRAVVLCSHE 182
                                       578999****************999...************************999999*********7 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 !   13.1   0.0   3.4e-05     0.046      23      44 ..      31      52 ..      16      59 .. 0.83
   2 !    8.7   0.0   0.00076         1     136     205 ..     123     189 ..      99     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.4e-05
                                      TSSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 23 sksftaivGpNGSGKsnlldAi 44
                                      s+ +t  +GpNGSGKs ll  +
  gi|344209985|ref|YP_004786161.1| 31 SDAVTGFIGPNGSGKSTLLRVL 52
                                      4568999*********998655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00076
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEE.E-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfiv.islreemleka 205
                                        LSgG   L+ +a  +A       p+++lDe ++ LD +  + + +++++  +    +v  s++  ++e+ 
  gi|344209985|ref|YP_004786161.1| 123 GLSGGMTRLLGIAQALA----GDPPIVMLDEPASGLDPAMSRLIFDIVESIADAGRAVVlCSHELPLVEET 189
                                       58999999999888776....567************************99888865555145666666554 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.1e-06    0.0029      17      43 ..      25      52 ..      21      56 .. 0.81
   2 ?    3.2   0.0     0.043        59     323     364 ..     141     181 ..     126     186 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.1e-06
                            AAA_15 17 veidlsee.ltvliGkNnsGKSsileal 43
                                      v++d+ ++ +t +iG+N+sGKS++l++l
  gi|344209985|ref|YP_004786161.1| 25 VSLDVPSDaVTGFIGPNGSGKSTLLRVL 52
                                      5555555569***************988 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.043
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       ++ i++++EP   L p + + +++   ++a+ ++  v++++H
  gi|344209985|ref|YP_004786161.1| 141 DPPIVMLDEPASGLDPAMSRLIFDIVESIADAGR-AVVLCSH 181
                                       6779*****************************9.9999999 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 !   18.6   0.0     8e-07    0.0011      18      39 ..      28      49 ..      20      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 8e-07
                            AAA_29 18 eidlkgatlltGpsGsGKSTll 39
                                      ++  + +t ++Gp+GsGKSTll
  gi|344209985|ref|YP_004786161.1| 28 DVPSDAVTGFIGPNGSGKSTLL 49
                                      454344899************8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   9.1e-07    0.0013      16      38 ..      28      51 ..      14      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.1e-07
                            AAA_23 16 dF.skgltlItGpNGaGKTTildA 38
                                      d  s+ +t ++GpNG+GK+T+l+ 
  gi|344209985|ref|YP_004786161.1| 28 DVpSDAVTGFIGPNGSGKSTLLRV 51
                                      4467889**************986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.9e-05     0.026      98     131 ..      31      64 ..      11      69 .. 0.81
   2 ?   -3.2   0.0       5.1     7e+03      13      39 ..     169     194 ..     163     199 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                                       TTSEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgevs 131
                                       +d ++ ++G+ G GKStL+ +ll+ ++   g vs
  gi|344209985|ref|YP_004786161.1|  31 SDAVTGFIGPNGSGKSTLLRVLLGVERPTSGTVS 64 
                                       458999****************998776666666 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.1
                                       EES--EEEEEEESTTTT--HHHHHHHH CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfL 39 
                                       +a   ++++++s +   l +++ dr++
  gi|344209985|ref|YP_004786161.1| 169 IADAGRAVVLCSHE-LPLVEETADRLV 194
                                       66777777777777.445555566655 PP

>> AAA_33  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     0.019       4      37 ..      37      74 ..      34     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                            AAA_33  4 lvGlpGsGKstlaerllkklg....avllssdtlrrrl 37
                                      ++G++GsGKstl++ ll  +     +v  s +++ r+l
  gi|344209985|ref|YP_004786161.1| 37 FIGPNGSGKSTLLRVLLGVERptsgTVSYSGPEAERQL 74
                                      99************997544444555556666655555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.9e-05     0.026      29     142 ..      37     148 ..      30     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                            AAA_16  29 lsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeal 105
                                       ++G+ G+GKs+l+r ll  +e+    +++    + e+++ y++   ++ r ++   + ++  ++++++++++l+e++
  gi|344209985|ref|YP_004786161.1|  37 FIGPNGSGKSTLLRVLL-GVERPTSGTVSYSGPEAERQLGYLPQRPTF-RPGFSVRETAAFYADLVDDDPDRLLERV 111
                                       58***************.688885444444444445666665555555.3344444444444556777777777777 PP

                            AAA_16 106 aavpelagaeasrllellkrll..allsrderplvlvlD 142
                                       +   e+ag   s l   ++rll  a++   ++p ++ lD
  gi|344209985|ref|YP_004786161.1| 112 G-LEEVAGRPVSGLSGGMTRLLgiAQALA-GDPPIVMLD 148
                                       7.555555555667777777774333333.334555555 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.3e-05     0.045      80     126 ..      26      69 ..       8      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.3e-05
                        Adeno_IVa2  80 slnyglqPviGviyGPtGsGksqllrnlissklisPiPetvifitPe 126
                                       sl++  + v G i GP GsGks llr l+  +   P+  tv +  Pe
  gi|344209985|ref|YP_004786161.1|  26 SLDVPSDAVTGFI-GPNGSGKSTLLRVLLGVE--RPTSGTVSYSGPE 69 
                                       6777777888877.**************9876..6888888887776 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.002       2.7      23      41 ..      39      57 ..      36      74 .. 0.84
   2 ?    3.8   0.0     0.013        18     525     570 ..     140     182 ..     132     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.002
                            AAA_13 23 GwNGaGKTtLSrllrslel 41
                                      G NG+GK+tL r+l  +e+
  gi|344209985|ref|YP_004786161.1| 39 GPNGSGKSTLLRVLLGVER 57
                                      99***********998865 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.013
                            AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHn 570
                                       g   iv++D P S LD  ++ ++f  ++s +   +  + + +  H 
  gi|344209985|ref|YP_004786161.1| 140 GDPPIVMLDEPASGLDPAMSRLIFDIVESIA---DAGRAVVLCSHE 182
                                       5678********************9999987...444555555555 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   0.1   0.00027      0.37       3      22 ..      36      55 ..      34      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
                                      EEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltge 22
                                      +++G   +GKStL++ l+g 
  gi|344209985|ref|YP_004786161.1| 36 GFIGPNGSGKSTLLRVLLGV 55
                                      799**************985 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 ?   10.2   0.3   0.00031      0.42       2      21 ..      34      53 ..      33      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00031
                                      EEEEEESTTCCHHHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnhll 21
                                      vt++ G+ GsGK+tLl+ ll
  gi|344209985|ref|YP_004786161.1| 34 VTGFIGPNGSGKSTLLRVLL 53
                                      78889999*********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); 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 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1792.29
//
Query:       gi|344209986|ref|YP_004786162.1|  [L=270]
Description: hypothetical protein HAH_5044 [Haloarcula hispanica ATCC 33960]
Scores for complete 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-07   30.3  21.1    1.2e-05   24.8  21.1    2.2  1  ABC2_membrane_2  ABC-2 family transporter protein
     0.0026   17.2   7.2     0.0026   17.2   7.2    2.2  2  ABC2_membrane    ABC-2 type transporter
  ------ inclusion threshold ------
       0.18   10.9  16.2      0.038   13.1  12.7    1.6  1  ABC2_membrane_3  ABC-2 family transporter protein
        0.2   11.3   0.2       0.43   10.3   0.2    1.6  1  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres


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 !   24.8  21.1   2.6e-09   1.2e-05      81     222 ..      60     205 ..       8     266 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.6e-09
                   ABC2_membrane_2  81 mavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvll............. 144
                                       + vl+p +a + g+ aia+   rg l +l ++P s ++++ g   g++++   ++ ++++ +l+             
  gi|344209986|ref|YP_004786162.1|  60 VEVLVPTLAFAVGYRAIADPAVRGELDILDTYPLSTWSYVGGVYAGRALL---LLTIVVVPLLAlgvnvattagpet 133
                                       56899***********************************9999999999...444444444445558999999986 PP

                   ABC2_membrane_2 145 alaiilalgivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaella 221
                                       +++ ++ + +++    ++++v+++vl++l  + l++++llS++ars+ +a+ lal+ ++vl + +++++++  +l +
  gi|344209986|ref|YP_004786162.1| 134 TVFASHRGVDSPF--LFIRFVALTVLYAL--TSLTIAFLLSALARSRGRALVLALAGLLVLTVGSDLAVFA--ALDT 204
                                       6666666666665..49************..77************************************76..4444 PP

                   ABC2_membrane_2 222 g 222
                                       g
  gi|344209986|ref|YP_004786162.1| 205 G 205
                                       3 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   7.2   5.8e-07    0.0026       3     173 ..       7     191 ..       5     195 .. 0.73
   2 ?   -0.6   2.6      0.16   7.4e+02      99     153 ..     212     267 ..     206     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.8e-07
                     ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgn...lg.nsedglnrpgllffsvlflafsaltsvapvf 75 
                                       +++++ re+++++r+++++ ++ l++ ++   +fg+++ +   +g     +++ + ++  +v +la +a+   a+  
  gi|344209986|ref|YP_004786162.1|   7 FWTVFVREVRSAVRTRTYL-ALGLVTGIV---LFGLAYAGggpAGgYVPTVVDTLVAVEVLVPTLA-FAVGYRAIAD 78 
                                       899*************999.778877755...45555554222443333344669***********.7778888*** PP

                     ABC2_membrane  76 erergvlerelvsplyslsayvlakvlve.lpvsllqalifllivyflv..............gldlsrf..flfll 135
                                       +  rg l+ + ++pl s+++yv + +++  l++ +++++ +l++ + +               g+d   f  + f++
  gi|344209986|ref|YP_004786162.1|  79 PAVRGELDILDTYPL-STWSYVGGVYAGRaLLLLTIVVVPLLALGVNVAttagpettvfashrGVDSP-FlfIRFVA 153
                                       ***************.******9999888544444444444443333323444444434444444443.2559999* PP

                     ABC2_membrane 136 lllltalaasslgllisalapsfedasqlaslvllpll 173
                                       l++l+al+++++++l+sala+s   a +la + ll+l+
  gi|344209986|ref|YP_004786162.1| 154 LTVLYALTSLTIAFLLSALARSRGRALVLALAGLLVLT 191
                                       ***********************999999999999887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.16
                     ABC2_membrane  99 akvlvelpvsllqalifllivyflvgldlsrf..flflllllltalaasslgllisa 153
                                       + +l++ p ++  +l+f  + y+ v  +   f   ++ +l ll+ + ++++g ++++
  gi|344209986|ref|YP_004786162.1| 212 GGALAMTPAGAYRGLVFDQVLYVAVPGRSA-FvpTWVAALSLLFWWGLTFVGAMLAT 267
                                       556777777788888888899998888885.66689999999999999999988875 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 ?   13.1  12.7   8.4e-06     0.038     192     316 ..      85     230 ..      48     266 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.4e-06
                   ABC2_membrane_3 192 kelqlvsgvsplqywlskilgdflvyllqlllill.lafgl................gipfgnlglllllfllfgla 251
                                       + ++ + ++s+++y+ + + g +l+ l+++++ ll l +++                  + + ++ ++ l +l++l+
  gi|344209986|ref|YP_004786162.1|  85 LDILDTYPLSTWSYVGGVYAGRALLLLTIVVVPLLaLGVNVattagpettvfashrgVDSPFLFIRFVALTVLYALT 161
                                       56667889**********************9977647677788899***9999988544444778888********* PP

                   ABC2_membrane_3 252 yialgyllsslfknsetaqilifivilllsgffgglfp..ledlp.....salkwifsiiPffapglgllrl 316
                                       ++++++lls+l ++ + a +l+++ +l+l + + + ++  l   +     ++l  ++ + P  a+  + ++ 
  gi|344209986|ref|YP_004786162.1| 162 SLTIAFLLSALARSRGRALVLALAGLLVLTVGSDLAVFaaL---DtgvttGTLGGALAMTPAGAYRGLVFDQ 230
                                       *******************9988888866555443333222...2122336666666666666665554444 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 ?   10.3   0.2   9.6e-05      0.43      51      67 ..      37      53 ..      22      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.6e-05
                      HrcA_DNA-bdg 51 gLvegvpGPkGGYkPtl 67
                                      gL  +  GP+GGY+Pt+
  gi|344209986|ref|YP_004786162.1| 37 GLAYAGGGPAGGYVPTV 53
                                      6666778*********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 2033.00
//
Query:       gi|344209987|ref|YP_004786163.1|  [L=168]
Description: transcription regulator [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-15   55.5   3.2    4.1e-09   36.4   1.0    2.6  2  HTH_20           Helix-turn-helix domain
    8.9e-13   47.6   0.0    2.5e-08   33.4   0.0    2.4  2  HTH_24           Winged helix-turn-helix DNA-binding
    1.1e-11   44.4   0.1    5.5e-07   29.4   0.1    2.3  2  HTH_5            Bacterial regulatory protein, arsR family
    2.2e-08   33.8   4.9    5.2e-06   26.3   0.7    3.0  3  MarR_2           MarR family
    2.5e-08   33.7   0.0    4.2e-05   23.3   0.0    2.2  2  TrmB             Sugar-specific transcriptional regulator Trm
    2.4e-06   27.4   0.1    2.6e-05   24.1   0.1    2.1  2  HTH_11           HTH domain
    5.5e-05   23.4   0.1     0.0047   17.3   0.0    2.1  2  Rrf2             Transcriptional regulator
    5.6e-05   22.9   0.0       0.22   11.3   0.0    2.7  2  HTH_10           HTH DNA binding domain
    7.2e-05   22.6   0.0    0.00035   20.4   0.0    2.0  2  MarR             MarR family
    9.9e-05   22.3   0.4    0.00021   21.2   0.2    1.8  2  HTH_Crp_2        Crp-like helix-turn-helix domain
    0.00019   21.2   1.2     0.0027   17.5   0.8    2.3  2  HTH_IclR         IclR helix-turn-helix domain
    0.00021   21.4   0.0       0.15   12.3   0.0    2.2  2  HTH_34           Winged helix DNA-binding domain
      0.001   19.2   0.0       0.17   12.1   0.0    2.2  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.005   16.5   0.0       0.19   11.3   0.0    2.4  2  RP-C             Replication protein C N-terminal domain
     0.0067   16.0   0.0      0.027   14.0   0.0    1.9  2  HTH_CodY         CodY helix-turn-helix domain
     0.0094   15.7   0.0      0.033   13.9   0.0    1.8  2  HTH_DeoR         DeoR-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.017   15.3   0.5        8.4    6.6   0.1    2.6  2  AbiEi_4          Transcriptional regulator, AbiEi antitoxin
      0.019   15.1   0.0       0.11   12.6   0.0    2.0  2  Phage_CI_repr    Bacteriophage CI repressor helix-turn-helix 
      0.021   15.2   0.1        4.5    7.7   0.0    2.2  2  FaeA             FaeA-like protein
      0.052   13.7   6.4       0.41   10.8   1.0    3.4  3  DprA_WH          DprA winged helix domain
      0.059   12.5   0.0       0.07   12.2   0.0    1.0  1  Glyco_transf_56  4-alpha-L-fucosyltransferase glycosyl transf
      0.062   13.8   0.3        3.3    8.3   0.2    2.3  2  HTH_27           Winged helix DNA-binding domain
        3.8    7.9   8.9         36    4.8   8.8    2.7  1  HTH_31           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 !   18.4   0.0   2.1e-06    0.0016      22      52 ..       8      38 ..       3      44 .. 0.87
   2 !   36.4   1.0   5.2e-12   4.1e-09       9      55 ..      68     115 ..      62     118 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.1e-06
                                      CTTB-HHHHHHHHTS-HHHHHHHHHHHHHCT CS
                            HTH_20 22 aegltaselaerldlskntlsyHLrvLeeag 52
                                      + g+ +++la+ ld++  ++ yHLr+L++ag
  gi|344209987|ref|YP_004786163.1|  8 KPGVHFNALAADLDIATGQAQYHLRKLRRAG 38
                                      56777899*********************88 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 5.2e-12
                                       -.HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20   9 h.PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55 
                                         ++ r il +L +ae l+a el +rl+++++t+s H+ +L++ag++e
  gi|344209987|ref|YP_004786163.1|  68 RrETARTILLHLLEAESLSADELTDRLGVARSTVSWHVSALADAGILE 115
                                       55799*****************************************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 !   12.0   0.0   0.00015      0.12      13      45 ..       6      38 ..       3      38 .. 0.92
   2 !   33.4   0.0   3.2e-11   2.5e-08       2      48 .]      69     115 ..      68     115 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                            HTH_24 13 qknprisqreLAerlglSpstvnrrlkrLeeeG 45
                                      + +p+   + LA  l++  +   ++l++L ++G
  gi|344209987|ref|YP_004786163.1|  6 ESKPGVHFNALAADLDIATGQAQYHLRKLRRAG 38
                                      6789999***********************998 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 3.2e-11
                            HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       +et r IL  L +  ++s  eL +rlg+ +stv++++  L ++G+++
  gi|344209987|ref|YP_004786163.1|  69 RETARTILLHLLEAESLSADELTDRLGVARSTVSWHVSALADAGILE 115
                                       689999**************************************975 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   9.9e-05     0.077      20      43 ..      15      38 ..      12      40 .. 0.93
   2 !   29.4   0.1     7e-10   5.5e-07       4      47 .]      72     116 ..      69     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.9e-05
                                      HHHHHHTS-HHHHHHHHHHHHHTT CS
                             HTH_5 20 elaeelglsqstvShHLkkLreaG 43
                                       la++l++  +   +HL+kLr aG
  gi|344209987|ref|YP_004786163.1| 15 ALAADLDIATGQAQYHLRKLRRAG 38
                                      599*******************99 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 7e-10
                                       HHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5   4 RlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                        + IL  L e ++l++ el++ lg+ +stvS H ++L +aG++ek
  gi|344209987|ref|YP_004786163.1|  72 ARTILLHLLEaESLSADELTDRLGVARSTVSWHVSALADAGILEK 116
                                       5556666666477*****************************986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0026         2      17      49 ..       8      38 ..       3      48 .. 0.88
   2 !   26.3   0.7   6.7e-09   5.2e-06       7      54 ..      60     117 ..      56     123 .. 0.79
   3 ?   -2.7   0.0       7.1   5.5e+03      43      50 ..     154     161 ..     140     166 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0026
                                      TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTT CS
                            MarR_2 17 rpgrdltvgelarrlglsksavsrilkrLvaaG 49
                                       pg  +  ++la+ l++  + ++++l++L +aG
  gi|344209987|ref|YP_004786163.1|  8 KPG--VHFNALAADLDIATGQAQYHLRKLRRAG 38
                                      677..8999***********************9 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 6.7e-09
                                       HHHHHHHHHCTTTS..........EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2   7 qarvLaaLgrrpgr..........dltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                       ++rvLa+ +r+  r           l++ el++rlg+ +s+vs ++  L +aG +e++
  gi|344209987|ref|YP_004786163.1|  60 ERRVLAFARRETARtillhlleaeSLSADELTDRLGVARSTVSWHVSALADAGILEKS 117
                                       5666666666666666666666666******************************998 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 7.1
                                       HHHHHTTS CS
                            MarR_2  43 krLvaaGL 50 
                                        rLv+ GL
  gi|344209987|ref|YP_004786163.1| 154 TRLVDGGL 161
                                       35555555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0026         2      26      62 ..      14      52 ..       7      59 .. 0.81
   2 !   23.3   0.0   5.4e-08   4.2e-05      14      59 ..      76     123 ..      70     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0026
                                      CHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..TTEE CS
                              TrmB 26 deiaeelgvprskvYevLrsLedkGlVerekgr..pklY 62
                                      + +a +l++   +++  Lr+L ++G V  e+ +  +++Y
  gi|344209987|ref|YP_004786163.1| 14 NALAADLDIATGQAQYHLRKLRRAGDVVAEEIQgkTHYY 52
                                      5689999999***************99888755435555 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 5.4e-08
                                       CHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..T CS
                              TrmB  14 YlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr..p 59 
                                        l Ll+ ++++ade+  +lgv rs+v   ++ L d+G+ e++ g+  +
  gi|344209987|ref|YP_004786163.1|  76 LLHLLEAESLSADELTDRLGVARSTVSWHVSALADAGILEKSYGErgR 123
                                       688**************************************9988543 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.48   3.8e+02      15      45 ..      10      44 ..       5      53 .. 0.68
   2 !   24.1   0.1   3.3e-08   2.6e-05       2      44 ..      72     113 ..      71     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.48
                            HTH_11 15 pisgeeLAeeLnvSrrtvrrdIkaLeelg....vp 45
                                       +  + LA  L++ +   + ++++L+ +g     +
  gi|344209987|ref|YP_004786163.1| 10 GVHFNALAADLDIATGQAQYHLRKLRRAGdvvaEE 44
                                      46667888888887777888999999999544444 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 3.3e-08
                            HTH_11   2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44 
                                       +++il  Llea++ +s++eL ++L+v r+tv  ++ aL ++g+
  gi|344209987|ref|YP_004786163.1|  72 ARTILLHLLEAES-LSADELTDRLGVARSTVSWHVSALADAGI 113
                                       578999999***9.************************99993 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.061        47      25      56 ..       9      41 ..       1      49 [. 0.83
   2 !   17.3   0.0     6e-06    0.0047      12      68 ..      74     127 ..      67     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.061
                                      -.B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 25 p.vsseeiaerqnispsylekilakLrkaglvk 56
                                      p v  +++a+  +i    ++  l+kLr+ag v 
  gi|344209987|ref|YP_004786163.1|  9 PgVHFNALAADLDIATGQAQYHLRKLRRAGDVV 41
                                      3488999**********************9775 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 6e-06
                                       HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEES CS
                              Rrf2  12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLa 68 
                                       ++ll+L + e+   +s++e+ +r ++ +s ++  ++ L+ ag+++   G +G ++ a
  gi|344209987|ref|YP_004786163.1|  74 TILLHLLEAES---LSADELTDRLGVARSTVSWHVSALADAGILEKSYGERGRVVVA 127
                                       55555555444...9*************************************97644 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00029      0.22      24      47 ..      11      34 ..       7      37 .. 0.90
   2 !    8.7   0.0    0.0019       1.5      25      45 ..      86     106 ..      81     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                            HTH_10 24 vtlkeLAkelGIskstlsehLrka 47
                                      v+ ++LA +l+I+   +++hLrk 
  gi|344209987|ref|YP_004786163.1| 11 VHFNALAADLDIATGQAQYHLRKL 34
                                      67789*****************95 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0019
                            HTH_10  25 tlkeLAkelGIskstlsehLr 45 
                                       +++eL ++lG+++st+s h++
  gi|344209987|ref|YP_004786163.1|  86 SADELTDRLGVARSTVSWHVS 106
                                       789**************9986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       2.1   1.6e+03      20      45 ..      13      38 ..       5      46 .. 0.73
   2 !   20.4   0.0   4.5e-07   0.00035       7      50 ..      74     117 ..      70     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.1
                                      HHHHHHHHTS-HHHHHHHHHHHHHTT CS
                              MarR 20 vseLakklgvskstvtrvldrLekkG 45
                                         La  l + ++ +   l++L ++G
  gi|344209987|ref|YP_004786163.1| 13 FNALAADLDIATGQAQYHLRKLRRAG 38
                                      55677778888888888888887666 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 4.5e-07
                                       HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR   7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                        iL  l e ++ls  eL ++lgv +stv+  + +L ++G +e+s
  gi|344209987|ref|YP_004786163.1|  74 TILLHLLEAESLSADELTDRLGVARSTVSWHVSALADAGILEKS 117
                                       5899999**********************************987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       6.6   5.1e+03      41      49 ..      30      38 ..      16      44 .. 0.77
   2 !   21.2   0.2   2.7e-07   0.00021      21      57 ..      84     126 ..      61     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6.6
                                      HHHHHHHTT CS
                         HTH_Crp_2 41 ilseLkreg 49
                                       l++L+r+g
  gi|344209987|ref|YP_004786163.1| 30 HLRKLRRAG 38
                                      578888887 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 2.7e-07
                                       EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE..ET.EE...E CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglis..rg.rr...i 57 
                                       +l+ +el ++lG+ r+tvs   s+L ++g+++   g r+   +
  gi|344209987|ref|YP_004786163.1|  84 SLSADELTDRLGVARSTVSWHVSALADAGILEksYGeRGrvvV 126
                                       7999****************************64233323433 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 ?    1.5   0.0      0.35   2.7e+02      17      46 ..       9      38 ..       6      43 .. 0.85
   2 !   17.5   0.8   3.4e-06    0.0027       8      50 ..      75     116 ..      67     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.35
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelG 46
                                      +++ +  lA+ ++++   +  +L+ L + G
  gi|344209987|ref|YP_004786163.1|  9 PGVHFNALAADLDIATGQAQYHLRKLRRAG 38
                                      5678899**************999998877 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 3.4e-06
                                       HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       iL +l ea   l+  el +r+g+++Stv+ +++ L   G++e+
  gi|344209987|ref|YP_004786163.1|  75 ILLHLLEAES-LSADELTDRLGVARSTVSWHVSALADAGILEK 116
                                       7888888888.9****************************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 !    7.1   0.0    0.0078       6.1      13      46 ..       9      42 ..       3      51 .. 0.87
   2 !   12.3   0.0   0.00019      0.15       5      49 ..      75     119 ..      73     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0078
                            HTH_34 13 deadfvelkealeatdgnLsvhlkkLekagYiev 46
                                        + f+ l + l + +g+   hl+kL  ag ++ 
  gi|344209987|ref|YP_004786163.1|  9 PGVHFNALAADLDIATGQAQYHLRKLRRAGDVVA 42
                                      5789**************************8865 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00019
                            HTH_34   5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdke 49 
                                       +l  L+++++ ++ el + l++  +  s h+++L +ag +e + +
  gi|344209987|ref|YP_004786163.1|  75 ILLHLLEAESLSADELTDRLGVARSTVSWHVSALADAGILEKSYG 119
                                       6778999*******************************8876555 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 ?    4.9   0.0     0.038        29      22      55 ..      10      43 ..       4      47 .. 0.83
   2 !   12.1   0.0   0.00021      0.17      22      53 ..      84     115 ..      73     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.038
                                      SB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                    Fe_dep_repress 22 vvktkdlaerLnvspssVsemlkkLekdGyveye 55
                                       v    la  L+++   ++  l+kL+++G v+ e
  gi|344209987|ref|YP_004786163.1| 10 GVHFNALAADLDIATGQAQYHLRKLRRAGDVVAE 43
                                      5667789**********************77665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00021
                                       SB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress  22 vvktkdlaerLnvspssVsemlkkLekdGyve 53 
                                         +  +l  rL+v+ s+Vs  ++ L+++G +e
  gi|344209987|ref|YP_004786163.1|  84 SLSADELTDRLGVARSTVSWHVSALADAGILE 115
                                       56778999********************9876 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 ?    2.7   0.0      0.11        87      76     102 ..      15      41 ..      11      56 .. 0.86
   2 !   11.3   0.0   0.00025      0.19      73     101 ..      86     114 ..      84     122 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.11
                              RP-C  76 qLsralglsestlrrhlaaLveaGlii 102
                                       +L+  l++++ + ++hl++L  aG ++
  gi|344209987|ref|YP_004786163.1|  15 ALAADLDIATGQAQYHLRKLRRAGDVV 41 
                                       68889999**************99766 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00025
                              RP-C  73 sNaqLsralglsestlrrhlaaLveaGli 101
                                       s+++L  +lg+++st++ h++aL++aG++
  gi|344209987|ref|YP_004786163.1|  86 SADELTDRLGVARSTVSWHVSALADAGIL 114
                                       8899***********************97 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.7   1.3e+03      25      32 ..      31      38 ..      20      51 .. 0.83
   2 !   14.0   0.0   3.5e-05     0.027       5      44 ..      85     123 ..      81     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.7
                          HTH_CodY 25 LrkLesaG 32
                                      LrkL  aG
  gi|344209987|ref|YP_004786163.1| 31 LRKLRRAG 38
                                      89999998 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.5e-05
                          HTH_CodY   5 LtaskiaDriGitrsvivnaLrkLesaGiiesrsLGmkGt 44 
                                       L a ++ Dr+G++rs +   +  L  aGi+e +s G +G 
  gi|344209987|ref|YP_004786163.1|  85 LSADELTDRLGVARSTVSWHVSALADAGILE-KSYGERGR 123
                                       88999*************************9.68887775 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 ?   -1.6   0.0         3   2.3e+03      15      28 ..      11      24 ..       4      37 .. 0.78
   2 !   13.9   0.0   4.3e-05     0.033       5      49 ..      75     119 ..      72     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3
                          HTH_DeoR 15 lsveelvellgvSe 28
                                      ++ + l++ l++++
  gi|344209987|ref|YP_004786163.1| 11 VHFNALAADLDIAT 24
                                      67778888888875 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.3e-05
                          HTH_DeoR   5 ilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRthG 49 
                                       il  l +  +ls +el+++lgv+  T+    + L+ +g+l++ +G
  gi|344209987|ref|YP_004786163.1|  75 ILLHLLEAESLSADELTDRLGVARSTVSWHVSALADAGILEKSYG 119
                                       6666778899********************************999 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.014        11      18      39 ..      19      41 ..      14      42 .. 0.81
   2 ?    6.6   0.1     0.011       8.4      14      40 ..      85     116 ..      75     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.014
                           AbiEi_4 18 el.eaaGispsalrrLvrkGwLv 39
                                      +l +a G   ++lr+L+r+G++v
  gi|344209987|ref|YP_004786163.1| 19 DLdIATGQAQYHLRKLRRAGDVV 41
                                      663458889999********986 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.011
                           AbiEi_4  14 fttrelea.aGispsa....lrrLvrkGwLvr 40 
                                       ++ +el+  +G+ +s+    ++ L ++G L++
  gi|344209987|ref|YP_004786163.1|  85 LSADELTDrLGVARSTvswhVSALADAGILEK 116
                                       578999999*******8999999999999885 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 ?    0.1   0.0       1.1   8.6e+02      16      28 ..      14      26 ..       9      44 .. 0.71
   2 ?   12.6   0.0   0.00014      0.11      13      31 ..      86     103 ..      75     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.1
                                      HHHHCCTT--HHH CS
                     Phage_CI_repr 16 keLAdlLgiakss 28
                                      ++LA+ L+ia   
  gi|344209987|ref|YP_004786163.1| 14 NALAADLDIATGQ 26
                                      5899999999765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00014
                                       SSCHHHHCCTT--HHHHHH CS
                     Phage_CI_repr  13 kmqkeLAdlLgiakssvst 31 
                                       +++ eL d+Lg+a+s+vs 
  gi|344209987|ref|YP_004786163.1|  86 SAD-ELTDRLGVARSTVSW 103
                                       455.9************93 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0058       4.5      10      45 ..       6      40 ..       2      54 .. 0.84
   2 ?    5.5   0.0     0.029        22       4      53 ..      74     122 ..      71     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0058
                                      HH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSE CS
                              FaeA 10 nsikapckTreiAdalglsaYQaRyYLeqLekegki 45
                                       s k +++ + +A  l ++  Qa y L +L+++g +
  gi|344209987|ref|YP_004786163.1|  6 ES-KPGVHFNALAADLDIATGQAQYHLRKLRRAGDV 40
                                      55.66677777899999999*************976 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.029
                                       HHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--SSS CS
                              FaeA   4 eIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrspvrrG 53 
                                        Il +l +   +    e+ d lg++   +      L  +g +++s   rG
  gi|344209987|ref|YP_004786163.1|  74 TILLHLLE-AESLSADELTDRLGVARSTVSWHVSALADAGILEKSYGERG 122
                                       69999999.999999*****************************988777 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.27   2.1e+02      26      49 ..      11      34 ..       6      43 .. 0.85
   2 ?   10.8   1.0   0.00052      0.41      13      43 ..      72     102 ..      53     108 .. 0.85
   3 ?    1.6   0.2      0.39     3e+02       9      24 ..     129     144 ..     126     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.27
                           DprA_WH 26 vhvDqLvrrtglpaaevsaaLleL 49
                                      vh+ +L++++ + +++ + +L  L
  gi|344209987|ref|YP_004786163.1| 11 VHFNALAADLDIATGQAQYHLRKL 34
                                      89**************99888665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00052
                           DprA_WH  13 lerrvLaaLgpePvhvDqLvrrtglpaaevs 43 
                                        +  +L +L++e+++ D+L  r+g+  ++vs
  gi|344209987|ref|YP_004786163.1|  72 ARTILLHLLEAESLSADELTDRLGVARSTVS 102
                                       566678*******************999998 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.39
                           DprA_WH   9 plddlerrvLaaLgpe 24 
                                       ++ d+ rr+Laa+ p+
  gi|344209987|ref|YP_004786163.1| 129 ADPDETRRLLAAVRPS 144
                                       567999******9987 PP

>> Glyco_transf_56  4-alpha-L-fucosyltransferase glycosyl transferase group 56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     9e-05      0.07     128     236 ..      29     143 ..      17     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9e-05
                   Glyco_transf_56 128 yllrrlaqkrvgrvfa..trGdleylaqrakkvkdsllyfPtrmdealt...laeekeeeeekltillGnsGdrsnr 199
                                       y+lr+l  +r g v a   +G  +y+++++   + ++l f  r + ++    l e+++ ++++lt  lG +      
  gi|344209987|ref|YP_004786163.1|  29 YHLRKL--RRAGDVVAeeIQGKTHYYSREYDPWERRVLAFARRETARTIllhLLEAESLSADELTDRLGVARSTVSW 103
                                       889998..677888874468********************99987765411156677888899************** PP

                   Glyco_transf_56 200 hiaalka...ikqqfgekvkvivPmGyPanneayieevee 236
                                       h++al+    +++++ge+ +v+v +  P++ ++ ++ v+ 
  gi|344209987|ref|YP_004786163.1| 104 HVSALADagiLEKSYGERGRVVVALADPDETRRLLAAVRP 143
                                       *****86454799****************99999988875 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      0.13     1e+02      23      48 ..      15      41 ..       4      52 .. 0.76
   2 ?    8.3   0.2    0.0043       3.3       8      63 ..      76     127 ..      70     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.13
                            HTH_27 23 dlcgrlnvedshisyslkkLtek.GLv 48
                                      +l+  l++   ++ y l+kL ++ ++v
  gi|344209987|ref|YP_004786163.1| 15 ALAADLDIATGQAQYHLRKLRRAgDVV 41
                                      67777888899999********94444 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0043
                            HTH_27   8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvr 63 
                                       +Lhl++   +  ++ +l +rl v  s++s  +++L  +G +e++  e  r+++ v+
  gi|344209987|ref|YP_004786163.1|  76 LLHLLE--AESLSADELTDRLGVARSTVSWHVSALADAGILEKSYGE--RGRVVVA 127
                                       466666..999999***************************999888..6666665 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   8.8     0.046        36      13      34 ..      72     104 ..      30     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.046
                            HTH_31  13 a...........GLsqeevAerlgvsestlsrl 34 
                                       a            Ls +e+ +rlgv +st+s+ 
  gi|344209987|ref|YP_004786163.1|  72 ArtillhlleaeSLSADELTDRLGVARSTVSWH 104
                                       255555555555*******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 1340.96
//
Query:       gi|344209988|ref|YP_004786164.1|  [L=186]
Description: nitrous oxide reductase [Haloarcula hispanica ATCC 33960]
Scores for 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  147.9   0.1    2.4e-43  147.6   0.1    1.1  1  NosL      NosL
     0.0077   16.0   0.0      0.012   15.4   0.0    1.3  1  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom
     0.0091   15.8   3.5      0.088   12.7   1.4    2.3  2  VATC      Vms1-associating treble clef domain


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 !  147.6   0.1     4e-47   2.4e-43       1     131 []      35     183 ..      35     183 .. 0.95

  Alignments for each domain:
  == domain 1  score: 147.6 bits;  conditional E-value: 4e-47
                              NosL   1 pveltaeaecdvCgMliaehpgpkgqifyede.....depakFcstrdlfafllepeerk.eikaiyvtDmsavdw. 70 
                                       pv+++++++cd+CgM+i +hpgp+gq++y+d+     d pa+Fcst++++++ +++e+++ +++++++tD+sa+d+ 
  gi|344209988|ref|YP_004786164.1|  35 PVAIESGQNCDQCGMVIDQHPGPVGQTYYQDNtpeghDPPARFCSTTCTYRHRFAKEQSGwTPAETFLTDYSATDYd 111
                                       899****************************556677**************************************** PP

                              NosL  71 ...........esp.daeafidakkalyVvgsdveGaMGpelvpFsdeadAeaFaaehgGkvlrfedvteelv 131
                                                  +   ++eaf+  +++++V++s+ eG+MG+ +vpFsd+adAe+Fa+e+gG++l  ed+t+elv
  gi|344209988|ref|YP_004786164.1| 112 vrtdggktiisR-HlESEAFASTEELTVVANSEIEGSMGTAIVPFSDSADAESFAEEYGGQTLPAEDITRELV 183
                                       ********9644.26*******************************************************986 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 !   15.4   0.0     2e-06     0.012      21      66 ..     129     175 ..     124     179 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-06
                                       TTSCEEEEEEEEE.TTTSEEEEEEEEESSHHHHHHHHHHHTTEEETT CS
                             RRM_1  21 kfGpiksiklvrd.etgkskgfafVeFeskedAekAlealngkklgg 66 
                                        f + +++++v + e + s+g+a+V F ++ dAe+  e++ g++l+ 
  gi|344209988|ref|YP_004786164.1| 129 AFASTEELTVVANsEIEGSMGTAIVPFSDSADAESFAEEYGGQTLPA 175
                                       48889999**********************************99875 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.017     1e+02       4      14 ..      42      52 ..      39      64 .. 0.75
   2 !   12.7   1.4   1.5e-05     0.088      25      40 ..      76      91 ..      74      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.017
                              VATC  4 lrCsiCgesle 14
                                      ++C++Cg  + 
  gi|344209988|ref|YP_004786164.1| 42 QNCDQCGMVID 52
                                      79****98765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.5e-05
                              VATC 25 rYCstkClraHRranf 40
                                      r+Cst C  +HR a++
  gi|344209988|ref|YP_004786164.1| 76 RFCSTTCTYRHRFAKE 91
                                      8***********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); 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:                         3  (0.000167327); expected 0.2 (1e-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: 1534.70
//
Query:       gi|344209989|ref|YP_004786165.1|  [L=91]
Description: hypothetical protein HAH_5047 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   4.9       0.12   11.8   4.9    1.2  1  LysE           LysE type translocator
       0.36   10.7   7.2        0.4   10.5   7.2    1.0  1  7TMR-DISM_7TM  7TM diverse intracellular signalling
        1.5    8.9   6.2        6.1    6.9   6.2    1.8  1  MARVEL         Membrane-associating domain
        2.6    8.4   6.8        5.2    7.4   6.8    1.6  1  DUF1772        Domain of unknown function (DUF1772)


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 ?   11.8   4.9   2.6e-05      0.12       3      73 ..       7      75 ..       1      88 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.6e-05
                              LysE  3 lllspGpqnllvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwl 73
                                      +l+++G   l+ ++ + ++ ++    v+l v+ig   l+l +++G+ ++l a p+v   l+  G+ +L+ l
  gi|344209989|ref|YP_004786165.1|  7 GLATLGTLALFFVAAASTHRRRSRPYVLLTVAIGL--LVLRSVVGIGTVLGAVPMVVHHLTEHGFDFLIAL 75
                                      56778888877777777888899999999999885..6667999***********************9976 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 ?   10.5   7.2   8.9e-05       0.4     128     197 ..       7      79 ..       1      85 [. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.9e-05
                     7TMR-DISM_7TM 128 llallvillllligikaw.rkgnkparyfliawlllligvlidilsllgllpsn..ffteyllqigvllevll 197
                                        la l+ l l++++ ++  r++ +p  ++++a+ ll++ +++ i ++lg +p     +te+++ + ++l vl+
  gi|344209989|ref|YP_004786165.1|   7 GLATLGTLALFFVAAASThRRRSRPYVLLTVAIGLLVLRSVVGIGTVLGAVPMVvhHLTEHGFDFLIALLVLS 79 
                                       4555666666666666667***********************9999999666554456779998866666654 PP

>> MARVEL  Membrane-associating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   6.2    0.0014       6.1      16      97 ..       6      84 ..       1      87 [. 0.68

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0014
                            MARVEL 16 faiiilgliasliakldqllgspssalnfavfvavfsfly..alfllvlylfknsaftsilwplidlivdalaallwlv 92
                                      +++  lg+ a +   ++   ++ + + ++++ + ++++l+  +++++   l+   a++   + l + ++d+l+all l 
  gi|344209989|ref|YP_004786165.1|  6 LGLATLGTLALFF--VAAASTHRRRSRPYVLLTVAIGLLVlrSVVGIGTVLG---AVPMVVHHLTEHGFDFLIALLVLS 79
                                      4444444444444..3334456666666666666666666678888888775...999999999999999999999999 PP

                            MARVEL 93 afial 97
                                      a + +
  gi|344209989|ref|YP_004786165.1| 80 AIYSV 84
                                      98765 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   6.8    0.0012       5.2      38      87 ..       5      58 ..       2      89 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
                           DUF1772 38 vfpplallsalafa.ylaaraasrgarllylaaaalllls..ivp.yTllvmvP 87
                                      v++++ l+++++f+ ++a+ +++r+++ ++l++a+ ll+   +v   T+l  vP
  gi|344209989|ref|YP_004786165.1|  5 VLGLATLGTLALFFvAAASTHRRRSRPYVLLTVAIGLLVLrsVVGiGTVLGAVP 58
                                      566777777777774444666666666666555555543322444345555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 736.04
//
Query:       gi|344209990|ref|YP_004786166.1|  [L=140]
Description: universal stress protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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-30  105.2   2.2    4.2e-30  105.1   2.2    1.0  1  Usp             Universal stress protein family
    0.00046   20.2   0.0    0.00057   19.9   0.0    1.1  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 !  105.1   2.2   4.7e-34   4.2e-30       1     139 [.       1     138 [.       1     140 [] 0.97

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 4.7e-34
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my++I+Va+Dgs ++ +A+ +Ale+a+++gael+++ v+d+++ ++ + +  e e+ e e+ +  + a+  +++ +a
  gi|344209990|ref|YP_004786166.1|   1 MYDTIVVATDGSADANRAATHALEQAEQHGAELHAVFVVDTDRHAEPALSSMELETIEIEEWGNDELAEV-AERGDA 76 
                                       9*********************************************************999999998886.9999** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                        gv+v++   +g+p  e + +a+e dadliV+G +g+s+ +   +GSv+++v+++a  pVlv
  gi|344209990|ref|YP_004786166.1|  77 LGVEVTTRCCHGKPYVEVISYADEVDADLIVLGYHGHSHTKTDQIGSVTDRVVQNAGRPVLV 138
                                       ******************************************99*****************9 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   6.4e-08   0.00057      15      96 ..      21     110 ..      17     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.4e-08
                                       HHHHHHHCTTSEEEEEEEE-HH.HHTCG....S-CHHHHH.HHHHHHHHHHHHHHHTT--EEEEESS..HHHHHHHH CS
                    DNA_photolyase  15 pALaaAaasgepvipvfvldpe.kahkl....rvgaarvd.fllesLadLdeeLrelgirLvvrrgd..padvlpel 83 
                                       +AL++A ++g+++++vfv+d++ +a++     +++ + ++ +    La+ +e+ ++lg++   r++   p  ++ ++
  gi|344209990|ref|YP_004786166.1|  21 HALEQAEQHGAELHAVFVVDTDrHAEPAlssmELETIEIEeWGNDELAEVAERGDALGVEVTTRCCHgkPYVEVISY 97 
                                       69********************6444447777788888879*****************99988865444999***** PP

                                       HHHCTECEEEEE- CS
                    DNA_photolyase  84 akelgasavvanr 96 
                                       a e++a+ +v+ +
  gi|344209990|ref|YP_004786166.1|  98 ADEVDADLIVLGY 110
                                       ******9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 1033.18
//
Query:       gi|344209991|ref|YP_004786167.1|  [L=159]
Description: pyridoxamine 5'-phosphate oxidase-like FMN-binding protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   64.2   0.0    1.4e-17   64.0   0.0    1.0  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.016   15.4   0.0    1.2  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase


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 !   64.0   0.0   1.6e-21   1.4e-17       1     140 [.      15     144 ..      15     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 1.6e-21
                                       -HHHHHHHHHC-SEEEEEEEETTEEEEEEEEEEEETTEEEEEEET...TSHCCHCCC.T--ECEEEEEEEEEEE-SE CS
                      Pyridox_ox_2   1 dreeilalLdegevgrlafvddgepvilPvnyvvdgdslyfhgak...gsrlaaalr.gapvcvvvtevdglvlars 73 
                                       d+e+i ++L+++++g+l++ + + p++lP++y++d+++++  ++    +sr+a++++ + +  + v+++d    a +
  gi|344209991|ref|YP_004786167.1|  15 DDEAIREFLATHSTGVLGLPTTDVPYLLPLSYGFDDGACLYFTYLlgeSSRKAELTErAGRGRFLVYDIDT---AFE 88 
                                       7899*********************************9888888777789999999965569999999888...666 PP

                                       GGEEEEEEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTTGGCSB---CCCCCTEEEEEEEEEEEEEE CS
                      Pyridox_ox_2  74 fnslnyrSVvvrGraeevtdeeekaealellvekivpgrwenlrpptrkelkatsvlrlkieevsgr 140
                                            ++SV++ G+++ v  +e++    +++++++    w+++  +t++     ++++++i+++ g 
  gi|344209991|ref|YP_004786167.1|  89 -----WQSVMLAGDISSV--PEDDWSDITAMTQNA----WRPNTLQTATTSGGVALYEFEITDLAGI 144
                                       .....*************..777777788899888....8866667777778899999999999886 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   1.8e-06     0.016       2      87 ..      16     104 ..      14     105 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-06
                                       HHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTT.TEEEEEEETTSHHHHHHHHH-EEEEEEEETT...GSEE CS
                    Putative_PNPOx   2 deelreflaeskavvlATvdedGrPnvspvllkagdgr.dgivfatnadsrklrnleenprvallfldde...lgrg 74 
                                       de++refla+++++vl+  + d  P++ p+++ ++dg   ++++   + srk++  e+  r  +l++d +     ++
  gi|344209991|ref|YP_004786167.1|  16 DEAIREFLATHSTGVLGLPTTDV-PYLLPLSYGFDDGAcLYFTYLLGESSRKAELTERAGRGRFLVYDIDtafEWQS 91 
                                       579***************99999.*********8888899999999***********************99999999 PP

                                       EEEEEEEEEESCH CS
                    Putative_PNPOx  75 vrieGtaelvsdg 87 
                                       v++ G +  v ++
  gi|344209991|ref|YP_004786167.1|  92 VMLAGDISSVPED 104
                                       *****99999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1265.51
//
Query:       gi|344209992|ref|YP_004786168.1|  [L=160]
Description: hypothetical protein HAH_5050 [Haloarcula hispanica ATCC 33960]
Scores for 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  124.4   0.7    4.1e-36  123.9   0.7    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 !  123.9   0.7   2.3e-40   4.1e-36       2     119 ..       4     119 ..       3     122 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.9 bits;  conditional E-value: 2.3e-40
                                       HHHHHHHHHHHT---HHHHHHHHHHHHHHHHTTS-HHHHHHHHTTS-HHHHHHHHTT--TTS-----SHHHHHHHHH CS
                           DUF2267   2 defleevqerlgledreeAeratravLrtLrdrlteeeaadlaaqLPeelrgllrdgwppvepgkrfdreeflerva 78 
                                       def++e+q+rl+l+ + eA ratra+L  L++r++ e+aad+aa+LP+e++++++ + ++  +g+rfd++ef++rva
  gi|344209992|ref|YP_004786168.1|   4 DEFTGEIQHRLELPGTGEAVRATRATLLPLGQRIPAENAADFAASLPMEIKWYMTGAVRD--HGQRFDWTEFVDRVA 78 
                                       89********************************************************99..*************** PP

                                       HTS.....EHHHHHHHHHHHHHHHS-HHHHHHHHHTS-HHH CS
                           DUF2267  79 eelgvdpedaeqaaraVfaalkealsegeiedvaaqLPkdl 119
                                       e +gv+p+da+++ar+V+++++ a+++++++d+++qLP++ 
  gi|344209992|ref|YP_004786168.1|  79 EIEGVEPSDAAYHARVVVDLMHTAVPAADFQDLRGQLPESA 119
                                       **************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1191.08
//
Query:       gi|344209993|ref|YP_004786169.1|  [L=300]
Description: universal stress protein [Haloarcula hispanica ATCC 33960]
Scores for 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-67  224.4   4.4    4.2e-33  114.8   0.9    2.0  2  Usp           Universal stress protein family
     0.0012   18.7   0.2       0.61   10.1   0.0    2.6  2  FR47          FR47-like protein
     0.0079   15.7   3.1       0.24   10.8   0.1    2.5  2  AP_endonuc_2  Xylose isomerase-like TIM barrel


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 !  114.8   0.9   6.9e-37   4.2e-33       1     141 []       1     141 [.       1     141 [. 0.98
   2 !  111.3   0.1   8.5e-36   5.1e-32       2     140 ..     152     290 ..     151     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 6.9e-37
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       m++ IlV++Dgse++++A+e++++la+a+ga l+++ vid+r+ g   ++d+ + e     ++++++  aa + a +
  gi|344209993|ref|YP_004786169.1|   1 MFDSILVPTDGSEHATRAAEHGAALARAFGASLHVIAVIDTRTAGGPFNGDDLEDETLDRMTADAEDTVAAITDAVD 77 
                                       899**************************************************************999999999999 PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       +  + +++++ gdp +ei+ + +++d++li +G++gr+g+ r+l GSv+e+v+r+a++pVl Vr
  gi|344209993|ref|YP_004786169.1|  78 AAGAIQTTIRKGDPVDEICAYRDDHDVELIAMGTHGRTGVGRYLAGSVTESVVRQADVPVLTVR 141
                                       99999********************************************************998 PP

  == domain 2  score: 111.3 bits;  conditional E-value: 8.5e-36
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeag 78 
                                       y+ IlV++Dgs  + +A+e A e a++++a++++l+v+  ++ ++ s++  +    e+ +++ e++ +  +a+a++ 
  gi|344209993|ref|YP_004786169.1| 152 YDDILVPTDGSAPAAAAIEPACEIAAQFDARVHALNVVNLSNIATGSEYTLPKDLIESLESQGEKVTERIAARARES 228
                                       899****************************************************99999999999999******** PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       gv++++ v++g pa  ile+a+e+d+dli +G+ gr+gl r+l+GS++e+++rha+ pVl+V
  gi|344209993|ref|YP_004786169.1| 229 GVETVTRVVSGFPAADILEYADENDIDLIAMGTAGRTGLNRFLVGSTTERIIRHADMPVLAV 290
                                       ************************************************************99 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0001      0.61      32      66 ..     111     145 ..      98     148 .. 0.91
   2 !    5.9   0.0    0.0022        13      33      67 ..     262     296 ..     256     299 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0001
                                       GG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-H CS
                              FR47  32 ehrrrGlgsrlvkalakeiaergktvllvvvasNt 66 
                                       +h r G g+ l+ ++++ ++++ + ++l v+a++ 
  gi|344209993|ref|YP_004786169.1| 111 THGRTGVGRYLAGSVTESVVRQADVPVLTVRATDR 145
                                       799***************************99985 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0022
                                       G-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HH CS
                              FR47  33 hrrrGlgsrlvkalakeiaergktvllvvvasNtp 67 
                                       + r Gl + lv + +++i++  + ++l v+a +++
  gi|344209993|ref|YP_004786169.1| 262 AGRTGLNRFLVGSTTERIIRHADMPVLAVNARDQR 296
                                       5689**************************99876 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 !    5.2   0.8    0.0022        13      65     136 ..      12      89 ..       2     108 .. 0.71
   2 !   10.8   0.1     4e-05      0.24      51     137 ..     152     242 ..      81     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0022
                                       HHHHHHHHHHHHHHHHHHTBSEEEEEBCC.....GBCTTTSGHHHHHHHHHHHHHH.HHHHHHHHTSEEEEE--TTT CS
                      AP_endonuc_2  65 reesvdalkraielaaaLGapllvlhpGt.....agagpkgseeeawerlaeslne.ladyaekegvklalEtlags 135
                                       +e++ +a+++ + la+a+Ga l v+ + +      ++ +++ e+e+++r+ ++ ++ +a+++++++   a++t+ ++
  gi|344209993|ref|YP_004786169.1|  12 SEHATRAAEHGAALARAFGASLHVIAVIDtrtagGPFNGDDLEDETLDRMTADAEDtVAAITDAVDAAGAIQTTIRK 88 
                                       45669999999***********9999887888886677777788888888765544155555566666666666655 PP

                                       T CS
                      AP_endonuc_2 136 g 136
                                       g
  gi|344209993|ref|YP_004786169.1|  89 G 89 
                                       5 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 4e-05
                                       CCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCC........GBCTTTSGHHHHHHHHHHHHHHHHHH CS
                      AP_endonuc_2  51 trfgypdederearreesvdalkraielaaaLGapllvlhpGt........agagpkgseeeawerlaeslnelady 119
                                       +++  +++d  +++     +a++ a+e+aa+++a++  l++ +           +pk+ +e+   +  ++ +++a+ 
  gi|344209993|ref|YP_004786169.1| 152 YDDILVPTDGSAPA----AAAIEPACEIAAQFDARVHALNVVNlsniatgsEYTLPKDLIESLESQGEKVTERIAAR 224
                                       44444555555555....9*****************99998889999999966888888888888888888888888 PP

                                       HHHHTSEEEEE--TTTTS CS
                      AP_endonuc_2 120 aekegvklalEtlagsgv 137
                                       a++ gv+ +     g+++
  gi|344209993|ref|YP_004786169.1| 225 ARESGVETVTRVVSGFPA 242
                                       888888776665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2117.45
//
Query:       gi|344209994|ref|YP_004786170.1|  [L=144]
Description: hypothetical protein HAH_5052 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   64.1   0.0    1.5e-17   63.9   0.0    1.0  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
     0.0058   16.8   0.0     0.0082   16.3   0.0    1.3  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase


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 !   63.9   0.0   1.6e-21   1.5e-17       2     140 ..      11     141 ..      10     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 1.6e-21
                                       HHHHHHHHHC-SEEEEEEEETTE.EEEEEEEEEEETTE..EEEEEETTS.HCCHCCCT--ECEEEEEEEEEEE-SEG CS
                      Pyridox_ox_2   2 reeilalLdegevgrlafvddge.pvilPvnyvvdgds..lyfhgakgs.rlaaalrgapvcvvvtevdglvlarsf 74 
                                       +ee +a+Ld+g++g l+++ +++ p+++Pv+y++d+ +  +yf+ a+g  r   +l+++ +++v ++  +    +  
  gi|344209994|ref|YP_004786170.1|  11 DEERDAFLDNGGTGILSLAAGDApPHSVPVSYGYDAPTttFYFRLAVGVeRSKGELDDRAATFVTYDETD----SG- 82 
                                       699*****************7778***********66666*******65144444444558888887222....34. PP

                                       GEEEEEEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTTGGCSB---CCCCCTEEEEEEEEEEEEEE CS
                      Pyridox_ox_2  75 nslnyrSVvvrGraeevtdeeekaealellvekivpgrwenlrpptrkelkatsvlrlkieevsgr 140
                                           ++SVv+ Gr+e v+ e  ++e le+l +  +p    ++ +   +e+   +++rl ++e++gr
  gi|344209994|ref|YP_004786170.1|  83 ----WQSVVANGRLEDVEREGIETETLEGLEHVDMP--MVDIFERPLREVDF-EFYRLVPNELTGR 141
                                       ....*************************9888899..66666444445554.88**********9 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   9.1e-07    0.0082       2      86 ..      11      97 ..       9      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.1e-07
                                      HHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTS..HHHHHHHHH-EEEEEEEETT..GSEEEE CS
                    Putative_PNPOx  2 deelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnads..rklrnleenprvallfldde..lgrgvr 76
                                      dee  +fl +  ++ l+ +  d  P+++pv++ ++  +++++f  +      k++    +  ++++ +d+     ++v 
  gi|344209994|ref|YP_004786170.1| 11 DEERDAFLDNGGTGILSLAAGDAPPHSVPVSYGYDAPTTTFYFRLAVGVerSKGE--LDDRAATFVTYDETdsGWQSVV 87
                                      44666899999***************************88888655444115555..6666666666666667777788 PP

                                      EEEEEEEESC CS
                    Putative_PNPOx 77 ieGtaelvsd 86
                                       +G+ e v++
  gi|344209994|ref|YP_004786170.1| 88 ANGRLEDVER 97
                                      8999888876 PP



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:                      208  (0.0116013); 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: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.41
# Mc/sec: 1058.45
//
Query:       gi|344209995|ref|YP_004786171.1|  [L=861]
Description: cation-transporting ATPase [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-56  189.9   2.7    2.8e-56  189.9   2.7    2.6  2  E1-E2_ATPase     E1-E2 ATPase
    1.4e-38  132.4   1.1    1.4e-38  132.4   1.1    1.9  2  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    4.1e-28   99.1   3.9    8.7e-28   98.0   3.9    1.6  1  Hydrolase        haloacid dehalogenase-like hydrolase
    4.8e-21   74.6   0.0    3.2e-20   72.0   0.0    2.1  2  Cation_ATPase    Cation transport ATPase (P-type)
    1.5e-13   50.2   0.0      3e-13   49.2   0.0    1.5  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    1.1e-05   25.3   0.8    9.2e-05   22.3   0.6    2.0  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
     0.0007   20.0   0.3     0.0014   19.1   0.3    1.5  1  HAD              haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.16   4.1e+02     106     136 ..      45      75 ..      38      92 .. 0.70
   2 !  189.9   2.7   1.1e-59   2.8e-56       1     180 [.     111     303 ..     111     304 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.16
                                       ----HHHHHHHHHHHHHHHHHHHHHHHHHHS CS
                      E1-E2_ATPase 106 skktplqkkldklgkvlvpvvlliallvfli 136
                                       sk+tpl   + ++ + l++v +++a+l + +
  gi|344209995|ref|YP_004786171.1|  45 SKRTPLDIAIAQFDSALIWVLVAAAILSVWA 75 
                                       7788888888888888888877777766544 PP

  == domain 2  score: 189.9 bits;  conditional E-value: 1.1e-59
                                       SSS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-............ CS
                      E1-E2_ATPase   1 kllpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek............ 64 
                                       +l++pta+v+rdg+ +e+da elvpGD+++l++gd+vpaDgr+++  + evde+aLTGEs+pv+k            
  gi|344209995|ref|YP_004786171.1| 111 ELTAPTATVRRDGQSVEVDATELVPGDVIELESGDVVPADGRLIDCRSlEVDEAALTGESTPVSKgtdpvdadapla 187
                                       5899************************************************************************* PP

                                       G-TTEE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTT CS
                      E1-E2_ATPase  65 ekgdmvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllg 141
                                       e++ mv+ Gt+v++g+  av tatg+dte+g iar+++ +++++tplq +ld lg++l + v+++a+lv+ +++++g
  gi|344209995|ref|YP_004786171.1| 188 EREPMVYKGTNVTRGSGAAVLTATGMDTEVGAIARQLAGTEETDTPLQTELDTLGRTLGVGVMVLAALVVPLLVFRG 264
                                       ***************************************************************************** PP

                                       SSTTHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 142 kslaeallralallvaaiPcaLplavplalalgarrlak 180
                                        +l++a l a++l+vaa+P++Lp++v+l+lalg+r++a+
  gi|344209995|ref|YP_004786171.1| 265 TELVQAALTAISLAVAAVPEGLPAVVTLTLALGVRKMAD 303
                                       *************************************97 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 ?   -3.8   0.2       3.5     9e+03     122     145 ..     659     683 ..     656     687 .. 0.80
   2 !  132.4   1.1   5.4e-42   1.4e-38       2     175 ..     690     850 ..     689     861 .] 0.89

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.5
                   Cation_ATPase_C 122 lfsnkllllaillsl.llqvlivyv 145
                                       +f n + +++ lls+ +  v+iv++
  gi|344209995|ref|YP_004786171.1| 659 IFDNVWKFVGYLLSAnVAEVAIVFI 683
                                       7889999999999988888888887 PP

  == domain 2  score: 132.4 bits;  conditional E-value: 5.4e-42
                   Cation_ATPase_C   2 lplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfgi 78 
                                       l+l a+q+LwinL+tD+lpalaL+ +p+++d+m+rpPr+++  +++  ml  i++ g++++ v l ++++tl   g+
  gi|344209995|ref|YP_004786171.1| 690 LVLPAVQLLWINLLTDGLPALALGADPKSDDVMQRPPRDPDRGIVDHDMLALIGGTGVISTTVMLGLLLVTLA--GA 764
                                       67899*******************************************************************9..55 PP

                   Cation_ATPase_C  79 sekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgta 155
                                        + +      ya+tm+F+ +v++++ +++++r +re       + sn++l  a+ +s+llq++++y+p ln +fgt+
  gi|344209995|ref|YP_004786171.1| 765 PAVT-----PYAMTMIFTGFVFLEFEKLYVIRWLRE-----TPTLSNRWLASAVGGSILLQLAVLYTP-LNVYFGTV 830
                                       5554.....47**********************444.....7778**********************9.******** PP

                   Cation_ATPase_C 156 plsleewlialllalvvllv 175
                                       pl+l++w ++ ++ l+ l++
  gi|344209995|ref|YP_004786171.1| 831 PLGLTDWGLIGGVLLLALPL 850
                                       *******7775555555544 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.0   3.9   3.4e-31   8.7e-28       1     210 []     320     620 ..     320     620 .. 0.82

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 3.4e-31
                                       SSEEEEESBTTTBCHHHHHHHHHHHH........................CHHHHHHHHHHHHCHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx........................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa........................alalaaaletgsehpigkalvaaakar 53 
                                       +++++ Dk+GTLt+g++sv +++v                          +l+  a le g   p  +a+v aa++ 
  gi|344209995|ref|YP_004786171.1| 320 VDVICTDKTGTLTEGRMSVSRIWVNDavvdsdeiegeplpdrvatvlragTLCSDATLEAG--DPTEQAIVMAADES 394
                                       689*********************9999999999999998888777777777777777766..99999999999999 PP

                                       HHHHHHHHHETTTE...................HHHHTHHHHHHHH...........HCHHHHHHHHHHHHHHCHHH CS
                                       xxxxxxxxxxxxxx...................xxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  54 sgaltgfatfigrg...................ayaigkpewltal...........dippdlgaaigsaqsqgrtv 100
                                       ++++++ ++   r                    +y +g pe + +            d +pd  ++i +  ++  + 
  gi|344209995|ref|YP_004786171.1| 395 GIDVERLREEHPRTaeipfsserkwmgtvhddtVYVKGAPEVILSKcsrvltdtgpaDLTPDRAEQIREQVGAFADD 471
                                       99998888855555777777777899999999999999999777776766666566666666666666666666666 PP

                                       HHH...........................TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHH CS
                                       xxx...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 101 all...........................qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaer 150
                                       al                            +    +++ + dp   ++e+a+a+a+  +ag+ v ++tgdn +ta +
  gi|344209995|ref|YP_004786171.1| 472 ALRvlavaytedtsvverndttgeaddvsaDLIFAGLVGMIDP--AREEVADAIAATERAGVAVKMVTGDNVRTAAA 546
                                       6669999****************98766665566666666699..******************************** PP

                                       HHHHTT..GGGE.SEEEEHHCES...........STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxx..xxxx.xxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 151 aanqlG..ddyf.daviasdiet...........vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       +a +lG  ++ +  + ++ + e+           +a  spe+kv++++ Lq++++ vam GDgvnDa+al++A+
  gi|344209995|ref|YP_004786171.1| 547 IAGELGlgQRVMeGHDVEECSEEalrdrvetvdvFARTSPEHKVRILQALQANGHTVAMTGDGVNDAPALKNAD 620
                                       *******9555545555555555666665569999999**********************************98 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.0   1.2e-23   3.2e-20      19      90 ..     378     443 ..     343     444 .. 0.93
   2 ?   -0.6   0.0      0.57   1.5e+03      10      45 ..     455     490 ..     450     506 .. 0.84

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 1.2e-23
                     Cation_ATPase  19 llGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiilkrCth 90 
                                         G++tE+A++ +a++ g+d+e+lree+++ +eipF+s+rK+m++v+  +      +yvKGApe+il++C++
  gi|344209995|ref|YP_004786171.1| 378 EAGDPTEQAIVMAADESGIDVERLREEHPRTAEIPFSSERKWMGTVHDDT------VYVKGAPEVILSKCSR 443
                                       68**********************************************85......**************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.57
                     Cation_ATPase  10 ensekdevkllGnktEsALlvlaeklgldteelree 45 
                                       ++  ++ ++ +G   + AL vla + ++dt+ ++++
  gi|344209995|ref|YP_004786171.1| 455 PDRAEQIREQVGAFADDALRVLAVAYTEDTSVVERN 490
                                       566677788999999**********99999988776 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   1.2e-16     3e-13       2      69 .]       6      72 ..       5      72 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.2e-16
                   Cation_ATPase_N  2 halsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                      h+++  +v+  L+ ++++GL+ +ea+ r+ ++G+Ne+++  k++ + + + qf + l+++L++aa++s
  gi|344209995|ref|YP_004786171.1|  6 HTQPTADVISGLD-SESDGLSASEARTRRDRHGENEITQGSKRTPLDIAIAQFDSALIWVLVAAAILS 72
                                      999*********9.9***************************************************98 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.13   3.4e+02      18      58 ..     517     557 ..     513     569 .. 0.90
   2 !   22.3   0.6   3.6e-08   9.2e-05     195     251 ..     592     649 ..     589     653 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                       Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                       e+ ++ai+  + +g+ v   TG ++r++  ++ elgl + v
  gi|344209995|ref|YP_004786171.1| 517 EEVADAIAATERAGVAVKMVTGDNVRTAAAIAGELGLGQRV 557
                                       67899******************************987654 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 3.6e-08
                                       HHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEET.TS-HHHHHHSSEEE--GGGTHH CS
                       Hydrolase_3 195 lakelnisleeviafGDgeNDieMLeaaglgvAmg.naseevkkaAdyvtksnnedGV 251
                                       +++ l+ +   v+  GDg ND + L+ a++gvAmg  +++ +k+a+d +  + n   +
  gi|344209995|ref|YP_004786171.1| 592 ILQALQANGHTVAMTGDGVNDAPALKNADIGVAMGvRGTDVAKQASDVILLDDNYATI 649
                                       789999****************************956788888888887776665555 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.3   5.4e-07    0.0014      83     188 .]     514     617 ..     454     617 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.4e-07
                               HAD  83 pklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd........rltgelglegkpvrg 151
                                       p+  ++++ +++aa  +aG+ v +v+g + + + +++ elg    l+ ++++ +         l  +++  + + r 
  gi|344209995|ref|YP_004786171.1| 514 PA--REEVADAIAATERAGVAVKMVTGDNVRTAAAIAGELG----LGQRVMEGHdveecseeALRDRVETVDVFART 584
                                       43..4799*********************************....66666655555555588777775555555555 PP

                               HAD 152 ..egkvaalrewlaaegegidleevvay.GDspsDlpllr 188
                                         e+kv+ l++ l+a+g+      +va  GD+++D p+l+
  gi|344209995|ref|YP_004786171.1| 585 spEHKVRILQA-LQANGH------TVAMtGDGVNDAPALK 617
                                       77777888888.666665......67777*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (861 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 6110.21
//
Query:       gi|344209996|ref|YP_004786172.1|  [L=474]
Description: NADH oxidase [Haloarcula hispanica ATCC 33960]
Scores for 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-58  197.0   1.8    5.1e-58  196.6   1.8    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      1e-26   93.3   1.9    6.5e-21   74.7   0.4    3.4  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    6.3e-13   48.9   0.0    3.4e-12   46.6   0.0    2.2  2  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    1.6e-08   34.2   0.0     0.0035   16.6   0.0    2.4  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.1e-06   28.8   0.9      0.012   15.9   0.0    3.5  4  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    6.6e-06   25.5  10.8       0.22   10.6   0.4    4.1  4  FAD_binding_2   FAD binding domain
    2.3e-05   23.3   0.1       0.17   10.6   0.0    3.6  4  HI0933_like     HI0933-like protein
    0.00015   21.2   0.2        1.8    7.8   0.0    3.0  3  Amino_oxidase   Flavin containing amine oxidoreductase
  ------ inclusion threshold ------
      0.025   13.8   0.1       0.35   10.1   0.0    2.6  3  Thi4            Thi4 family
      0.028   13.5   0.3       0.48    9.4   0.0    2.5  3  Lycopene_cycl   Lycopene cyclase protein
      0.086   12.4   0.1        6.1    6.4   0.0    2.3  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.099   12.5   0.0       0.19   11.6   0.0    1.5  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD 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 !  196.6   1.8   3.4e-61   5.1e-58       3     280 ..       5     311 ..       3     332 .. 0.93

  Alignments for each domain:
  == domain 1  score: 196.6 bits;  conditional E-value: 3.4e-61
                                       EEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH....HHHHCHHHHCCCCHCC CS
                                       xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   3 vvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias....evvkklnqgielllge 73 
                                        vviGg +AGl+aa +  +     +v+++e+++ + + +c  ++ + g+ e+   ++    e+    + gi+l+ ++
  gi|344209996|ref|YP_004786172.1|   5 FVVIGGDAAGLSAASKFTReaPDRDVIVFEKGEWVSYAHCGTPYYVKGTVERLTDLLslspEQ--ASERGIDLRRNH 79 
                                       59**************9997559*****************************99888998744..567789999999 PP

                                       TCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T........ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                       Pyr_redox_2  74 evvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp........ 142
                                       evv++d+++++v++ +  +g++++  y+ l++AtG+++ + +ipG++ ++ + ++ ldsa a++ +l +        
  gi|344209996|ref|YP_004786172.1|  80 EVVGVDTDAETVTVAQ--DGETFSQPYGDLLVATGAHAVTGPIPGAELDGAFTMHGLDSAAAVRAALSEpgdstvdt 154
                                       9*************64..599*************************88888999*********************** PP

                                       ...................SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEE CS
                                       ...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 ...................krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvev 200
                                                          +r+++vGgGy+GvE+A a++   +e++l ++  +ll++++++++++++++l+++Gv++
  gi|344209996|ref|YP_004786172.1| 155 sieyvdtalvekyadweppERVAIVGGGYVGVEMAEAFRAHDVETHLFQRSGHLLPPFGEAVGERVADHLREQGVTL 231
                                       ***************************************************************************** PP

                                       EESCEEEEEEETTE.EEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-G CS
                                       xxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 201 klgtsvkeidgnge.kle.vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiG 275
                                       +l+t v+e+ g++  ++  vv++dg++ d+dl +v++G++p+t+l+ e+  +el   g+i vde+++t+v+g+ya+G
  gi|344209996|ref|YP_004786172.1| 232 HLNTAVEELVGDEGgRVAsVVHGDGNT-DVDLALVGIGIKPNTALV-EDTPVELGASGAIAVDEYGATSVDGVYAAG 306
                                       **************96666*******7.******************.****************************** PP

                                       GGCTE CS
                                       xxxxx RF
                       Pyr_redox_2 276 Dvagg 280
                                       D+a++
  gi|344209996|ref|YP_004786172.1| 307 DCAED 311
                                       ***33 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0     0.002       2.9       3      34 ..       6      39 ..       4      46 .. 0.85
   2 !    7.6   0.0    0.0036       5.4      48      78 ..      66      93 ..      54      97 .. 0.84
   3 !   74.7   0.4   4.3e-24   6.5e-21       1      77 [.     175     252 ..     175     256 .. 0.97

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.002
                                      EEECSSHHHHHHHHHHHHTT..SEEEEEESSSSS CS
                         Pyr_redox  3 vvvGgGyiglElAgalaelg..kkVtvversdkl 34
                                      vv+Gg+  gl +A+ +++ +   +V v+e ++++
  gi|344209996|ref|YP_004786172.1|  6 VVIGGDAAGLSAASKFTREApdRDVIVFEKGEWV 39
                                      9***************998866788888877765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0036
                                      HHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox 48 eklekngievllntkveeiegsedgvesvkl 78
                                      e+ +++gi+++ n++v+ +++++++   v++
  gi|344209996|ref|YP_004786172.1| 66 EQASERGIDLRRNHEVVGVDTDAET---VTV 93
                                      78899***************99997...444 PP

  == domain 3  score: 74.7 bits;  conditional E-value: 4.3e-24
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.vesv 76 
                                       +v++vGgGy+g+E+A+a++++  ++++++rs +ll+ ++e+++++++++l+++g++++lnt vee++g+e g v sv
  gi|344209996|ref|YP_004786172.1| 175 RVAIVGGGYVGVEMAEAFRAHDVETHLFQRSGHLLPPFGEAVGERVADHLREQGVTLHLNTAVEELVGDEGGrVASV 251
                                       79**********************************************************************99999 PP

                                       E CS
                         Pyr_redox  77 k 77 
                                       +
  gi|344209996|ref|YP_004786172.1| 252 V 252
                                       7 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 ?   -1.7   0.1       2.3   3.4e+03      62      78 ..     178     194 ..     174     220 .. 0.54
   2 !   46.6   0.0   2.3e-15   3.4e-12       4     104 ..     355     457 ..     352     461 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.3
                                       EEEEEEECTTHHHHHHH CS
                     Pyr_redox_dim  62 vlGahivGpgageliqe 78 
                                       ++G   vG +++e++ +
  gi|344209996|ref|YP_004786172.1| 178 IVGGGYVGVEMAEAFRA 194
                                       55666666655554433 PP

  == domain 2  score: 46.6 bits;  conditional E-value: 2.3e-15
                                       EEESSSEEEEEES-H.HHHHHHHSGEEEEEEEEECGHHHCHTTH.TEEEEEEEEETTTTBEEEEEEEC.TTHHHHHH CS
                     Pyr_redox_dim   4 vvftdpevasvGlte.eeAkaagieikvgkfpfkangralayae.tkgfvKlvadaktgkvlGahivG.pgageliq 77 
                                       v+ +d+e + vGl   e+A aag  ++ ++ +++a +r+ +y+  +++ v lvad+++g++lG  ivG ++a+ +i+
  gi|344209996|ref|YP_004786172.1| 355 VKAFDLECGRVGLLDhEQASAAG--FDPVSKTVTAGSRSGYYPGgDDTDVTLVADRESGRLLGGAIVGaDRAAIRID 429
                                       67799*******86549******..88888888899999999999***********************677888*** PP

                                       HHHHHHHTTSBHH.HHHTSBSSSSSTGG CS
                     Pyr_redox_dim  78 elavaikagltve.dladtihihPtlse 104
                                        la+ai+a++t++ +   +++++P++s 
  gi|344209996|ref|YP_004786172.1| 430 TLATAIEADMTIDeLERLDLAYAPPFSP 457
                                       *************66788********94 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   6.8e-06      0.01     165     272 ..       3     118 ..       1     131 [. 0.83
   2 !   16.6   0.0   2.3e-06    0.0035     155     305 .]     166     306 ..     150     306 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.8e-06
                       Pyr_redox_3 165 qkvvViGgknSavDaAlelvrk..gaeVtvvtrgseiekeesdpsyslkpdienrleelvke......ekikvlfna 233
                                       + +vViGg   +  aA ++ r+  + +V v+ +g+ ++  +    y +k ++e   + l+ +      + i++  n+
  gi|344209996|ref|YP_004786172.1|   3 DPFVVIGGDAAGLSAASKFTREapDRDVIVFEKGEWVSYAHCGTPYYVKGTVERLTDLLSLSpeqaseRGIDLRRNH 79 
                                       568*****************998899********999999999999999988754443333365776544******* PP

                       Pyr_redox_3 234 evkeikekeeeykvktedgkkvevkddvvlatGykpdls 272
                                       ev  ++++ e+++v ++ ++  + + d ++atG +  + 
  gi|344209996|ref|YP_004786172.1|  80 EVVGVDTDAETVTVAQDGETFSQPYGDLLVATGAHAVTG 118
                                       ********999999888777777799*******997665 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.3e-06
                       Pyr_redox_3 155 kvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlf 231
                                       k+ +++    ++v+++Gg+  +v++A  + +++ e +++ r+ ++      +       + +r+++ ++e+ ++++ 
  gi|344209996|ref|YP_004786172.1| 166 KYADWE--PPERVAIVGGGYVGVEMAEAFRAHDVETHLFQRSGHLLPP---FGEA----VGERVADHLREQGVTLHL 233
                                       555664..3589*****************************9866654...4444....4555555555566***** PP

                       Pyr_redox_3 232 naevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                       n+ v+e+  +e     +  +g+  +  d  ++ +G kp++ ++++  +el ++g ++++e    t v+g++ aG
  gi|344209996|ref|YP_004786172.1| 234 NTAVEELVGDEGGRVASVVHGDGNTDVDLALVGIGIKPNTALVEDTPVELGASGAIAVDEY-GATSVDGVYAAG 306
                                       ******998777766666666665555666667**********************999875.5688*****999 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   7.8e-06     0.012       1      29 [.       7      37 ..       7      47 .. 0.92
   2 ?   -3.4   0.0       8.3   1.2e+04      37      54 ..     101     118 ..      97     125 .. 0.72
   3 !    9.3   0.0   0.00086       1.3       1      30 [.     178     207 ..     178     210 .. 0.95
   4 ?   -1.5   0.0         2     3e+03      30      46 ..     243     261 ..     217     264 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.8e-06
                                      EE--SHHHHHHHHHHHCC..TEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllekrd 29
                                      ++G+ ++Gl+aA+  +++  ++dv ++ek++
  gi|344209996|ref|YP_004786172.1|  7 VIGGDAAGLSAASKFTREapDRDVIVFEKGE 37
                                      8*************999889*********86 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.3
                                       EECETTCEECTS---EEE CS
                     NAD_binding_8  37 syevpgvrvdygahifhg 54 
                                       s  +++  v +gah+++g
  gi|344209996|ref|YP_004786172.1| 101 SQPYGDLLVATGAHAVTG 118
                                       445566788899999877 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00086
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                       IvG+G  G  +A + + ++++ +l++++ +
  gi|344209996|ref|YP_004786172.1| 178 IVGGGYVGVEMAEAFRAHDVETHLFQRSGH 207
                                       9*************************9877 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 2
                                       SSSGGG-EECE.TT.CEEC CS
                     NAD_binding_8  30 rlGGraasyev.pg.vrvd 46 
                                       + GGr+as+ + +g   vd
  gi|344209996|ref|YP_004786172.1| 243 DEGGRVASVVHgDGnTDVD 261
                                       5599999999953345555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00031      0.46       3      32 ..       6      37 ..       5      44 .. 0.84
   2 ?    4.4   0.2     0.011        17     148     239 ..      65     145 ..      42     156 .. 0.84
   3 !   10.6   0.4   0.00015      0.22     100     180 ..     185     254 ..     146     273 .. 0.75
   4 !    5.8   0.4     0.004         6     369     407 ..     282     313 ..     266     317 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00031
                                      EEE--SHHHHHHHHHHHH.TTT.-EEEEESSS CS
                     FAD_binding_2  3 iViGsGlAGLaAAleaae.aGl.kvavvekeq 32
                                      +ViG+ +AGL+AA + ++ a   +v+v ek++
  gi|344209996|ref|YP_004786172.1|  6 VVIGGDAAGLSAASKFTReAPDrDVIVFEKGE 37
                                      8*************998854445*******97 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.011
                                       HHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGTT CS
                     FAD_binding_2 148 vesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnapa 224
                                        e+a ++g+d++ ++e++ +   d ++ +++v+  ++g+++      +++atg+         +g+++ ae  +a +
  gi|344209996|ref|YP_004786172.1|  65 PEQASERGIDLRRNHEVVGV---DTDAETVTVA--QDGETFSQPYGDLLVATGAHAV------TGPIPGAELDGAFT 130
                                       5789999*************...8899999999..9999986555588888888775......89999999999999 PP

                                       -S-HHHHHHHCTTSS CS
                     FAD_binding_2 225 vtGdglalalragaa 239
                                         G + a+a+ra+++
  gi|344209996|ref|YP_004786172.1| 131 MHGLDSAAAVRAALS 145
                                       999999999999886 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00015
                                       T----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTT.EEE CS
                     FAD_binding_2 100 gvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarkagvdfqerteadeLivedg.rvt 175
                                       gv + +    ++++ ++ ++  + r++h  + +       g a+ +r+++++r+ gv+++ +t+++eL+ ++g rv 
  gi|344209996|ref|YP_004786172.1| 185 GVEMAE----AFRAHDVETHLFQ-RSGH-LLPP------FGEAVGERVADHLREQGVTLHLNTAVEELVGDEGgRVA 249
                                       344444....8888888888998.9999.8887......9****************************997665888 PP

                                       EEEEE CS
                     FAD_binding_2 176 Gavve 180
                                        +v  
  gi|344209996|ref|YP_004786172.1| 250 SVVHG 254
                                       77755 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.004
                                       EEEES-EEEBETTSBESTTEEESSBTEEE-STCEESSSS CS
                     FAD_binding_2 369 qhytmgGvetdengrvldadgqpipGLYAaGevaaggvh 407
                                        ++  g +++de g +       ++G YAaG +a  + h
  gi|344209996|ref|YP_004786172.1| 282 ELGASGAIAVDEYGAT------SVDGVYAAGDCA-EDTH 313
                                       5666677889999999......************.7776 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00011      0.17       4      33 ..       6      37 ..       3      40 .. 0.89
   2 !    5.8   0.0    0.0032       4.8     116     167 ..      65     116 ..      54     132 .. 0.78
   3 ?    0.5   0.0      0.12   1.9e+02       2      32 ..     175     205 ..     174     212 .. 0.88
   4 ?    1.8   0.0     0.053        79      85     146 ..     191     251 ..     182     270 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                      EEE--SHHHHHHHHHH..HHTT--EEEE-SSS CS
                       HI0933_like  4 iviGgGaAGlmaAisa..akrgkrVlllekak 33
                                      +viGg aAGl aA +   ++ +++V+++ek++
  gi|344209996|ref|YP_004786172.1|  6 VVIGGDAAGLSAASKFtrEAPDRDVIVFEKGE 37
                                      9*************99767889*******986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0032
                                       HHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEE..SEEEE----SS- CS
                       HI0933_like 116 lkelkeagvklrletevksvekeedgkfrvktkseeelea..dklvlAtGGlSi 167
                                        ++++e+g++lr ++ev +v+++++  ++v+  ++e+++     l++AtG  ++
  gi|344209996|ref|YP_004786172.1|  65 PEQASERGIDLRRNHEVVGVDTDAET-VTVAQ-DGETFSQpyGDLLVATGAHAV 116
                                       578899**************887666.77777.666666412579*****9876 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.12
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVllleka 32 
                                       +v+++GgG  G+  A++ ++++ ++ l+ + 
  gi|344209996|ref|YP_004786172.1| 175 RVAIVGGGYVGVEMAEAFRAHDVETHLFQRS 205
                                       699*************999999999998776 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.053
                                       HHHHTT--EEE.-STTEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEE CS
                       HI0933_like  85 lveelgvelke.edsgrlFpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvk 146
                                        +++++ve++  ++sg l p     e + +    +l+e+gv+l+l+t+v+++  +e+g++   
  gi|344209996|ref|YP_004786172.1| 191 AFRAHDVETHLfQRSGHLLPPF--GEAVGERVADHLREQGVTLHLNTAVEELVGDEGGRVASV 251
                                       5666666666435667777766..56677888899****************988887765544 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.044        66       2      23 ..      13      36 ..      12      39 .. 0.90
   2 !    7.4   0.0    0.0015       2.3     216     259 ..      68     111 ..      48     128 .. 0.80
   3 !    7.8   0.0    0.0012       1.8     210     264 ..     218     271 ..     161     306 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.044
                                      HHHHHHHHHHHTT..EEEEEEESS CS
                     Amino_oxidase  2 aGLaaArqLlsaG..fdVtvlEar 23
                                      aGL+aA++ ++    +dV+v+E  
  gi|344209996|ref|YP_004786172.1| 13 AGLSAASKFTREApdRDVIVFEKG 36
                                      9********99999********76 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0015
                                       HHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEE...EESEEEE- CS
                     Amino_oxidase 216 laeelrgldirlntrVkeikregdgvtvtledgevv...eaDaVvvT 259
                                          ++rg d+r n++V  +++++++vtv  +dge++    +D  v T
  gi|344209996|ref|YP_004786172.1|  68 A--SERGIDLRRNHEVVGVDTDAETVTVA-QDGETFsqpYGDLLVAT 111
                                       3..4699*********************5.89999988655555555 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEE.EESEEEE-S-HHH CS
                     Amino_oxidase 210 sqlpealaeelrgldirlntrVkeikregdgvtvtledgevv.eaDaVvvTvplgv 264
                                       ++++++l e   g++++lnt V e+  +++g    +++g+ + ++D  +v + +  
  gi|344209996|ref|YP_004786172.1| 218 ERVADHLRE--QGVTLHLNTAVEELVGDEGGRVASVVHGDGNtDVDLALVGIGIKP 271
                                       455555555..***************977775555555555558998888776655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00023      0.35      20      49 ..       5      35 ..       1      45 [. 0.91
   2 ?   -1.6   0.0      0.88   1.3e+03      20      48 ..     176     203 ..     163     207 .. 0.78
   3 ?   -0.1   0.0      0.31   4.6e+02     108     137 ..     224     253 ..     214     273 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00023
                                      EEEE--SHHHHHHHHHHHHC.TTS-EEEEES CS
                              Thi4 20 vvivGaGssGLtaayylakk.pdlkvailer 49
                                       v++G+ ++GL+aa  ++++ pd  v+++e+
  gi|344209996|ref|YP_004786172.1|  5 FVVIGGDAAGLSAASKFTREaPDRDVIVFEK 35
                                      5899***************99********97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.88
                                       EEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                              Thi4  20 vvivGaGssGLtaayylakkpdlkvaile 48 
                                       v+ivG+G  G+  a  +  + d+++ ++ 
  gi|344209996|ref|YP_004786172.1| 176 VAIVGGGYVGVEMAEAFRAH-DVETHLFQ 203
                                       899****9999999887666.66666665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.31
                                       HTSTTEEEEESEEEEEEEEETBTEEEEEEE CS
                              Thi4 108 lqlanvkllnavaveDlivregegvaGvvi 137
                                       l   +v l   +ave+l+  eg +va vv 
  gi|344209996|ref|YP_004786172.1| 224 LREQGVTLHLNTAVEELVGDEGGRVASVVH 253
                                       55678999999***************9995 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00032      0.48       3      38 ..       6      41 ..       4      64 .. 0.88
   2 ?    0.9   0.0      0.13   1.9e+02       2      18 ..     176     192 ..     175     210 .. 0.81
   3 ?   -1.6   0.1      0.71   1.1e+03      91     140 ..     218     268 ..     214     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00032
                     Lycopene_cycl  3 vviGaGpAglslAarlteakpglkvvlieaspsllf 38
                                      vviG+ +Agls A + t+++p+  v++ e ++ + +
  gi|344209996|ref|YP_004786172.1|  6 VVIGGDAAGLSAASKFTREAPDRDVIVFEKGEWVSY 41
                                      8***************************99987755 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.13
                     Lycopene_cycl   2 vvviGaGpAglslAarl 18 
                                       v+++G+G  g+ +A+  
  gi|344209996|ref|YP_004786172.1| 176 VAIVGGGYVGVEMAEAF 192
                                       89************987 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.71
                     Lycopene_cycl  91 eellerlvengvkll.eakvesveeeeageslvvleggrkirarlvvdarg 140
                                       e+++ +l e+gv+l+ +  ve+ + +e g++  v++g+ + +  l++++ g
  gi|344209996|ref|YP_004786172.1| 218 ERVADHLREQGVTLHlNTAVEELVGDEGGRVASVVHGDGNTDVDLALVGIG 268
                                       677788888888875277899999999999998888888777777777766 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 ?    3.7   0.0     0.027        41      22      43 ..      77      98 ..      73     107 .. 0.87
   2 ?    6.4   0.0    0.0041       6.1       2      20 ..     175     193 ..     174     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.027
                                      CTSEEEEE-S-HHHHHHHCTTS CS
                    UDPG_MGDP_dh_N 22 ighevigvDideekvdklnsgk 43
                                      + hev+gvD d+e+v   + g+
  gi|344209996|ref|YP_004786172.1| 77 RNHEVVGVDTDAETVTVAQDGE 98
                                      579************9877765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0041
                                       EEEEE--STTHHHHHHHHH CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavla 20 
                                       +++++G GYvG+ +a ++ 
  gi|344209996|ref|YP_004786172.1| 175 RVAIVGGGYVGVEMAEAFR 193
                                       89*********99887765 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 ?   11.6   0.0   0.00013      0.19       2      42 ..     176     216 ..     175     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekaleki 42 
                                       va++G G +G ++a++f ++++e++l+++s + l    e++
  gi|344209996|ref|YP_004786172.1| 176 VAIVGGGYVGVEMAEAFRAHDVETHLFQRSGHLLPPFGEAV 216
                                       9*************************999877665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); 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 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2894.29
//
Query:       gi|344209997|ref|YP_004786173.1|  [L=261]
Description: hypothetical protein HAH_5055 [Haloarcula hispanica ATCC 33960]
Scores for 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-18   65.1  37.9    8.9e-18   64.8  37.9    1.0  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 !   64.8  37.9   4.9e-22   8.9e-18       3     236 .]      15     253 ..      13     253 .. 0.75

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 4.9e-22
                              TauE   3 lagllaGfvagllGiGggliavPlLllllppavavatsllavvatslsgalahrrr.gnvdwrlllllllgsliGal 78 
                                       +++l+aG+ +gl+G+G++++ + +L+++++pa+av+  +l ++a ++s +    rr  +   +++ +l++++l+G++
  gi|344209997|ref|YP_004786173.1|  15 AIVLVAGATNGLAGFGFAVVGTMALATVIDPATAVVFMILPILAVNVSLVRDLSRReLRTCSQRFGPLIAAALVGTV 91 
                                       68899**********************88******************9777766653566689************** PP

                              TauE  79 lGallllllpsellkllfgvlllllallmllrkkr......srakgrerrptaillvligglvGllsGllGiG.gGf 148
                                       +G  +l +lp++ l++ +g+l l +++    r         s   ++   +t++++v   g++G+ ++l+G+  +G+
  gi|344209997|ref|YP_004786173.1|  92 VGMAVLDRLPEAPLRVGLGLLTLGFVATAQQR--VplpgwvS-VGNSDLGKTPLAMV---GIGGVSGALFGGTnVGV 162
                                       *******************9998877766322..12333331.11223333333333...33444444444321334 PP

                              TauE 149 llvpllllllglplkkavatslllilvislagalgyalagavdwpllll....llpgallGallGarlarrlsertl 221
                                        lv++l + + l+  ++v++ +l++l  s++ +++  ++g +   +++     ++++a++G+ +G+rl++ +s+r+ 
  gi|344209997|ref|YP_004786173.1| 163 QLVAYLRS-FDLSHSVFVGVVALVFLGLSVTRVAFAGVFGLYPNAVVAGtsvlAAVPAVAGVAVGKRLRTAVSDRVR 238
                                       44444443.5777777***************99998555554433333247669999*****************999 PP

                              TauE 222 rrlfallllvlgvkl 236
                                       r+++++ll ++g +l
  gi|344209997|ref|YP_004786173.1| 239 RAAVLALLSIIGFRL 253
                                       999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); 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:                         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 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1611.39
//
Query:       gi|344209998|ref|YP_004786174.1|  [L=118]
Description: hypothetical protein HAH_5056 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   37.3   0.0    3.3e-09   37.1   0.0    1.0  1  DrsE      DsrE/DsrF-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 !   37.1   0.0   1.9e-13   3.3e-09       8     117 .]      11     118 .]       3     118 .] 0.81

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1.9e-13
                                       -S-TTTBSHHHHHHHHHHHHHTTT...-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEHHHH CS
                              DrsE   8 tggpygseaarealelalaaaalg...hevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvCgqaa 81 
                                        +  + +  +r+a  l  a  +++    +++++f g+G++++ +     + ++++++el++++ke      vC  + 
  gi|344209998|ref|YP_004786174.1|  11 GTEGH-ENLGRLANGLEAATEFAEndeDDLELIFDGAGTQWIPE----LEDEDSDYHELYQTVKED---TAVCDYCS 79 
                                       32333.333777777777777777779*****************....77899************8...59****** PP

                                       HHTT--GGG....E-T-.-EEEE-HHHHHHHHHH-SEEEE- CS
                              DrsE  82 kargldede....dlgv.gvevsglgelaelqnegdrvitf 117
                                        a+g++++     +  v   e  g +++  l+++ + vitf
  gi|344209998|ref|YP_004786174.1|  80 GAFGVEDAVadsgL--VtLDEHDGHPSIRSLVDDDYEVITF 118
                                       ******88776533..259*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 748.44
//
Query:       gi|344209999|ref|YP_004786175.1|  [L=119]
Description: thioredoxin [Haloarcula hispanica ATCC 33960]
Scores for complete 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   94.2   0.0    4.4e-27   94.1   0.0    1.1  1  Thioredoxin    Thioredoxin
    8.8e-11   42.2   0.1    3.9e-09   36.9   0.1    2.1  1  Thioredoxin_2  Thioredoxin-like domain
      8e-07   29.1   0.0    9.8e-07   28.8   0.0    1.1  1  TraF           F plasmid transfer operon protein
    1.1e-05   25.4   0.0    1.7e-05   24.7   0.0    1.3  1  Thioredoxin_3  Thioredoxin domain
    2.3e-05   24.2   0.3    3.8e-05   23.5   0.1    1.5  2  DSBA           DSBA-like thioredoxin domain
    7.1e-05   23.1   0.0       0.44   10.9   0.0    2.2  2  Thioredoxin_8  Thioredoxin-like
    9.4e-05   22.2   0.0    0.00012   21.9   0.0    1.1  1  Thioredoxin_9  Thioredoxin
     0.0011   19.2   0.0     0.0023   18.0   0.0    1.6  1  Thioredoxin_7  Thioredoxin-like
     0.0018   18.2   0.0     0.0031   17.5   0.0    1.4  1  HyaE           Hydrogenase-1 expression protein HyaE
     0.0027   17.1   0.0     0.0033   16.8   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
     0.0032   17.8   0.0     0.0043   17.4   0.0    1.3  1  DUF836         Glutaredoxin-like domain (DUF836)
     0.0056   16.4   0.0      0.013   15.2   0.0    1.6  2  Thioredoxin_5  Thioredoxin
     0.0069   16.6   0.0      0.012   15.9   0.0    1.4  1  Glutaredoxin   Glutaredoxin
  ------ inclusion threshold ------
      0.012   15.3   0.1        1.3    8.7   0.1    2.0  2  Redoxin        Redoxin
      0.013   15.4   0.0       0.55   10.2   0.0    2.0  2  AhpC-TSA       AhpC/TSA family
      0.065   13.4   0.0       0.14   12.3   0.0    1.5  2  Thioredoxin_4  Thioredoxin
       0.17   12.0   0.0       0.23   11.5   0.0    1.2  1  TrbC_Ftype     Type-F conjugative transfer system pilin assem


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 !   94.1   0.0   4.2e-30   4.4e-27       8     102 ..      23     115 ..      16     116 .. 0.92

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 4.2e-30
                                       HHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEE CS
                       Thioredoxin   8 enFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngke 84 
                                       +++ ++v ++++ vl +FyA+wCg+C++l+P++e+la e+    ++akvdvd+n++la+ y+v+g+Ptl+lf +g++
  gi|344209999|ref|YP_004786175.1|  23 TDHLDDVVDKHDVVLTDFYADWCGPCQMLEPTVETLAAETG--ATVAKVDVDANQQLAQSYGVRGVPTLILFADGEQ 97 
                                       5566677777*****************************99..99******************************** PP

                                       EEEEESS-HHHHHHHHHH CS
                       Thioredoxin  85 vkkyegarekeklaaflk 102
                                       v++++g + +e+l+a ++
  gi|344209999|ref|YP_004786175.1|  98 VEEVVGLEGEEALRALIE 115
                                       *********9**999886 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.1   3.7e-12   3.9e-09       4     108 ..      32     113 ..      29     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 3.7e-12
                     Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrg 80 
                                       ++  vl++f++++C+ C+ l+ ++++l             ++  + +++++ ++           n++la++ygvrg
  gi|344209999|ref|YP_004786175.1|  32 KHDVVLTDFYADWCGPCQMLEPTVETL------------AAETGATVAKVDVDA-----------NQQLAQSYGVRG 85 
                                       67889**********************............222233344444444...........4569******** PP

                     Thioredoxin_2  81 tPtiv.fldgkeivarlpGyvpaeeleal 108
                                       +Pt++ f dg+  v++++G+  +e l+al
  gi|344209999|ref|YP_004786175.1|  86 VPTLIlFADGE-QVEEVVGLEGEEALRAL 113
                                       ***66699**9.88899999988888876 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   9.3e-10   9.8e-07     130     205 ..      34      98 ..      26     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 9.3e-10
                              TraF 130 eygLlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqk 205
                                       ++ L  Fy+  c+ c+++ p+++ +a ++g +v  V+vd ++   l++          +gv+ +P+l+l+   +q 
  gi|344209999|ref|YP_004786175.1|  34 DVVLTDFYADWCGPCQMLEPTVETLAAETGATVAKVDVDANQQ--LAQ---------SYGVRGVPTLILFADGEQV 98 
                                       566777***********************************88..777.........************9988655 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.6e-08   1.7e-05      10      75 ..      45     114 ..      40     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.6e-08
                                       STTCHHHHHHHHHHCHCCTCECEEECCTTHHHH.HHCT-SSSSEE..ECTTCEE..EESS---CCHHHHHH CS
                     Thioredoxin_3  10 CakCpklekavkeaaaekgikaevekvtdfeei.ekygVmsvPal..vidgkvv..vsGkvpseeeirkll 75 
                                       C  C+ le  v+ +aae g ++  ++v  ++++ ++ygV+ vP+l  + dg+ v  v+G +  ee +r+l+
  gi|344209999|ref|YP_004786175.1|  45 CGPCQMLEPTVETLAAETGATVAKVDVDANQQLaQSYGVRGVPTLilFADGEQVeeVVG-LEGEEALRALI 114
                                       999*****************************************955568765433778.67777777776 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.6   1.6e+03       5      29 ..      41      63 ..      38      70 .. 0.69
   2 !   23.5   0.1   3.6e-08   3.8e-05     147     191 ..      65     113 ..      54     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                                      EEBTTBHHHHHHHHHHHHHHHHCCT CS
                              DSBA  5 ffDvlCPyCylgkerleklaarspd 29
                                      + D  C+ C + ++ +e laa   +
  gi|344209999|ref|YP_004786175.1| 41 YAD-WCGPCQMLEPTVETLAAET-G 63
                                      444.4888999999888888776.4 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 3.6e-08
                                       HHHHHHHHHHHHHHHHTT-SSSSEEEE..TTC..EEEESSSSHHHHHHH CS
                              DSBA 147 eavkeavrentaaaqslgvtGvPtvvv..dgk..rmvfGadrldtlada 191
                                         +k +v+ n+++aqs+gv+GvPt ++  dg+    v+G +  + l+  
  gi|344209999|ref|YP_004786175.1|  65 TVAKVDVDANQQLAQSYGVRGVPTLILfaDGEqvEEVVGLEGEEALRAL 113
                                       567889*******************999988767788888888887765 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00042      0.44       2      28 ..      34      60 ..      32      71 .. 0.83
   2 !   10.8   0.0   0.00045      0.48      66      90 ..      69      93 ..      62      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00042
                                      SEEEEEE--SSSHHHHHHHHHHHHHHH CS
                     Thioredoxin_8  2 kvvlLyfgaswcppckaftpklkelye 28
                                      +vvl  f+a+wc pc+   p++  l  
  gi|344209999|ref|YP_004786175.1| 34 DVVLTDFYADWCGPCQMLEPTVETLAA 60
                                      78999***********99999987755 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00045
                                      E-TT-HHHHTT-S--TT-SEEEEE- CS
                     Thioredoxin_8 66 fddkkrnklkkkynvkaiPtlvvld 90
                                      +d + +++l++ y+v ++Ptl++  
  gi|344209999|ref|YP_004786175.1| 69 VDVDANQQLAQSYGVRGVPTLILFA 93
                                      4556799***************976 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.1e-07   0.00012      49     110 ..      41      98 ..      30     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.1e-07
                                       --TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT--E CS
                     Thioredoxin_9  49 tedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliildeegee 110
                                        +dwCg +++  P ++ +a ++ + +v  +  d+n++l ++y   g r +Ptli++ ++ ++
  gi|344209999|ref|YP_004786175.1|  41 YADWCGPCQMLEPTVETLAAET-GATVAKVDVDANQQLAQSY---GVRGVPTLILFADGEQV 98 
                                       579*******************.*******************...99*******99766443 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.2e-06    0.0023      20      81 ..      36      92 ..      28      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-06
                                      EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT-.--SSEEEEE CS
                     Thioredoxin_7 20 vlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanilelde.qgvPvvafl 81
                                      vl +f a+wc++Cq le ++++      a+     + +vdv+ +++   + ++ +gvP+++++
  gi|344209999|ref|YP_004786175.1| 36 VLTDFYADWCGPCQMLEPTVETL-----AAETGATVAKVDVDANQQLA-QSYGvRGVPTLILF 92
                                      6779*************999988.....35677777788887777744.44445789999887 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.9e-06    0.0031      63     100 ..      64     102 ..      50     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.9e-06
                                       EEEEE.THHHHHHHHHCCT-TSSSEEEEEETTEEEEEEE CS
                              HyaE  63 aavva.dreqeealaerfgvlktPsllflrdgeylgvla 100
                                       a+v++ d + +++la+ +gv+ +P+l++++dge +  + 
  gi|344209999|ref|YP_004786175.1|  64 ATVAKvDVDANQQLAQSYGVRGVPTLILFADGEQVEEVV 102
                                       4445568999**********************9886655 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.1e-06    0.0033      46     106 ..      45      96 ..      35     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.1e-06
                         OST3_OST6  46 CelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfppkk 106
                                       C +C+ +ep +e++a    ++          akvd+d ++++ q++g++ +P l+lf   +
  gi|344209999|ref|YP_004786175.1|  45 CGPCQMLEPTVETLAAETGAT---------VAKVDVDANQQLAQSYGVRGVPTLILFADGE 96 
                                       999999999999999988888.........69*************************8744 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.1e-06    0.0043       9      49 ..      44      84 ..      37     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.1e-06
                                      T-HHHHHHHHHHHHHCCCTTEEEEEEETTT-CCCHCCCCTT CS
                            DUF836  9 gChlCeqakekLkelkleegleleviDIakdeeleakYgle 49
                                       C+ C+ ++  ++ l+ e g ++ ++D++ +++l + Yg++
  gi|344209999|ref|YP_004786175.1| 44 WCGPCQMLEPTVETLAAETGATVAKVDVDANQQLAQSYGVR 84
                                      5*************************************986 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.41   4.3e+02       7      29 ..      44      66 ..      39      70 .. 0.86
   2 !   15.2   0.0   1.3e-05     0.013     128     177 ..      56     106 ..      48     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.41
                     Thioredoxin_5  7 lcseCweiEpelkklkveygeki 29
                                      +c  C  +Ep +  l  e g  +
  gi|344209999|ref|YP_004786175.1| 44 WCGPCQMLEPTVETLAAETGATV 66
                                      899************99988765 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.3e-05
                     Thioredoxin_5 128 eefkeDlesklakkafqcDlklakemgvtevPtlvffn.eneeeeglkveg 177
                                       e++ +   +++ak   ++ ++la+ +gv+ vPtl++f   ++ ee + +eg
  gi|344209999|ref|YP_004786175.1|  56 ETLAAETGATVAKVDVDANQQLAQSYGVRGVPTLILFAdGEQVEEVVGLEG 106
                                       66666777889999999******************9983444455555555 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.1e-05     0.012       7      54 ..      43      90 ..      35      98 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                                      TSSHHHHHHHHHHHHTTGG....EEEEEGCCSHHHHHHHHHHHTSSSSSEEE CS
                      Glutaredoxin  7 ptCpyCkkakrlLkelgvk....feeidvdkdeeireelkelsgvrtvPqvf 54
                                       +C+ C++   + ++l ++    ++ +dvd++    ++l +  gvr vP++ 
  gi|344209999|ref|YP_004786175.1| 43 DWCGPCQMLEPTVETLAAEtgatVAKVDVDAN----QQLAQSYGVRGVPTLI 90
                                      79****99877776665444433999999999....5555555******986 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0013       1.3      23      58 ..      26      62 ..       4      70 .. 0.79
   2 ?    5.0   0.0     0.018        19      91     127 ..      71      98 ..      67     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0013
                                      HHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHH CS
                           Redoxin 23 lse.fkgkkvvvnfvpgafcPtCsaehpyleklaell 58
                                      l++ + ++ vv++ + + +c++C+   p +e+la++ 
  gi|344209999|ref|YP_004786175.1| 26 LDDvVDKHDVVLTDFYADWCGPCQMLEPTVETLAAET 62
                                      667677888999877777*****98777888887764 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.018
                                       E-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEE CS
                           Redoxin  91 sDgsaaftkalGlrleedaseglrtpryavidedgkv 127
                                       +D+++++++++G+r         + p+++++ +  +v
  gi|344209999|ref|YP_004786175.1|  71 VDANQQLAQSYGVR---------GVPTLILFADGEQV 98 
                                       69**********99.........88888888776655 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00052      0.55      16      55 ..      22      62 ..       3      71 .. 0.66
   2 ?    3.4   0.0     0.064        67      88     113 ..      71      90 ..      67     101 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00052
                                      EEEECHHH..TTSEEEEEEESTST-CCHHHHHHHHHHCHHHC CS
                          AhpC-TSA 16 etvslsdy..kgkpvvlffypkdwcpvCttelpalaklyeef 55
                                      +t +l+d+  k ++v+  fy+  wc +C+   p  + l+ e 
  gi|344209999|ref|YP_004786175.1| 22 GTDHLDDVvdKHDVVLTDFYAD-WCGPCQMLEPTVETLAAET 62
                                      5667899963334555556666.*****98888777777665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.064
                                       E-TTSHHHHHTT-EETTTTECSCEEE CS
                          AhpC-TSA  88 sDeegkvakaygvlkeekglalratf 113
                                        D ++++a++ygv        +++ +
  gi|344209999|ref|YP_004786175.1|  71 VDANQQLAQSYGVR------GVPTLI 90 
                                       699**********9......555554 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.9     2e+03      15      41 ..      35      61 ..      31      68 .. 0.80
   2 ?   12.3   0.0   0.00013      0.14     123     158 ..      68     105 ..      54     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.9
                                      EEEEEEE-TT-HHHHHHHHHHHHHHHH CS
                     Thioredoxin_4 15 vtvieyedlrCphCakfeeevekllee 41
                                      v+++ +    C  C  +e +ve l +e
  gi|344209999|ref|YP_004786175.1| 35 VVLTDFYADWCGPCQMLEPTVETLAAE 61
                                      677778888899999999999988766 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHHHT--SS-EEEE..TTEEE-TT--HH CS
                     Thioredoxin_4 123 dalveaeskeakkagiestPtfii..ngekveepqtye 158
                                       + +v a+++ a+  g+ ++Pt+i+  +ge+vee    e
  gi|344209999|ref|YP_004786175.1|  68 KVDVDANQQLAQSYGVRGVPTLILfaDGEQVEEVVGLE 105
                                       5678999***************9999****98766544 PP

>> TrbC_Ftype  Type-F conjugative transfer system pilin assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00022      0.23      37      85 ..      51      99 ..      45     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                        TrbC_Ftype 37 lketvkalaklleeemekasvqidPllFrqfkitaVPalvlaeedkase 85
                                      l++tv++la+ + ++ +k++v+ + +l + ++++ VP+l+l ++ ++ e
  gi|344209999|ref|YP_004786175.1| 51 LEPTVETLAAETGATVAKVDVDANQQLAQSYGVRGVPTLILFADGEQVE 99
                                      67899999999999999999999*****************998876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); 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 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 707.12
//
Query:       gi|344210000|ref|YP_004786176.1|  [L=134]
Description: hypothetical protein HAH_5058 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   65.1   0.0    5.2e-18   64.7   0.0    1.2  1  TrmB             Sugar-specific transcriptional regulator Trm
    1.5e-07   31.1   0.1      3e-07   30.1   0.1    1.5  1  HTH_IclR         IclR helix-turn-helix domain
    1.8e-06   27.8   0.0    3.7e-06   26.8   0.0    1.5  1  MarR             MarR family
    4.6e-06   26.5   0.0      8e-06   25.7   0.0    1.3  1  HTH_11           HTH domain
    8.6e-05   22.9   0.0    0.00011   22.6   0.0    1.2  1  Penicillinase_R  Penicillinase repressor
    0.00012   21.9   0.0    0.00038   20.3   0.1    1.7  2  MarR_2           MarR family
     0.0003   20.8   0.2    0.00067   19.7   0.1    1.6  1  HTH_20           Helix-turn-helix domain
     0.0009   18.8   0.0     0.0016   18.0   0.0    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0011   18.8   0.0     0.0022   17.9   0.0    1.4  1  RuvB_C           RuvB C-terminal winged helix domain
     0.0028   17.2   0.1     0.0046   16.5   0.1    1.3  1  UMPH-1           Pyrimidine 5'-nucleotidase (UMPH-1)
  ------ inclusion threshold ------
      0.016   15.2   0.0       0.03   14.3   0.0    1.6  1  HTH_29           Winged helix-turn helix
      0.016   14.8   0.1      0.037   13.7   0.1    1.6  1  GntR             Bacterial regulatory proteins, gntR family
      0.018   15.1   0.0      0.041   14.0   0.0    1.6  1  HTH_28           Helix-turn-helix domain
       0.03   14.0   0.1       0.11   12.2   0.0    1.8  2  DUF4423          Domain of unknown function (DUF4423)
      0.037   14.0   0.1      0.073   13.1   0.1    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.047   13.3   0.4        1.2    8.7   0.0    2.4  2  SMC_ScpB         Segregation and condensation complex subunit
      0.047   13.5   0.0       0.12   12.2   0.0    1.7  2  HTH_23           Homeodomain-like domain
      0.078   13.3   0.0       0.17   12.3   0.0    1.6  2  Rrf2             Transcriptional regulator
      0.085   12.9   0.0       0.24   11.5   0.0    1.7  2  Dimerisation     Dimerisation domain
       0.15   12.6   0.0       0.24   11.9   0.0    1.4  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 !   64.7   0.0   5.8e-21   5.2e-18       1      67 [.      19      93 ..      19      94 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 5.8e-21
                                      HH.HCHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEEEE--H CS
                              TrmB  1 Lq.klGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......pklYravdp 67
                                      L+  +GL+e + +++ aL+ +++p+t+de+ae+++++rs++Y+++++L++ G++e+ + +      +++Y+++dp
  gi|344210000|ref|YP_004786176.1| 19 LEcFHGLKELDKECFRALVeAEEPLTVDELAEAVDRERSTAYRAVQRLLQTGFIEKDQINydqggyYHVYSPTDP 93
                                      67689**************99********************************************999*****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 !   30.1   0.1   3.4e-10     3e-07      10      51 ..      34      75 ..      33      76 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 3.4e-10
                                      CT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 10 dalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      +al ea ++lt+ elA++ +  +St++R +q L + G++e+d
  gi|344210000|ref|YP_004786176.1| 34 RALVEAEEPLTVDELAEAVDRERSTAYRAVQRLLQTGFIEKD 75
                                      68889***********************************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   4.2e-09   3.7e-06      13      55 ..      38      80 ..      35      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 4.2e-09
                                      HHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTS CS
                              MarR 13 yeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeD 55
                                      + ++pl+v eLa+++  ++st+ r++ rL + G+ie+ +   D
  gi|344210000|ref|YP_004786176.1| 38 EAEEPLTVDELAEAVDRERSTAYRAVQRLLQTGFIEKDQINYD 80
                                      56799*******************************9887655 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   8.9e-09     8e-06       9      54 ..      36      84 ..      31      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 8.9e-09
                            HTH_11  9 LleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....vpIesepgrGY 54
                                      L ea++p++ +eLAe  ++ r+t +r +++L  +g    ++I  ++g GY
  gi|344210000|ref|YP_004786176.1| 36 LVEAEEPLTVDELAEAVDRERSTAYRAVQRLLQTGfiekDQINYDQG-GY 84
                                      7799*******************************888888888888.88 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.2e-07   0.00011       6     102 ..      30     125 ..      25     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.2e-07
                                       SHHHHHHHHHS-.EEHHHHHHT--GGG---HHHHHHHHHH.HHHTTS-EEEEETTEEEEE----XXXXXXXXXXXXX CS
                   Penicillinase_R   6 aevmeilwekge.atvkevveeleeekelaysTVktllrr.LvkKgllsrekegrafiYsplvseeeavasavkqll 80 
                                       +e  ++l e++e +tv+e+ e++++e+++ay  V+ ll+    +K+ ++ ++ g  ++Ysp+      +a +++ +l
  gi|344210000|ref|YP_004786176.1|  30 KECFRALVEAEEpLTVDELAEAVDRERSTAYRAVQRLLQTgFIEKDQINYDQGGYYHVYSPTDPS--QIADEMQRML 104
                                       5666777776666*************************744********************8554..5778999999 PP

                                       XXXXXXXXXXXXXXXXXXXXXX CS
                   Penicillinase_R  81 dklfegsvkelvaafveeekls 102
                                       +  ++ ++ +l+++f ++ + s
  gi|344210000|ref|YP_004786176.1| 105 NDWYA-KMGQLIQEFENKYEQS 125
                                       99996.9999999997765544 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   4.3e-07   0.00038      16      53 ..      39      74 ..      32      76 .. 0.87
   2 ?   -2.0   0.0       3.7   3.3e+03      24      32 ..      93     101 ..      88     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.3e-07
                                      CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 16 rrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      ++++  ltv ela++ + ++s++ r+++rL + G++e+
  gi|344210000|ref|YP_004786176.1| 39 AEEP--LTVDELAEAVDRERSTAYRAVQRLLQTGFIEK 74
                                      4445..******************************96 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.7
                                       HHHHHHHHT CS
                            MarR_2  24 vgelarrlg 32 
                                       ++++a++++
  gi|344210000|ref|YP_004786176.1|  93 PSQIADEMQ 101
                                       789999887 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   7.5e-07   0.00067      16      56 ..      33      74 ..      25      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.5e-07
                                      HHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 16 lraL.araegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      +raL   +e+lt+ elae++d  ++t+++ ++ L + g++e 
  gi|344210000|ref|YP_004786176.1| 33 FRALvEAEEPLTVDELAEAVDRERSTAYRAVQRLLQTGFIEK 74
                                      56677899********************************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 !   18.0   0.0   1.7e-06    0.0016      13      48 .]      38      73 ..      34      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.7e-06
                            HTH_24 13 qknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +++  ++  eLAe+++  +st  r ++rL + G+I+
  gi|344210000|ref|YP_004786176.1| 38 EAEEPLTVDELAEAVDRERSTAYRAVQRLLQTGFIE 73
                                      567789****************************96 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 !   17.9   0.0   2.4e-06    0.0022       3      57 ..      24      75 ..      22      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.4e-06
                                      ---HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEE CS
                            RuvB_C  3 GLdeldikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIert 57
                                      GL+eld+++ ++l e   ++p+ ++ la++++ e++t    +   Ll++g+Ie++
  gi|344210000|ref|YP_004786176.1| 24 GLKELDKECFRALVE--AEEPLTVDELAEAVDRERSTAYRAVQR-LLQTGFIEKD 75
                                      9*************9..69********************99986.89******97 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 !   16.5   0.1   5.1e-06    0.0046      18      81 ..      65     126 ..      53     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.1e-06
                            UMPH-1  18 gildesklineevkkklkeLyhkYrpieidpsltieekvkymveWwskshaLlieqklkkeeia 81 
                                        +l+ + + +++++ ++   yh Y p   dps   +e  +++ +W++k ++L+ e++ k+e+ +
  gi|344210000|ref|YP_004786176.1|  65 RLLQTGFIEKDQINYDQGGYYHVYSP--TDPSQIADEMQRMLNDWYAKMGQLIQEFENKYEQSE 126
                                       5677777788899999999*******..59*************************998887755 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.4e-05      0.03      10      40 ..      38      70 ..      30      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.4e-05
                            HTH_29 10 eGvs..tvsqiAkllglsrrtvyrwlkrfeegG 40
                                      e++   tv ++A++++  r+t yr++ r  ++G
  gi|344210000|ref|YP_004786176.1| 38 EAEEplTVDELAEAVDRERSTAYRAVQRLLQTG 70
                                      4444479*********************99998 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.1e-05     0.037      18      55 ..      37      73 ..      26      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.1e-05
                                      S-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR 18 lrpGdkLPsereLaaefgVsrttvReALrrLeaeglve 55
                                      ++++++L ++ eLa++ +  r+t  +A +rL + g +e
  gi|344210000|ref|YP_004786176.1| 37 VEAEEPL-TVDELAEAVDRERSTAYRAVQRLLQTGFIE 73
                                      6899***.***********************9999886 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   4.6e-05     0.041      14      41 ..      44      71 ..      33      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-05
                            HTH_28 14 svreaArelgisrrtvyrWikryeegGi 41
                                      +v+e+A+++   r+t yr ++r+ + G+
  gi|344210000|ref|YP_004786176.1| 44 TVDELAEAVDRERSTAYRAVQRLLQTGF 71
                                      99***********************996 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    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      27      80 ..      34      83 ..      31     107 .. 0.80
   2 ?   -0.4   0.0      0.89     8e+02      64      82 ..     110     128 ..      92     133 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                           DUF4423 27 rellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqte 80
                                      r+l+++++   +++ela+++      + + +a+++Ll++g+++kd+  +y q  
  gi|344210000|ref|YP_004786176.1| 34 RALVEAEEP-LTVDELAEAVD--RERSTAYRAVQRLLQTGFIEKDQI-NYDQGG 83
                                      788888888.9999*******..99999******************9.998865 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.89
                           DUF4423  64 klgllkkdedgkyrqteks 82 
                                       k+g+l ++ ++ky+q+e+s
  gi|344210000|ref|YP_004786176.1| 110 KMGQLIQEFENKYEQSESS 128
                                       4555555555577777665 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 ?   13.1   0.1   8.1e-05     0.073      19      55 ..      40      76 ..      15      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.1e-05
                                      EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                         HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglisrgr 55
                                      e plt +elA+ +   r+t  r+ ++L + g i++ +
  gi|344210000|ref|YP_004786176.1| 40 EEPLTVDELAEAVDRERSTAYRAVQRLLQTGFIEKDQ 76
                                      569******************************9754 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 ?    8.7   0.0    0.0014       1.2      11     128 ..      40      76 ..      35      93 .. 0.50
   2 ?    2.6   0.0       0.1        94      17      46 ..      98     127 ..      85     133 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0014
                          SMC_ScpB  11 geplsleeLakilelskeeveealeeLkeeyeeedrglelvevaggyrlvtkpelaevvkklvkekkktrLsqaale 87 
                                       +epl+++eLa++++ ++++                                                          
  gi|344210000|ref|YP_004786176.1|  40 EEPLTVDELAEAVDRERST---------------------------------------------------------- 58 
                                       4444444444444444444.......................................................... PP

                          SMC_ScpB  88 tLaiIaykqpvtraeieeiRGvnsdsvvrtLlerglieekg 128
                                                              ++++v++Ll++g+ie+ +
  gi|344210000|ref|YP_004786176.1|  59 -----------------------AYRAVQRLLQTGFIEKDQ 76 
                                       .......................555666666666666555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.1
                          SMC_ScpB  17 eeLakilels.keeveealeeLkeeyeeedr 46 
                                       +e++++l+ +  +++ ++++e++++ye++++
  gi|344210000|ref|YP_004786176.1|  98 DEMQRMLN-DwYAKMGQLIQEFENKYEQSES 127
                                       45555554.2588899999999999977765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014      0.12      18      46 ..      43      71 ..      33      73 .. 0.84
   2 ?   -2.7   0.0       6.5   5.8e+03      21      27 ..      94     100 ..      93     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                            HTH_23 18 lsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      l+v e A++ ++ r+T yr ++r  + G+
  gi|344210000|ref|YP_004786176.1| 43 LTVDELAEAVDRERSTAYRAVQRLLQTGF 71
                                      6899*******************987874 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.5
                            HTH_23  21 reIAreL 27 
                                       ++IA+e+
  gi|344210000|ref|YP_004786176.1|  94 SQIADEM 100
                                       7999987 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       9.8   8.8e+03      40      60 ..       4      24 ..       2      26 .. 0.72
   2 ?   12.3   0.0   0.00019      0.17      19      56 ..      36      73 ..      32      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 9.8
                                      HHHHHHHHHHHHTTSEEEETT CS
                              Rrf2 40 sylekilakLrkaglvksvrG 60
                                      s+ e++ + ++ +gl++   G
  gi|344210000|ref|YP_004786176.1|  4 SMSEQLRRDMQCEGLLECFHG 24
                                      566777788888888887666 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00019
                                      HSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 19 keeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      + e eep++++e+ae ++ ++s + + +++L + g+++
  gi|344210000|ref|YP_004786176.1| 36 LVEAEEPLTVDELAEAVDRERSTAYRAVQRLLQTGFIE 73
                                      5577889*****************************98 PP

>> Dimerisation  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00027      0.24      14      47 ..      35      67 ..      31      69 .. 0.90
   2 ?   -2.2   0.0       4.8   4.3e+03      26      47 ..      94     104 ..      88     105 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                      Dimerisation 14 iiakaggkplspsEiaskLptknpeapvlldRlL 47
                                      ++++a  +pl++ E+a+++   +++a   ++RlL
  gi|344210000|ref|YP_004786176.1| 35 ALVEAE-EPLTVDELAEAVDRERSTAYRAVQRLL 67
                                      677886.9*************************9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.8
                      Dimerisation  26 sEiaskLptknpeapvlldRlL 47 
                                       s+ia           +  +R+L
  gi|344210000|ref|YP_004786176.1|  94 SQIA-----------DEMQRML 104
                                       4444...........3345555 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   0.0   0.00027      0.24      16      60 ..      40      84 ..      31      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrek 60
                                      +++ +  +l++++++e s++  ++ +L   G++e+ +   d++  
  gi|344210000|ref|YP_004786176.1| 40 EEPLTVDELAEAVDRERSTAYRAVQRLLQTGFIEKDQINYDQGGY 84
                                      57778899*************************998877777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 839.19
//
Query:       gi|344210001|ref|YP_004786177.1|  [L=153]
Description: hypothetical protein HAH_5059 [Haloarcula hispanica ATCC 33960]
Scores for 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-07   31.8   9.0      1e-07   31.8   9.0    2.1  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 !    4.9   3.4    0.0009        16      57      70 ..      13      26 ..       3      29 .. 0.82
   2 !   31.8   9.0   5.8e-12     1e-07      16     104 ..      41     136 ..      26     150 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0009
                       Sulf_transp 57 livGGllFGvGMal 70
                                      ++vGGl+FG+G+a 
  gi|344210001|ref|YP_004786177.1| 13 ILVGGLIFGFGLAY 26
                                      69*********986 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 5.8e-12
                       Sulf_transp  16 ekdgrllralllaiavaavgfqlla.aaglidlpksaf.....pv.vglivGGllFGvGMalaGgCasgtlyrvGeG 85 
                                       ++d+ l+ +++   av+ v+f l    +g ++l++ +f     ++   ++vGG +FGvG  l+G C++ +++ +G G
  gi|344210001|ref|YP_004786177.1|  41 FEDFGLVFVMFGGAAVTGVAFVLGPrLLGRAPLTGDTFerrlkSFdRNVLVGGAIFGVGWGLSGICPGAAYASLGIG 117
                                       4444444333333333333333332244555665554422222224789**************************** PP

                       Sulf_transp  86 slralitllffilgavall 104
                                       +++ l++l+++ lga++ +
  gi|344210001|ref|YP_004786177.1| 118 NVTILWALAGMFLGAYLQG 136
                                       ***************9744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); 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:                         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 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 983.05
//
Query:       gi|344210002|ref|YP_004786178.1|  [L=163]
Description: hypothetical protein HAH_5060 [Haloarcula hispanica ATCC 33960]
Scores for 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-14   52.0  11.9    1.1e-13   51.5  11.9    1.2  1  Sulf_transp   Sulphur transport
  ------ inclusion threshold ------
      0.026   14.3   0.7      0.026   14.3   0.7    1.9  2  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr
        1.8    9.3   8.0       0.63   10.8   3.3    2.4  2  DUF4282       Domain of unknown function (DUF4282)


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 !   51.5  11.9   1.8e-17   1.1e-13     176     306 ..      19     147 ..       4     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1.8e-17
                       Sulf_transp 176 pwslvlgavllgllavlawllsaktgrsfglgftvpgakilqylvl...gtskf..lnwgvvlvlGiilGaflaall 247
                                         ++++g++l+gl  v+++l    tg+  + g ++ ++++l+y+     +++ +   +w vv+ lGiilGa++ a++
  gi|344210002|ref|YP_004786178.1|  19 ISRYAVGGLLVGLGTVVIYLG---TGI--SAGASTFLESTLSYVSDrsrFQQYVssRDWRVVFTLGIILGAAVYAVV 90 
                                       455778999999888887763...344..445566788888887521112222222589****************** PP

                       Sulf_transp 248 sgefkleapkarellaallGGllMGfGarlAgGCniGaglsgiaslslsgwlalvflll 306
                                        +  +++     + ++ llGG+++G+G+r++ GC++G+g+ g+ s s +++  ++++l+
  gi|344210002|ref|YP_004786178.1|  91 YQGGAWT--TDVQPWRLLLGGVFVGIGTRVGKGCTSGHGVCGVGSASKTSIAGVLTFLA 147
                                       *****96..789999*****************************999999987766665 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 ?   14.3   0.7   4.3e-06     0.026      60     144 ..      14      97 ..       8     104 .. 0.80
   2 ?   -1.2   0.8      0.26   1.5e+03      42      53 ..     140     151 ..     123     161 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.3e-06
                      Trp_oprn_chp  60 lavrglgrrvvgvllalagagaavaalslltdpadaaraaaaaatgvasaaaaveltawpvlalaggvllllagvll 136
                                       l  +g+ r++vg ll+ +g ++++ +  + +++++  +++ + +++ ++ ++ v+  +w v+  +g +l   a+v +
  gi|344210002|ref|YP_004786178.1|  14 LFPNGISRYAVGGLLVGLGTVVIYLGTGISAGASTFLESTLSYVSDRSRFQQYVSSRDWRVVFTLGIIL--GAAVYA 88 
                                       5668999*************************9999999998888888888888888899999998554..455555 PP

                      Trp_oprn_chp 137 ll.rarswp 144
                                       ++ ++++w+
  gi|344210002|ref|YP_004786178.1|  89 VVyQGGAWT 97 
                                       540456665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.26
                      Trp_oprn_chp  42 apaltalAlvll 53 
                                       a++lt lA++++
  gi|344210002|ref|YP_004786178.1| 140 AGVLTFLAVAII 151
                                       222222222222 PP

>> DUF4282  Domain of unknown function (DUF4282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.43   2.6e+03      20      32 ..      25      37 ..      14      57 .. 0.55
   2 ?   10.8   3.3   0.00011      0.63       3      40 ..      62     126 ..      61     161 .. 0.61

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.43
                           DUF4282 20 givlialvllsli 32
                                      g +l++l+ +++ 
  gi|344210002|ref|YP_004786178.1| 25 GGLLVGLGTVVIY 37
                                      3333333333222 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
                           DUF4282   3 sFnrfitpkllkvlYilgivlialvllslivgafaal...........................s 40 
                                       +F++++++   +v++ lgi+l a v  ++  g+ ++                             
  gi|344210002|ref|YP_004786178.1|  62 RFQQYVSSRDWRVVFTLGIILGAAVYAVVYQGGAWTTdvqpwrlllggvfvgigtrvgkgctsgH 126
                                       7*******************988777755555555553444444444444444555566666662 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1021.03
//
Query:       gi|344210003|ref|YP_004786179.1|  [L=416]
Description: beta-lactamase domain-containing protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   4.5    2.4e-12   47.3   4.5    1.4  1  Lactamase_B    Metallo-beta-lactamase superfamily
    3.8e-10   40.2   0.0    6.8e-10   39.4   0.0    1.4  1  Rhodanese      Rhodanese-like domain
    0.00066   19.3   0.1     0.0013   18.3   0.1    1.5  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 !   47.3   4.5   4.1e-16   2.4e-12       9     196 ..     149     328 ..     142     329 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 4.1e-16
                                       EEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCH CS
                       Lactamase_B   9 yliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfme 85 
                                       yl+ +dg++ +iD++       +     ++   + ++++ + TH H+DHi+g+++l  +    v+ +a++++  ++ 
  gi|344210003|ref|YP_004786179.1| 149 YLLYDDGEAAIIDPLRAFTDRYLD----DAAELGVELKYALDTHIHADHISGVRDLDAEGVEGVIPEAAVDRGVTYA 221
                                       9999**************999975....6************************************************ PP

                                       HHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE.TTCCEEEECTTTSSHHCCCCC CS
                       Lactamase_B  86 eaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey.gggkvlftGDallagetgrid 161
                                       +++++++  +       +++ d  +  +dg+++ +++  +    ++gh+ g  +y  +g++l tGD l++++ +r d
  gi|344210003|ref|YP_004786179.1| 222 AEQGSTGPAS-----QARQDTDDLTTAEDGDTFQVGDATIETVSTPGHTTGMTSYlVDGSLLATGDGLFIESVARPD 293
                                       **99999976.....78888888888888888888888888888888888887777********************* PP

                                       C...TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE.S CS
                       Lactamase_B 162 l..tlrgaevrdpsdaekyldsllklaglkaevlvp.g 196
                                       l     ga+   + ++e++ +++l   +l++ +l+  +
  gi|344210003|ref|YP_004786179.1| 294 LeeGDEGAPEAARMLYESLQERVL---TLPDGTLIGgA 328
                                       977444444444444444443333...77777777655 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   1.1e-13   6.8e-10       2     106 ..      21     120 ..      20     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.1e-13
                         Rhodanese   2 akelkellekgkva.llDvRppeeYekghI....pgAvnvskdtlsrakkseapllelpeellelgidnkktvvvyc 73 
                                       ++ lk+++++g+ + llD+R + +Y++++I      ++n+     +++++ e++ + ++ +     i ++++v v+c
  gi|344210003|ref|YP_004786179.1|  21 PESLKDRIDAGEDVtLLDARMQSDYDEWRIdgenVTSLNI-----PYFEFLEDDIDSDVLAQ----IPDDREVTVLC 88 
                                       789*****7766557***************4433334444.....55555555555555555....556******** PP

                         Rhodanese  74 dgggraaaaaallkklGyknvsvldGGfkawke 106
                                       ++gg ++ +a +l ++G ++v +l+ G+++w++
  gi|344210003|ref|YP_004786179.1|  89 AKGGASEYVAGTLAEHG-YDVNHLEDGMNGWAS 120
                                       *****9999999999**.8************85 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 !   18.3   0.1   2.2e-07    0.0013      30     113 ..     180     264 ..     158     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.2e-07
                                       SEEEEE-SS--HHHHGGGGCCCC.C--EEEE.EEEEHHHHHHCCTTCGHHHCHTT.TTEEEEEE-TTSEEEECSTTE CS
                     Lactamase_B_2  30 pidaVllthaHyDHlaglltlre.lrpkklp.lyapkgvlavleanfvylaleee.pavnvheldwgesfelgdggl 103
                                       +++  l th H+DH+ g+ +l + + +  +p   +++gv    e+++   a++   ++ ++++ + g++f++gd+  
  gi|344210003|ref|YP_004786179.1| 180 ELKYALDTHIHADHISGVRDLDAeGVEGVIPeAAVDRGVTYAAEQGSTGPASQARqDTDDLTTAEDGDTFQVGDAT- 255
                                       5677788****************7555447735589999999988877666666678999*************765. PP

                                       EEEEEEE-EE CS
                     Lactamase_B_2 104 eitatparhk 113
                                        i+++  ++ 
  gi|344210003|ref|YP_004786179.1| 256 -IETVSTPGH 264
                                       .665555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2490.45
//
Query:       gi|344210004|ref|YP_004786180.1|  [L=81]
Description: SirA family protein [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-21   76.1   0.0    1.6e-21   75.9   0.0    1.0  1  TusA      Sulfurtransferase TusA
  ------ inclusion threshold ------
      0.029   14.2   0.1      0.057   13.3   0.0    1.5  2  DUF2249   Uncharacterized conserved protein (DUF2249)


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 !   75.9   0.0   1.8e-25   1.6e-21       1      70 []       9      79 ..       9      79 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 1.8e-25
                                      EEEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHH.HHTEEEEEEE-GCC-EEEEEEE CS
                              TusA  1 ielDlrGlvCPePllklkkalekleegevlevladdpaatediprfak.klghelveveeedgeyrivirk 70
                                      ++lD++G +CP+P++k+k a + l+eg+vlevla+dp+++ di  +a   +g elv++ee d++y+ ++rk
  gi|344210004|ref|YP_004786180.1|  9 ETLDVKGASCPMPVVKTKSATDDLAEGDVLEVLATDPGSMSDIDGWAAgTEGVELVDQEEGDDVYKHYVRK 79
                                      58********************************************8725677****************98 PP

>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    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       1      33 [.      10      42 ..      10      45 .. 0.95
   2 ?   -2.3   0.0      0.46   4.1e+03      57      68 ..      66      77 ..      57      79 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.3e-06
                           DUF2249  1 tlDvRelppperhaaIfeafeaLapGetlelvn 33
                                      tlDv + + p +  ++ +a ++La+G++le+++
  gi|344210004|ref|YP_004786180.1| 10 TLDVKGASCPMPVVKTKSATDDLAEGDVLEVLA 42
                                      79****************************987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.46
                           DUF2249 57 lergpgewrvli 68
                                      +e+g+++++  +
  gi|344210004|ref|YP_004786180.1| 66 QEEGDDVYKHYV 77
                                      567777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 587.10
//
Query:       gi|344210005|ref|YP_004786181.1|  [L=190]
Description: hypothetical protein HAH_5063 [Haloarcula hispanica ATCC 33960]
Scores for 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-54  181.9   0.7    8.7e-54  181.6   0.7    1.1  1  DrsE_2        DsrE/DsrF/DrsH-like family
    4.7e-07   30.2   0.0    2.1e-06   28.1   0.0    1.9  1  DrsE          DsrE/DsrF-like family
  ------ inclusion threshold ------
       0.04   13.3   0.0      0.053   13.0   0.0    1.2  1  aGPT-Pplase1  alpha-glutamyl/putrescinyl thymine pyrophosphor


Domain annotation for each model (and alignments):
>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.6   0.7   1.5e-57   8.7e-54       2     153 .]      39     189 ..      38     189 .. 0.97

  Alignments for each domain:
  == domain 1  score: 181.6 bits;  conditional E-value: 1.5e-57
                                       T-EEEEEE----H.HHHHHHHHHHHHHHTT-EEEEEE-GGGGGGGB-GGG---TT--HHHHHHHHHS-SS--SSS-G CS
                            DrsE_2   2 kkklaiifskgtldkalaalilAsgAaalglevtiFftFwGLnilrkeekkkvkkkslekmamkmvtrksklskmnm 78 
                                       +kk++ii++kgtld+a+++lilAs+Aaa+g+evt+F+tFwGL il++e++k++k +s+++++m+m+++    + + m
  gi|344210005|ref|YP_004786181.1|  39 TKKMSIIATKGTLDMAYPPLILASTAAAFGYEVTVFHTFWGLDILHEERSKNLKLSSVGNPNMPMPNA--VAAIPGM 113
                                       79**************************************************************9875..578899* PP

                                       GGHHHHHHHHHHHHCT---HHHHHHHHHHTT-EEEEEHHHHHHHT--GGGB-TT-.EEE-HHHHHHHHHC-SEEEE CS
                            DrsE_2  79 agigtkmmkkvmkekgvasleeLleaakeagvklvaCqmtmdlmglkkeelidgv.eiagaatylkeaeeadvnLf 153
                                       ++++tkmm+k + ++++a++eeLle++ ++gv+++aCqmt+dlm++++ +++dgv + +gaat l+++++ad++L+
  gi|344210005|ref|YP_004786181.1| 114 DRVTTKMMEKRIANNDTATIEELLETSLDMGVEFQACQMTIDLMDYDEADFYDGVtTGVGAATALQDMADADIQLL 189
                                       *******************************************************999****************96 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   3.6e-10   2.1e-06       1     108 [.      40     182 ..      40     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.6e-10
                                       -EEEEEE-S-TTTBSHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS............................. CS
                              DrsE   1 kkvfilvtggpygseaarealelalaaaalghevsvffygdGvllllk............................. 48 
                                       kk  i+ t+g  + ++a+ +l la  aaa+g+ev vf++  G  +l++                             
  gi|344210005|ref|YP_004786181.1|  40 KKMSIIATKG--TLDMAYPPLILASTAAAFGYEVTVFHTFWGLDILHEersknlklssvgnpnmpmpnavaaipgmd 114
                                       5677888876..88999************************************************************ PP

                                       .......---TGGGTS---GGGGGGCGGGT-EEEEEHHHHHHTT--GGGE-..T--EEEE-HHHHHHHH CS
                              DrsE  49 .......gqtanpadeknlaellkalkeygvklyvCgqaakargldededl..gvgvevsglgelaelq 108
                                              ++  + +d   + ell++  ++gv++ +C+++ + + +de++ +  gv+  v+++++l +++
  gi|344210005|ref|YP_004786181.1| 115 rvttkmmEKRIANNDTATIEELLETSLDMGVEFQACQMTIDLMDYDEAD-FydGVTTGVGAATALQDMA 182
                                       ****99866677778888999*************************886.4255777777777776654 PP

>> aGPT-Pplase1  alpha-glutamyl/putrescinyl thymine pyrophosphorylase clade 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.8e-06     0.053     151     216 ..     119     182 ..      84     187 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.8e-06
                      aGPT-Pplase1 151 eklpekllkakslkevyellrkipglG.pFlayqllldlnysellnfsendfvvaGpGarsglkklf 216
                                       + + +++++ ++ +++ ell++   +G +F a+q+++dl   ++ +f   d v+ G+Ga   l+ + 
  gi|344210005|ref|YP_004786181.1| 119 KMMEKRIAN-NDTATIEELLETSLDMGvEFQACQMTIDLMDYDEADFY--DGVTTGVGAATALQDMA 182
                                       333344444.5566788999985555538************9999999..669*********99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1214.03
//
Query:       gi|344210006|ref|YP_004786182.1|  [L=208]
Description: hypothetical protein HAH_5064 [Haloarcula hispanica ATCC 33960]
Scores for 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   58.0   0.3    1.5e-15   56.8   0.3    1.7  1  DUF1641   Protein of unknown function (DUF1641)


Domain annotation for each model (and alignments):
>> DUF1641  Protein of unknown function (DUF1641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.3   8.2e-20   1.5e-15       2      39 .]     163     200 ..     162     200 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 8.2e-20
                           DUF1641   2 gleepkpvGlfgLlraLrDPDVqrGLGfllalLKalGk 39 
                                       ++e+++pvG+ gLlr LrDPDVq+GLG+llal+ a+G+
  gi|344210006|ref|YP_004786182.1| 163 EREPAEPVGPVGLLRGLRDPDVQYGLGYLLALAGAVGR 200
                                       799**********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1442.33
//
Query:       gi|344210007|ref|YP_004786183.1|  [L=381]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Haloarcula hispanica ATCC 33960]
Scores for complete 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    1.1e-21   77.4   0.0    1.8  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      0.002   18.1   0.2       0.24   11.4   0.0    2.6  3  NAD_binding_9  FAD-NAD(P)-binding
     0.0076   15.8   0.0       0.02   14.4   0.0    1.6  1  Pribosyltran   Phosphoribosyl transferase domain
     0.0095   16.5   0.1        3.9    8.1   0.1    2.4  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 !   77.4   0.0   2.3e-25   1.1e-21       2     294 .]       4     307 ..       3     307 .. 0.79

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 2.3e-25
                                       SEEEE--SHHHHHHHHHHHH........HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHH.CCC CS
                                       xxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq........agakvtlvelegtclnggcllskallgvaedaeiasevvkklnqg.iel 69 
                                       +vv++GgG +G+ +a +la           +++tl++++  +++  ++l ++  g +e+a+ ++  +++l  + ++l
  gi|344210007|ref|YP_004786183.1|   4 HVVIVGGGTGGTVLANDLADrldvelaaDDVRITLINDGPDHVYKPVWL-YVPFGQREPADGRRP-LDELVDDaVDL 78 
                                       79******************9**999877*******9999999996666.777777888877773.45666666999 PP

                                       CHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                       Pyr_redox_2  70 llgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.... 142
                                       + +  v++id++++++  +    g    ++yd+lvlAtGs+     ipG+a+++++  +++ s  al+++ll     
  gi|344210007|ref|YP_004786183.1|  79 RID-RVTAIDTEAQRLRFN----GTAPAVDYDYLVLATGSTLEPERIPGLADGGHDYYSESGS-TALRDELLGfteg 149
                                       999.9*************5....66679***********988888*****9999999555555.5788888889996 PP

                                       .SEEEEES-SHHHHHHHHHH..........HHHT-..EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEE CS
                                       .xxxxxxxxxxxxxxxxxxx..........xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 .krivvvGgGyiGvElAaal..........aklgk..evtlveardrllraldkelsaaleealekeGvevklgtsv 206
                                          + v+G+         ++          +      +v + +  ++     ++ ++++++  + ++G+ev +  ++
  gi|344210007|ref|YP_004786183.1| 150 hLVLSVIGSPHMCPAAPLEFvfmaddwlreRG--LrdDVDITYTYPIQRVHGNPHIAEWARPIMDERGIEVETFFNA 224
                                       55568999665543333334334454454433..25545555555544333569*********************** PP

                                       EEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS.BES.STTEEE-GGGCTEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxxx RF
                       Pyr_redox_2 207 keidgngeklevvledgeeidadlvvvavGvrpstelleeklglelderggivvdefl.rtn.vpgiyaiGDvaggk 281
                                       +e+d+++e  +++  +g+ +d+dl+v+        +l+ e++gl   ++g++ vd++  + +  +++ya+GD a ++
  gi|344210007|ref|YP_004786183.1| 225 EEVDPDSE--TLTSMEGTDLDYDLLVTIP-PHGGIDLI-EEAGL--GDDGWVDVDKHTlEAEaAENVYALGDTA-DT 294
                                       *******9..9999*********999765.55555666.9***9..67*******99875555***********.99 PP

                                       CSS--HHHHHHHH CS
                                       xxxxxxxxxxxxx RF
                       Pyr_redox_2 282 ggpelaqaAvqqG 294
                                       g+p+   +A+ q+
  gi|344210007|ref|YP_004786183.1| 295 GVPNAGSVAHYQA 307
                                       9999999999886 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 !   11.4   0.0   5.2e-05      0.24       1      34 [.       6      42 ..       6      52 .. 0.86
   2 ?    4.0   0.0      0.01        46     117     155 ..      76     113 ..      66     114 .. 0.74
   3 ?   -3.0   0.0       1.4   6.3e+03      70      79 ..     174     183 ..     148     214 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.2e-05
                     NAD_binding_9  1 aivGaGprGlavlerLlara...kkkspleitlfdps 34
                                      +ivG+G  G+ +++ L++r      +++++itl+++ 
  gi|344210007|ref|YP_004786183.1|  6 VIVGGGTGGTVLANDLADRLdveLAADDVRITLINDG 42
                                      7*******************99888899*****9874 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.01
                     NAD_binding_9 117 vevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       v++  ++v++++++a++ ++   +   +++d++vLA+G 
  gi|344210007|ref|YP_004786183.1|  76 VDLRIDRVTAIDTEAQRLRF-NGTAPAVDYDYLVLATGS 113
                                       56667899999988887544.3444568**********6 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.4
                     NAD_binding_9  70 aeWlrergal 79 
                                       ++Wlrerg  
  gi|344210007|ref|YP_004786183.1| 174 DDWLRERGLR 183
                                       4677777642 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   4.4e-06      0.02      30      61 ..       4      35 ..       2      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.4e-06
                                      GEEEEEEETTTHHHHHHHHHHSTT-EE-EEEE CS
                      Pribosyltran 30 pdvvvgiargGvpfakiladeLevplayvrkv 61
                                       +v+vg  +gG ++a++lad+L+v+la  +++
  gi|344210007|ref|YP_004786183.1|  4 HVVIVGGGTGGTVLANDLADRLDVELAADDVR 35
                                      689**********************9865554 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1   0.00086       3.9       1      20 [.       4      23 ..       4      43 .. 0.83
   2 !    5.9   0.0    0.0042        19      39      75 ..     200     236 ..     180     241 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00086
                                      EEEEECSSHHHHHHHHHHHH CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalae 20
                                      +vv+vGgG+ g  lA+ la+
  gi|344210007|ref|YP_004786183.1|  4 HVVIVGGGTGGTVLANDLAD 23
                                      89**************9976 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0042
                                       SHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEE CS
                         Pyr_redox  39 Deeaskilqeklekngievllntkveeiegsedgves 75 
                                       ++ ++++ +  + ++giev +  ++ee++ ++++++s
  gi|344210007|ref|YP_004786183.1| 200 NPHIAEWARPIMDERGIEVETFFNAEEVDPDSETLTS 236
                                       57799999999******************99987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2191.24
//
Query:       gi|344210008|ref|YP_004786184.1|  [L=78]
Description: SirA family protein [Haloarcula hispanica ATCC 33960]
Scores for 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-18   63.8   0.0    1.1e-17   63.6   0.0    1.0  1  TusA      Sulfurtransferase TusA
  ------ inclusion threshold ------
      0.017   14.8   0.0       0.02   14.5   0.0    1.1  1  DSHCT     DSHCT (NUC185) domain


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 !   63.6   0.0   1.2e-21   1.1e-17       2      70 .]       9      77 ..       8      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1.2e-21
                                      EEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEEEE CS
                              TusA  2 elDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelveveeedgeyrivirk 70
                                      ++D+rG +CP+Pl+ l  +++ +e+g+v+++l+d  ++  d+p++a++ g+el+++ee d+   ++++k
  gi|344210008|ref|YP_004786184.1|  9 TVDARGAACPGPLMDLIGQIRDAEAGDVVRLLSDTDQSLTDVPEWAEEAGNELLAIEELDDHNAFYLEK 77
                                      89*******************************************************988777777765 PP

>> DSHCT  DSHCT (NUC185) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.3e-06      0.02     113     146 ..      29      62 ..      16      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-06
                             DSHCT 113 tdldeGdiVRllrrleellrqlakaakvigneeL 146
                                        d+++Gd+VRll  +++ l ++++ a+  gne L
  gi|344210008|ref|YP_004786184.1|  29 RDAEAGDVVRLLSDTDQSLTDVPEWAEEAGNELL 62 
                                       5899************************999977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.48
# Mc/sec: 491.50
//
Query:       gi|344210009|ref|YP_004786185.1|  [L=197]
Description: type 11 methyltransferase/S-adenosylmethionine-dependent methyltransferase 3-like protein 1 [Haloarcula hispanica ATCC 33960]
Scores for complete 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-12   46.7   0.0    3.2e-12   46.5   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
      7e-12   45.9   0.0    9.9e-12   45.4   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
      2e-11   44.4   0.0    2.7e-11   43.9   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
    6.8e-09   35.4   0.0    8.1e-09   35.2   0.0    1.0  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    8.1e-08   32.9   0.0      1e-07   32.6   0.0    1.1  1  Methyltransf_12  Methyltransferase domain
    7.5e-07   29.1   0.0    9.7e-07   28.7   0.0    1.1  1  Met_10           Met-10+ like-protein
    1.5e-05   24.9   0.0    1.9e-05   24.6   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.7e-05   24.4   0.0    2.6e-05   23.8   0.0    1.2  1  MTS              Methyltransferase small domain
    0.00017   21.1   0.0    0.00022   20.7   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00017   21.4   0.0    0.00021   21.1   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00042   19.5   0.0     0.0018   17.4   0.0    1.8  2  Fibrillarin      Fibrillarin
     0.0014   18.4   0.0     0.0026   17.6   0.0    1.4  2  DUF938           Protein of unknown function (DUF938)
     0.0036   16.8   0.0      0.005   16.3   0.0    1.2  1  Methyltransf_4   Putative methyltransferase
  ------ inclusion threshold ------
      0.054   12.8   0.0      0.069   12.4   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
      0.078   13.0   0.0      0.094   12.7   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.081   12.9   0.0       0.11   12.4   0.0    1.1  1  Methyltransf_18  Methyltransferase domain
      0.088   12.6   0.0       0.45   10.3   0.0    1.8  1  Methyltransf_8   Hypothetical methyltransferase
        0.1   11.9   0.0       0.14   11.4   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase


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 !   46.5   0.0   3.3e-15   3.2e-12       3     112 ..      33     140 ..      32     171 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 3.3e-15
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlil 79 
                                       +g +v ++GCG+G++++ +a ++ +   v+ +D ++  +   +  a++++++nv   +gd+ +l+++l+ +++D ++
  gi|344210009|ref|YP_004786185.1|  33 SGESVAEVGCGSGYFALPAA-RIVEPEPVYALDLDAALLDELEDLADQQEIENVVPIHGDARNLPSALT-ARVDTLM 107
                                       578899**************.8888899*************************************8777.89***** PP

                   Methyltransf_31  80 snevlnaladpdkileeiervlkpggilliedp 112
                                         ++l+ + d+  ++++++r+++ gg ll+ + 
  gi|344210009|ref|YP_004786185.1| 108 IANTLHGVDDQSGFIRQAFRAIEAGGSLLVVNW 140
                                       ***************************998765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0     1e-14   9.9e-12       1      97 []      37     133 ..      37     133 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1e-14
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS.SSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlp.fedgsfDlvvssgalh 75 
                                       v ++GcG+G ++l +a+ ++ + v+++D+++++l++ +  a+++++ nv  ++gda++lp    +++D  +++++lh
  gi|344210009|ref|YP_004786185.1|  37 VAEVGCGSGYFALPAARIVEPEPVYALDLDAALLDELEDLADQQEIeNVVPIHGDARNLPsALTARVDTLMIANTLH 113
                                       789***************978**********************999*************944788*******99999 PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                        ++  d+  ++++++r+++ gG
  gi|344210009|ref|YP_004786185.1| 114 GVD--DQSGFIRQAFRAIEAGG 133
                                       987..678**********9999 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   2.8e-14   2.7e-11       2      95 ..      39     136 ..      38     137 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 2.8e-14
                                       EET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTS.S-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklp.fednsfDlvvssevlhhv 74 
                                       +vGcG+G++a + a+ +  + v+++Dl++++l+  ++ a ++++ +v  +++da++lp    + +D  ++ ++lh v
  gi|344210009|ref|YP_004786185.1|  39 EVGCGSGYFALPAARIVepEPVYALDLDAALLDELEDLADQQEIeNVVPIHGDARNLPsALTARVDTLMIANTLHGV 115
                                       79************99999***************999999999898888********845568************** PP

                                       CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllv 95 
                                       +d++ +++++ R  + gG l+
  gi|344210009|ref|YP_004786185.1| 116 DDQSGFIRQAFRAIEAGGSLL 136
                                       ******************997 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   8.1e-12   8.1e-09      34     154 ..      18     140 ..      15     151 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 8.1e-12
                                       HHHH..HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TT CS
                   Ubie_methyltran  34 lWkk..fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanae 108
                                       lW +   + ++ +v +g++v +v +G+g +a+  ++ v+ +  v  lD+++ +L++ e+ + ++   n+  ++++a 
  gi|344210009|ref|YP_004786185.1|  18 LWPTpgATLRTLGVASGESVAEVGCGSGYFALPAARIVEPE-PVYALDLDAALLDELEDLADQQEIENVVPIHGDAR 93 
                                       565555678889999******************99999886.699******************************** PP

                                       T-TTS-.T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE CS
                   Ubie_methyltran 109 eLpfed.dsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlef 154
                                       +Lp       D++ ++  l  v D++  +++a+r + +GG l+v++ 
  gi|344210009|ref|YP_004786185.1|  94 NLPSALtARVDTLMIANTLHGVDDQSGFIRQAFRAIEAGGSLLVVNW 140
                                       ***9974779********************************99875 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   1.1e-10     1e-07       2      99 .]      39     135 ..      38     135 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.1e-10
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhh 78 
                                       e+GcG+G ++ + ++  ++  ++++D++++ ++  +    ++e +n+  ++ +a++l +    + +D+  ++n+lh 
  gi|344210009|ref|YP_004786185.1|  39 EVGCGSGYFALPAARIVEPEPVYALDLDAALLDELEDLADQQEIENVVPIHGDARNLPSALT-ARVDTLMIANTLHG 114
                                       9*************999***************777778888888999999999999876655.6************* PP

                   Methyltransf_12  79 lkdirevldnirklLkpgGrl 99 
                                       ++d   +++++ +++  gG l
  gi|344210009|ref|YP_004786185.1| 115 VDDQSGFIRQAFRAIEAGGSL 135
                                       ******************975 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   9.8e-10   9.7e-07      98     192 ..      31     130 ..      23     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 9.8e-10
                                       --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---..TT-EEEE CS
                            Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir..eqladrv 172
                                       v  ge V +v  G G+fa+p+a+  +++ v+a dl+ +    l++     ++e+vv pi +D+r++    +  +d +
  gi|344210009|ref|YP_004786185.1|  31 VASGESVAEVGCGSGYFALPAARIVEPEPVYALDLDAALLDELEDLADQQEIENVV-PIHGDARNLPSalTARVDTL 106
                                       789*****************************************************.********986443333332 PP

                                       .EE--...TTTGGGGHHHHHHHEE CS
                            Met_10 173 .vmnl...pksaieFldkvlaalk 192
                                        + n    ++    F+ ++++a++
  gi|344210009|ref|YP_004786185.1| 107 mIANTlhgVDDQSGFIRQAFRAIE 130
                                       122321113444556666666555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.9e-08   1.9e-05      22     120 ..      33     140 ..      18     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.9e-08
                   Methyltransf_23  22 aggrvLdiGcGtGillevlrengf..svtgvDlspeaveiaekakkaqkdqfdeqeaae..............pqgk 82 
                                       +g +v ++GcG+G+++  +++ +    v++ Dl+ ++ +++        d +d+qe+++                ++
  gi|344210009|ref|YP_004786185.1|  33 SGESVAEVGCGSGYFALPAARIVEpePVYALDLDAALLDEL-------EDLADQQEIENvvpihgdarnlpsaLTAR 102
                                       566899***********9988765569*******9988876.......4555555555555555544444333556* PP

                   Methyltransf_23  83 fdlIvlrevlehvpdppellrqiatllkpgGylllsep 120
                                        d+    ++l+ v+d    +rq+++ ++ gG ll+  +
  gi|344210009|ref|YP_004786185.1| 103 VDTLMIANTLHGVDDQSGFIRQAFRAIEAGGSLLVVNW 140
                                       ******************************99998775 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   2.7e-08   2.6e-05      25     142 ..      27     142 ..      22     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.7e-08
                                       HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC....EEEEE-STTTTSTTS- CS
                               MTS  25 etlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle....vevvasdvleeveekk 97 
                                       +tl  +  ++v+ +GcG G+ ++ +a+  +   v ++d da+ l+  +  + ++++e    ++  a+++ ++++ ++
  gi|344210009|ref|YP_004786185.1|  27 RTLGVASGESVAEVGCGSGYFALPAARIVEPEPVYALDLDAALLDELEDLADQQEIEnvvpIHGDARNLPSALT-AR 102
                                       5666667889******************99999************99999999999986556777788888888.99 PP

                                       EEEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETT CS
                               MTS  98 fdlivsNPPfhagkatelavaeeliaeAkeaLkegGeLliVanrk 142
                                       +d+++    +h   +        +i++A +a + gG+Ll+V  + 
  gi|344210009|ref|YP_004786185.1| 103 VDTLMIANTLHGVDD-----QSGFIRQAFRAIEAGGSLLVVNWHD 142
                                       999988878887777.....789*****************97655 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.2e-07   0.00022     159     255 ..      31     134 ..      22     139 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.2e-07
                              PrmA 159 vkegeevlDvGtGSGiLaiaaak.LgakkvvavDiDevAvkvakeNaelNkveakleva.lseellk..eekad.vi 230
                                       v +ge+v  vG+GSG  a+ aa+ ++ + v+a+D+D   ++  ++ a++ ++e+ + ++  +++l++  ++++d ++
  gi|344210009|ref|YP_004786185.1|  31 VASGESVAEVGCGSGYFALPAARiVEPEPVYALDLDAALLDELEDLADQQEIENVVPIHgDARNLPSalTARVDtLM 107
                                       56799**************7666168899********9999999999999999988887333444434445566267 PP

                              PrmA 231 vaNILaevlie..laedikklvkeggl 255
                                       +aN L  v  +  ++ ++ ++++ gg+
  gi|344210009|ref|YP_004786185.1| 108 IANTLHGVDDQsgFIRQAFRAIEAGGS 134
                                       899887653322266666666666665 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.1e-07   0.00021      66     134 ..      26      93 ..      21     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.1e-07
                                       HHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG CS
                              PCMT  66 lellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr 134
                                       l  l +  g++v evG+GsGy +   ar+v+++  v +++  + l +e +    ++++env+ ++gD r
  gi|344210009|ref|YP_004786185.1|  26 LRTLGVASGESVAEVGCGSGYFALPAARIVEPEP-VYALDLDAALLDELEDLADQQEIENVVPIHGDAR 93 
                                       56788999*************************9.99*****************************986 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.8e-06    0.0018      63     130 ..      26      94 ..      17     111 .. 0.85
   2 ?   -0.6   0.0      0.58   5.7e+02     192     216 ..     168     192 ..     166     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                                       -S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTS..TTEEEEES-TTS CS
                       Fibrillarin  63 lkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakkR..knivPileDArk 130
                                       l++l + +g++v  +G +sG  +   + iv++e  vya++     l el ++a++   +n+vPi +DAr+
  gi|344210009|ref|YP_004786185.1|  26 LRTLGVASGESVAEVGCGSGYFALPAARIVEPE-PVYALDLDAALLDELEDLADQQeiENVVPIHGDARN 94 
                                       677889999**********************66.79**************999776337*********96 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.58
                                       HHHHHHHHTTEEEEEEEE-TTTSTT CS
                       Fibrillarin 192 eeveklkeeglkvleqvklepyekd 216
                                       +e   l+ ++++ + qv+l py+  
  gi|344210009|ref|YP_004786185.1| 168 TEDAVLSASEFTLERQVELPPYHYA 192
                                       567789999*************864 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.6e-06    0.0026      24     138 ..      32     136 ..      23     149 .. 0.85
   2 ?   -2.6   0.0       3.8   3.8e+03     180     203 ..     173     196 ..     155     197 .] 0.69

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-06
                            DUF938  24 kttervLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnlkpPleldvtaevapvereappap 100
                                       +++e v E++ G+G  A   A  +++    + d d  l + ++  ad++ ++n+  P++ d+ + +           
  gi|344210009|ref|YP_004786185.1|  32 ASGESVAEVGCGSGYFALPAARIVEPEPVYALDLDAALLDELEDLADQQEIENV-VPIHGDARNLPSALT------- 100
                                       445569***********************************************9.69**99988755544....... PP

                            DUF938 101 asidailsinllHispwsaveglfagagellkkkavlv 138
                                       a +d+++ +n+lH  + +   g+++ a + ++ ++ l+
  gi|344210009|ref|YP_004786185.1| 101 ARVDTLMIANTLH--GVDDQSGFIRQAFRAIEAGGSLL 136
                                       789**********..55666788888888777777765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.8
                            DUF938 180 aaaqgLqleklvdmPannkllvfq 203
                                         a++ +le++v++P     lvf 
  gi|344210009|ref|YP_004786185.1| 173 LSASEFTLERQVELPPYHYALVFT 196
                                       456777888888888877777775 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     5e-06     0.005       4      68 ..      36      99 ..      33     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5e-06
                                      EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS CS
                    Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllell 68
                                       v+e+GcG+G f +  A       + ++++   +++++ + ++++e++N+  ++gda + l+++l
  gi|344210009|ref|YP_004786185.1| 36 SVAEVGCGSGYFALPAARIVEPEPVYALDLDAALLDELEDLADQQEIENVVPIHGDA-RNLPSAL 99
                                      689***************98888999*******************************.7777665 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.9e-05     0.069      64     168 ..      35     141 ..      23     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.9e-05
                                       SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHHHHHHHS.-----TTEEEEES-TTTS-----.....SEEEEE CS
                    Methyltransf_2  64 kslvDvGGGtGalakaivsayPtikvivfDlpeVveaAkehl.sageeervefvgGdffkdslPea.....Daillk 134
                                       +s+ +vG G+G +a  +++      v  +Dl     +  e l +++e e+v  + Gd +  +lP+a     D ++++
  gi|344210009|ref|YP_004786185.1|  35 ESVAEVGCGSGYFALPAARIVEPEPVYALDLDAALLDELEDLaDQQEIENVVPIHGDAR--NLPSAltarvDTLMIA 109
                                       57789999999999888888888889999999888888888768889999*******99..7886655566****** PP

                                       SSGGGS-HHHHHHHHHHHHHH--TT-EEEEEE-- CS
                    Methyltransf_2 135 rvlhDwsdekcvklLkrvkkalpagGkvivveav 168
                                       + lh  +d++   ++++  +a+ agG ++vv+  
  gi|344210009|ref|YP_004786185.1| 110 NTLHGVDDQS--GFIRQAFRAIEAGGSLLVVNWH 141
                                       ******9985..799****************964 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.5e-05     0.094      27      78 ..      35      82 ..      25     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.5e-05
                   Methyltransf_32 27 ltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkf 78
                                      ++v++vG+G gY +   a      +  v+++d+ ++l ++ e++a++ +  +
  gi|344210009|ref|YP_004786185.1| 35 ESVAEVGCGSGYFALPAAR--IVEPEPVYALDLDAALLDELEDLADQQE--I 82
                                      6899********9999888..44689****************9999877..4 PP

>> Methyltransf_18  Methyltransferase 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      12      88 ..      31     108 ..      28     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                   Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklk..eeevdtv 86 
                                       v +g++va +G+  gy ++ +++    + v+a D+ +  l++ ++ ++++++e+ +  + +d  +  +  +  vdt+
  gi|344210009|ref|YP_004786185.1|  31 VASGESVAEVGCGSGYFALPAARIVEPEPVYALDLDAALLDELEDLADQQEIENVV-PIHGDARNLPSalTARVDTL 106
                                       66799********************************************9997654.44555544333213346666 PP

                   Methyltransf_18  87 vi 88 
                                       +i
  gi|344210009|ref|YP_004786185.1| 107 MI 108
                                       66 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00045      0.45      74     162 ..      35     143 ..      26     153 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00045
                                       S-EEEES-TT-HHH...HH--S-..EEEEESS-S.........S....TTEEE..S-TTS-S--.TT-EEEEEEES- CS
                    Methyltransf_8  74 lvvadlGcGeakia...eavrekekvrsfdlvav.........n....ervva..cdlakvPle.desvdvavfcls 131
                                        +va++GcG    a    ++ e+e v ++dl a          +    e+vv+   d +++P +    vd  ++  +
  gi|344210009|ref|YP_004786185.1|  35 ESVAEVGCGSGYFAlpaARIVEPEPVYALDLDAAlldeledlaDqqeiENVVPihGDARNLPSAlTARVDTLMIANT 111
                                       5899*****9998877689999999****997632222222221111223443225778888762456999999999 PP

                                       --SS-.HHHHHHHHHHHEEEEEEEEEEEEGGG CS
                    Methyltransf_8 132 lmgtn.ladflkeanrvlkvGGllkvaevksr 162
                                       l g +    f+++a r +  GG l v + + r
  gi|344210009|ref|YP_004786185.1| 112 LHGVDdQSGFIRQAFRAIEAGGSLLVVNWHDR 143
                                       98765155699999999999999999877666 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   0.00014      0.14      54     165 ..      25     138 ..      23     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                                       HHTTTT--TT-EEEEES-TTSHHHHHHHHHH--E.EEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---.-- CS
                              CMAS  54 ileklelkpGmtlLdiGcGWGslvrraverydvk.vvglTlSkeqaklakkrvdeldlerkvevklldyedlde.kv 128
                                       +l+ l++  G+ + ++GcG G+ +  a++  + + v +l l +      ++  d++++e+ v ++  d ++l+    
  gi|344210009|ref|YP_004786185.1|  25 TLRTLGVASGESVAEVGCGSGYFALPAARIVEPEpVYALDLDAALLDELEDLADQQEIENVVPIH-GDARNLPSaLT 100
                                       68899********************9999876544778888888888888888888877777775.46777777333 PP

                                       SEEEEES-GGGT.SGGGHHHHHHHHHHHS-TT-EEEEE CS
                              CMAS 129 drvvsvgafehv.gkenydtffkklkkllkedGllllh 165
                                        rv ++ + + + g++    f+++++++++++G ll+ 
  gi|344210009|ref|YP_004786185.1| 101 ARVDTLMIANTLhGVDDQSGFIRQAFRAIEAGGSLLVV 138
                                       44444444444457788888888888888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 1060.74
//
Query:       gi|344210010|ref|YP_004786186.1|  [L=72]
Description: hypothetical protein HAH_5068 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   7.7    1.6e-16   60.0   7.7    1.1  1  DUF2892          Protein of unknown function (DUF2892)
  ------ inclusion threshold ------
      0.014   15.4   2.8      0.015   15.3   2.8    1.0  1  Chlorosome_CsmC  Chlorosome envelope protein C
       0.34    8.9   1.0       0.37    8.8   1.0    1.0  1  MSP1b            Major surface protein 1B


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 !   60.0   7.7   2.7e-20   1.6e-16       1      64 [.       1      70 [.       1      72 [] 0.96

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 2.7e-20
                           DUF2892  1 MkkNvgtldRilrivvGlvllllallglsggw......gwllglvGavllltgltgfCplyallgintck 64
                                      M+ N+g +dR+ ri+vGlvl++++l++l+g        g ++ l+G+vl++tgl+++C ly+llgi+t++
  gi|344210010|ref|YP_004786186.1|  1 MENNIGATDRLTRIAVGLVLAVAGLATLGGLLgfgttvGAVATLLGVVLVATGLVRMCLLYRLLGIDTSG 70
                                      99**************************888899****999***************************76 PP

>> Chlorosome_CsmC  Chlorosome envelope protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   2.8   2.5e-06     0.015      15      66 ..       5      57 ..       2      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.5e-06
                   Chlorosome_CsmC 15 leltdrlaflaeavlltGqs.avvgglelaGsvvetvagtvgslidatGiskl 66
                                      +  tdrl+ +a + +l+  + a  ggl  +G+ v +va+ +g ++ atG+ ++
  gi|344210010|ref|YP_004786186.1|  5 IGATDRLTRIAVGLVLAVAGlATLGGLLGFGTTVGAVATLLGVVLVATGLVRM 57
                                      567**********99976654788999999********************987 PP

>> MSP1b  Major surface protein 1B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.0   6.2e-05      0.37     287     321 ..      16      50 ..       8      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 6.2e-05
                             MSP1b 287 igaaiavaaqatweglamtgkfmgavaklagavsm 321
                                       +g  +ava  at  gl   g  +gava l g v +
  gi|344210010|ref|YP_004786186.1|  16 VGLVLAVAGLATLGGLLGFGTTVGAVATLLGVVLV 50 
                                       78899************************999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 454.26
//
Query:       gi|344210011|ref|YP_004786187.1|  [L=416]
Description: succinyl-diaminopimelate desuccinylase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-40  138.0   0.2      5e-40  137.4   0.2    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    2.3e-18   66.1   0.0    4.4e-18   65.2   0.0    1.4  1  M20_dimer      Peptidase dimerisation domain
    5.8e-10   39.2   0.1    1.1e-07   31.8   0.1    2.1  2  Peptidase_M28  Peptidase family M28
      0.005   15.9   0.1        2.8    6.9   0.0    2.3  2  Peptidase_M42  M42 glutamyl aminopeptidase


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 !  137.4   0.2   1.1e-43     5e-40       2     204 ..      80     406 ..      79     408 .. 0.93

  Alignments for each domain:
  == domain 1  score: 137.4 bits;  conditional E-value: 1.1e-43
                                       EEEES-BSS.TTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT. CS
                                       xxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                     Peptidase_M20   2 lgsHlDvVp.eeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr. 75 
                                        ++HlD+Vp e++   wt+ p   ++e +++yGrGa+dmkg v+++l a++a++++  +p+ t+ ++f+ dEE+g+ 
  gi|344210011|ref|YP_004786187.1|  80 YNGHLDTVPfEADA--WTHaPLGERVE-DRVYGRGATDMKGAVASMLLAIQAFAATDAEPPVTLLFAFVSDEEVGGd 153
                                       68*******77777..*********99.*********************************************8778 PP

                                       THHHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE..................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                     Peptidase_M20  76 gGakallegleerekvdavfelhieepgileagklaigvv..................................... 115
                                       +G +alle    +ek+da   ++i+ep+    g+ +++v                                      
  gi|344210011|ref|YP_004786187.1| 154 AGLPALLE----AEKLDADA-CVIGEPTCEA-GRHSVTVAdrgsiwltleasgegahgsrpmlginavdrlydavet 224
                                       9*******....88888866.99******99.99888888************************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|344210011|ref|YP_004786187.1| 225 lrdrfgsrrldiapkvepivdesveyyapslgedvardlfryptinlgifeggdavnsvpqsaraeidirltagvet 301
                                       ***************************************************************************** PP

                                       ...............EEEEEEE.EEESHEEECCHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH..TTTEEE.E CS
                                       ...............xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx.x RF
                     Peptidase_M20 116 ...............kvevell.eggapvtlndsplvkalaeaaeelfgekvelivsgpggtdarff..agiptv.m 173
                                                       ++++++ ++   ++ +dsplv+a+ ++a +++ge+v +    +gg da+ +  agiptv +
  gi|344210011|ref|YP_004786187.1| 302 pdvlseirscvtdceGITITDVsWSVGTAEESDSPLVEAVTSTAADVTGERVFRRSA-TGGGDAKTLrnAGIPTVeF 377
                                       **************659999994555555555***************9977555544.49*******99999***55 PP

                                       EEESSGGCTTSTTTEEEHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 174 ifgpgsglaHspnEyvdledlekgikvlarl 204
                                        +g+  +++H+p+Eyv ++ l++ ++v++rl
  gi|344210011|ref|YP_004786187.1| 378 ALGT--DTVHTPDEYVPVDVLVDNAAVYTRL 406
                                       5884..6*********************997 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.0   9.8e-22   4.4e-18       2     101 ..     187     312 ..     186     315 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 9.8e-22
                                       EB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC...............................T CS
                         M20_dimer   2 ghkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia..........................eers 52 
                                       + +G+++ ++++ g+++H++ p  g+NA+  l ++++ l+d  g+                            ++  
  gi|344210011|ref|YP_004786187.1| 187 ADRGSIWLTLEASGEGAHGSRPMLGINAVDRLYDAVETLRDRFGSRRldiapkvepivdesveyyapslgedvARDL 263
                                       679***************************************77777****************************** PP

                                       CCTCCCCCEECCE-CCCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHH CS
                         M20_dimer  53 lprttlnvtgiegGsaknvipdeaeakidiRllpgedpeevleeieeil 101
                                       ++++t+n++++egG+a n++p++a+a+idiRl  g +  +vl ei++ +
  gi|344210011|ref|YP_004786187.1| 264 FRYPTINLGIFEGGDAVNSVPQSARAEIDIRLTAGVETPDVLSEIRSCV 312
                                       *********************************************9876 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.1   2.4e-11   1.1e-07       1      74 [.      65     151 ..      65     172 .. 0.88
   2 !    5.3   0.0    0.0032        14     114     176 ..     333     388 ..     310     395 .. 0.67

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 2.4e-11
                                       EEEEEESTTCESEEEEEEEE--B-TTT.............TCC..T---TTTTHHHHHHHHHHHHHCHHGGCCSSEE CS
                     Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvg.............rgp..ifvGAdDnAsgvaalLelarvlaasgsrpkrg 62 
                                       N+++ ++g++ d++ll+++H+D+v+++             + +     GA+D    va++L  ++++aa   +p  +
  gi|344210011|ref|YP_004786187.1|  65 NLLVGIPGES-DRTLLYNGHLDTVPFEadawthaplgervE-DrvYGRGATDMKGAVASMLLAIQAFAATDAEPPVT 139
                                       7888999999.*********************888877651.154667*********************999***** PP

                                       EEEEEESSCSGS CS
                     Peptidase_M28  63 vrflffdaEEag 74 
                                       + f+f++ EE g
  gi|344210011|ref|YP_004786187.1| 140 LLFAFVSDEEVG 151
                                       **********84 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0032
                                       HHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHHTTT--EEEECTSSS-TTTTSTT CS
                     Peptidase_M28 114 kssselekelkalakpvgraaaedpfdersgrgrsDhspflkagvpvldlaetgfpevyHtpr 176
                                       ++s+ +e+ ++++a+ +g+     +  +rs +g  D+  +++ag+p++ + + g +++ Htp+
  gi|344210011|ref|YP_004786187.1| 333 SDSPLVEAVTSTAADVTGE----RV-FRRSATGGGDAKTLRNAGIPTVEF-ALG-TDTVHTPD 388
                                       3444444444444443333....44.567789****************99.333.34447665 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0   0.00063       2.8     132     172 ..     112     154 ..      95     186 .. 0.81
   2 !    6.7   0.0   0.00068       3.1     226     284 ..     338     394 ..     315     401 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00063
                                       THHHHHHHHHHHHHHHHHCTSS-S..SEEEEEEESTCTTTSHH CS
                     Peptidase_M42 132 alDdragvavllellkelkeeele..atvylvatvqEEvGlrG 172
                                       a D + +va +l ++++++ ++ e  +t+ +++   EEvG  +
  gi|344210011|ref|YP_004786187.1| 112 ATDMKGAVASMLLAIQAFAATDAEppVTLLFAFVSDEEVGGDA 154
                                       6788999**********999999889**************765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00068
                                       HHHHHHHHHHTT--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHH CS
                     Peptidase_M42 226 rkkllelAkknnipyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahld 284
                                       ++ ++ +A++   +  ++  ++gg DA+++   ++g+pt+  + +t+ +H+p e + +d
  gi|344210011|ref|YP_004786187.1| 338 VEAVTSTAADVTGERVFRRSATGGGDAKTLR--NAGIPTVEFALGTDTVHTPDEYVPVD 394
                                       5555555555555555556667777887655..56*****************9988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2823.25
//
Query:       gi|344210012|ref|YP_004786188.1|  [L=137]
Description: thioredoxin [Haloarcula hispanica ATCC 33960]
Scores for complete 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   0.0    2.7e-27   94.8   0.0    1.1  1  Thioredoxin    Thioredoxin
    5.7e-12   46.1   0.1    1.4e-10   41.6   0.1    2.1  1  Thioredoxin_2  Thioredoxin-like domain
    4.1e-06   26.7   0.0    6.3e-06   26.1   0.0    1.3  1  Thioredoxin_3  Thioredoxin domain
    4.2e-05   23.6   0.0    8.3e-05   22.7   0.0    1.5  1  Thioredoxin_7  Thioredoxin-like
    4.9e-05   23.3   0.0    6.3e-05   22.9   0.0    1.2  1  TraF           F plasmid transfer operon protein
      6e-05   23.3   0.0      0.072   13.4   0.0    2.2  2  Thioredoxin_8  Thioredoxin-like
    0.00011   22.1   0.2    0.00023   21.0   0.0    1.6  2  DSBA           DSBA-like thioredoxin domain
    0.00013   21.7   0.0    0.00017   21.4   0.0    1.2  1  Thioredoxin_9  Thioredoxin
     0.0002   21.3   0.1    0.00035   20.5   0.0    1.5  1  HyaE           Hydrogenase-1 expression protein HyaE
    0.00072   19.9   0.0     0.0011   19.3   0.0    1.4  1  DUF836         Glutaredoxin-like domain (DUF836)
      0.004   16.5   0.0      0.005   16.2   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.086   12.8   0.0    2.0  1  AhpC-TSA       AhpC/TSA family
      0.012   15.8   0.0      0.025   14.8   0.0    1.6  1  Glutaredoxin   Glutaredoxin
      0.029   14.1   0.1       0.41   10.3   0.1    2.0  2  Redoxin        Redoxin
      0.042   13.5   0.0      0.056   13.1   0.0    1.3  1  Thioredoxin_5  Thioredoxin
      0.056   13.1   0.4       0.54    9.9   0.4    2.1  1  DUF953         Eukaryotic protein of unknown function (DUF953
       0.15   11.8   0.0       0.23   11.2   0.0    1.2  1  KaiB           KaiB domain


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.0   2.5e-30   2.7e-27      15     103 .]      50     135 ..      37     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 2.5e-30
                                       TTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS CS
                       Thioredoxin  15 akekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyega 91 
                                         +++ vlv+FyA+wCg+C++l+P++e++a e++   ++ak+dvd+n++la++y+v+g+Ptl+lf +g+ v++++g 
  gi|344210012|ref|YP_004786188.1|  50 T-DHDVVLVDFYADWCGPCQMLEPVVETVAAETA--ATVAKIDVDANQELAAEYGVRGVPTLLLFADGEPVERLVGM 123
                                       4.4899**************************99..99*************************************** PP

                                       -HHHHHHHHHHH CS
                       Thioredoxin  92 rekeklaaflkk 103
                                       +++++l+a ++k
  gi|344210012|ref|YP_004786188.1| 124 QDESQLRAVIEK 135
                                       *******99975 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.1   1.3e-13   1.4e-10       4     108 ..      51     132 ..      48     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1.3e-13
                     Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrg 80 
                                       ++  vlv+f++++C+ C+ l+ +++++               + + a+ + + +         ++n+ela +ygvrg
  gi|344210012|ref|YP_004786188.1|  51 DHDVVLVDFYADWCGPCQMLEPVVETV---------------AAETAATVAKIDV--------DANQELAAEYGVRG 104
                                       57789**********************...............2233333333332........33679********* PP

                     Thioredoxin_2  81 tPt.ivfldgkeivarlpGyvpaeeleal 108
                                       +Pt ++f dg+ +v+rl+G+ ++ +l+a+
  gi|344210012|ref|YP_004786188.1| 105 VPTlLLFADGE-PVERLVGMQDESQLRAV 132
                                       ***555*****.999**********9987 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0     6e-09   6.3e-06      10      75 ..      64     133 ..      55     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6e-09
                                       STTCHHHHHHHHHHCHCCTCECEEECCTTHHHH.HHCT-SSSSEE..ECTTC..EEEESS---CCHHHHHH CS
                     Thioredoxin_3  10 CakCpklekavkeaaaekgikaevekvtdfeei.ekygVmsvPal..vidgk..vvvsGkvpseeeirkll 75 
                                       C  C+ le +v+ +aae   ++  ++v  ++e+ ++ygV+ vP+l  + dg+   + +G + +e ++r+++
  gi|344210012|ref|YP_004786188.1|  64 CGPCQMLEPVVETVAAETAATVAKIDVDANQELaAEYGVRGVPTLllFADGEpvERLVG-MQDESQLRAVI 133
                                       999*****************************************977779872246889.88999988887 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   7.9e-08   8.3e-05      16      81 ..      51     111 ..      40     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7.9e-08
                                       HT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT-.--SSEEEEE CS
                     Thioredoxin_7  16 rgkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanilelde.qgvPvvafl 81 
                                       ++  vlv+f a+wc++Cq le ++++      a+     + ++dv+ +++   + ++ +gvP+++++
  gi|344210012|ref|YP_004786188.1|  51 DHDVVLVDFYADWCGPCQMLEPVVETV-----AAETAATVAKIDVDANQELA-AEYGvRGVPTLLLF 111
                                       56679****************999987.....35677777788887777744.32335779998876 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0     6e-08   6.3e-05     129     202 ..      52     114 ..      41     128 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6e-08
                              TraF 129 keygLlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpk 202
                                       +++ L+ Fy+  c+ c+++ p+++ +a ++  +v  ++vd ++   l++         ++gv+ +P+l+l+   
  gi|344210012|ref|YP_004786188.1|  52 HDVVLVDFYADWCGPCQMLEPVVETVAAETAATVAKIDVDANQE--LAA---------EYGVRGVPTLLLFADG 114
                                       5678999***********************************77..777.........***********98765 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   6.8e-05     0.072       2      25 ..      53      76 ..      51      90 .. 0.83
   2 !    8.4   0.0    0.0026       2.7      67      89 ..      89     111 ..      75     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.8e-05
                                      SEEEEEE--SSSHHHHHHHHHHHH CS
                     Thioredoxin_8  2 kvvlLyfgaswcppckaftpklke 25
                                      +vvl+ f+a+wc pc+   p +  
  gi|344210012|ref|YP_004786188.1| 53 DVVLVDFYADWCGPCQMLEPVVET 76
                                      79*************998888765 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0026
                                       -TT-HHHHTT-S--TT-SEEEEE CS
                     Thioredoxin_8  67 ddkkrnklkkkynvkaiPtlvvl 89 
                                       d + +++l+ +y+v ++Ptl++ 
  gi|344210012|ref|YP_004786188.1|  89 DVDANQELAAEYGVRGVPTLLLF 111
                                       456799**************986 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.37   3.9e+02       2      31 ..      57      84 ..      56      91 .. 0.76
   2 !   21.0   0.0   2.2e-07   0.00023     141     191 ..      78     132 ..      73     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.37
                                      EEEEEBTTBHHHHHHHHHHHHHHHHCCTEE CS
                              DSBA  2 vdeffDvlCPyCylgkerleklaarspdvk 31
                                      vd++ D  C+ C + ++++e +aa    ++
  gi|344210012|ref|YP_004786188.1| 57 VDFYAD-WCGPCQMLEPVVETVAAET-AAT 84
                                      788888.5999******999999877.444 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.2e-07
                                       HHHHTSHHHHHHHHHHHHHHHHTT-SSSSEEEE..TTC..EEEESSSSHHHHHHH CS
                              DSBA 141 dealeseavkeavrentaaaqslgvtGvPtvvv..dgk..rmvfGadrldtlada 191
                                       ++ ++   +k +v+ n+++a+++gv+GvPt ++  dg+    ++G ++  +l+  
  gi|344210012|ref|YP_004786188.1|  78 AAETAATVAKIDVDANQELAAEYGVRGVPTLLLfaDGEpvERLVGMQDESQLRAV 132
                                       555666677889******************999989988889*****99999876 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.6e-07   0.00017      48     106 ..      59     113 ..      36     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.6e-07
                                       E--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-T CS
                     Thioredoxin_9  48 ltedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliilde 106
                                       + +dwCg +++  Pv++ +a ++   +v  +  d+n+el  +y   g r +Ptl+++ +
  gi|344210012|ref|YP_004786188.1|  59 FYADWCGPCQMLEPVVETVAAET-AATVAKIDVDANQELAAEY---GVRGVPTLLLFAD 113
                                       679********************.9******************...8899999987744 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   3.3e-07   0.00035      60     104 ..      80     125 ..      67     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.3e-07
                                       S-EEEEEE.THHHHHHHHHCCT-TSSSEEEEEETTEEEEEEESSST CS
                              HyaE  60 alraavva.dreqeealaerfgvlktPsllflrdgeylgvlakird 104
                                        + a+v++ d + +++la ++gv+ +P+ll+++dge +  l +++d
  gi|344210012|ref|YP_004786188.1|  80 ETAATVAKiDVDANQELAAEYGVRGVPTLLLFADGEPVERLVGMQD 125
                                       4455556569999****************************99998 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.1e-06    0.0011      10      54 ..      64     109 ..      59     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.1e-06
                                       -HHHHHHHHHHHHHCCCTTEEEEEEETTT-CCCHCCCCTT.TTEEE CS
                            DUF836  10 ChlCeqakekLkelkleegleleviDIakdeeleakYgle.ipvla 54 
                                       C+ C+ ++ +++ ++ e   ++ +iD++ ++el a+Yg++ +p l+
  gi|344210012|ref|YP_004786188.1|  64 CGPCQMLEPVVETVAAETAATVAKIDVDANQELAAEYGVRgVPTLL 109
                                       9************************************986466665 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.8e-06     0.005      46     104 ..      64     113 ..      54     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.8e-06
                         OST3_OST6  46 CelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfpp 104
                                       C +C+ +ep +e+va    ++          ak+d+d ++++ +++g++ +P lllf  
  gi|344210012|ref|YP_004786188.1|  64 CGPCQMLEPVVETVAAETAAT---------VAKIDVDANQELAAEYGVRGVPTLLLFAD 113
                                       99*************999999.........69*************************87 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.2e-05     0.086      16      56 ..      41      82 ..      32     117 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.2e-05
                                      EEEECHHH.TT.SEEEEEEESTST-CCHHHHHHHHHHCHHHCC CS
                          AhpC-TSA 16 etvslsdy.kg.kpvvlffypkdwcpvCttelpalaklyeefk 56
                                      ++ +lsd   + ++v++ fy+  wc +C+   p  + ++ e +
  gi|344210012|ref|YP_004786188.1| 41 GKAELSDTtTDhDVVLVDFYAD-WCGPCQMLEPVVETVAAETA 82
                                      5678999975547888889988.*****987777766666655 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.4e-05     0.025       7      54 ..      62     109 ..      54     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                                       TSSHHHHHHHHHHHHTTGG....EEEEEGCCSHHHHHHHHHHHTSSSSSEEE CS
                      Glutaredoxin   7 ptCpyCkkakrlLkelgvk....feeidvdkdeeireelkelsgvrtvPqvf 54 
                                        +C+ C++   + ++  ++    ++ idvd+++e+ +e     gvr vP++ 
  gi|344210012|ref|YP_004786188.1|  62 DWCGPCQMLEPVVETVAAEtaatVAKIDVDANQELAAEY----GVRGVPTLL 109
                                       79******999997777544445999*****98888887....9999**975 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00039      0.41      22      56 ..      44      79 ..      33      90 .. 0.71
   2 ?    2.2   0.0      0.13   1.3e+02      91     114 ..      90     104 ..      71     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00039
                                      EHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHH CS
                           Redoxin 22 slse.fkgkkvvvnfvpgafcPtCsaehpyleklae 56
                                      +ls+  +++ vv++ + + +c++C+   p +e++a+
  gi|344210012|ref|YP_004786188.1| 44 ELSDtTTDHDVVLVDFYADWCGPCQMLEPVVETVAA 79
                                      6788878888777666666*****865555655555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.13
                                       E-TTSHHHHHTT-TTEEE.GGGEE CS
                           Redoxin  91 sDgsaaftkalGlrleedaseglr 114
                                       +D+++++++++G+r         +
  gi|344210012|ref|YP_004786188.1|  90 VDANQELAAEYGVR---------G 104
                                       799*********88.........3 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.3e-05     0.056     133     165 ..      80     112 ..      63     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.3e-05
                     Thioredoxin_5 133 DlesklakkafqcDlklakemgvtevPtlvffn 165
                                          +++ak   ++ ++la+e+gv+ vPtl +f 
  gi|344210012|ref|YP_004786188.1|  80 ETAATVAKIDVDANQELAAEYGVRGVPTLLLFA 112
                                       55677888899999***************9997 PP

>> DUF953  Eukaryotic protein of unknown function (DUF953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.4   0.00051      0.54      36      67 ..      62      93 ..      42     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00051
                                      BSSHHHHHHHHHHHHHHHH-SS-EEEEEEE-- CS
                            DUF953 36 sWCPdCvkaepvieealkeapedvklvrvdvG 67
                                       WC  C   epv+e +  e ++ v  + vd+ 
  gi|344210012|ref|YP_004786188.1| 62 DWCGPCQMLEPVVETVAAETAATVAKIDVDAN 93
                                      5***************9999999998888764 PP

>> KaiB  KaiB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00022      0.23      25      77 ..      78     131 ..      68     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                       HCTTTEEEEEEETTTSHCHHCCTCEESCCCCCCC.CSCCHCCCCCCHHHCCHHC CS
                              KaiB  25 dlgfqyeLqvvdvleqPelaeedrlvatPaLikl.sPePkqrlaGdlilqqlkl 77 
                                       +++   ++  +dv  + ela e+ +  +P+L    + eP+ rl+G ++  ql  
  gi|344210012|ref|YP_004786188.1|  78 AAETAATVAKIDVDANQELAAEYGVRGVPTLLLFaDGEPVERLVGMQDESQLRA 131
                                       56677788889*******************98752789*********9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); 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:                        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 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1023.40
//
Query:       gi|344210013|ref|YP_004786189.1|  [L=146]
Description: hypothetical protein HAH_5071 [Haloarcula hispanica ATCC 33960]
Scores for 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   54.8   0.0      1e-14   54.1   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 !   54.1   0.0   5.7e-19     1e-14       4      61 ..      51     110 ..      48     112 .. 0.92

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 5.7e-19
                                       HHHHHCTT-S--S-EEEEEEE-HHHHHHHHCC-.GGGGGG-SEEEEEEE.ETTEEEEEEE CS
                            DUF302   4 qatlkkklgedlrpykilgaCnPklatealqad.peiglllPcrvvVye.kdgkttvsyv 61 
                                       ++ l++k+++d +py++lgaCnP++a++al+a   ++g+l+ c+vv++e + g+ +v+ v
  gi|344210013|ref|YP_004786189.1|  51 SEMLNEKIDADRDPYYVLGACNPEVADRALDATdNKLGALMACNVVIWEeEPGQQRVYHV 110
                                       68899*************************9876***************777**999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        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 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1148.95
//
Query:       gi|344210014|ref|YP_004786190.1|  [L=186]
Description: type 11 methyltransferase [Haloarcula hispanica ATCC 33960]
Scores for 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   61.4   0.0    1.7e-16   60.7   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    4.3e-15   56.2   0.0      1e-14   55.0   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    5.4e-08   32.8   0.0    1.3e-07   31.5   0.0    1.6  2  Methyltransf_31  Methyltransferase domain
    4.6e-06   26.1   0.0      6e-06   25.8   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      4e-05   22.8   0.0    6.5e-05   22.1   0.0    1.3  1  DREV             DREV methyltransferase
    9.3e-05   22.3   0.0    0.00013   21.8   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
     0.0032   18.2   0.0     0.0068   17.1   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
     0.0092   16.1   0.0      0.016   15.3   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
  ------ inclusion threshold ------
      0.073   12.1   0.0      0.086   11.9   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
       0.13   12.1   0.0       0.24   11.2   0.0    1.6  1  Methyltransf_8   Hypothetical 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 !   60.7   0.0   9.3e-20   1.7e-16       2      96 .]      43     134 ..      42     134 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 9.3e-20
                                       EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHH CS
                   Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpe 78 
                                       d+G+GtG ++ ++a ++++v++vD+ ++m+++ +ek+++++  v++v + + +lpf  +s D  +s+++ h ++  +
  gi|344210014|ref|YP_004786190.1|  43 DLGSGTGFYTDDIAPAVESVYAVDIQEAMHDYYREKGVPDN--VDLVTSAVDDLPFDTGSLDGAFSTMTYHEFA-SD 116
                                       9*************999***********************9..9*****************************5.9* PP

                                       HHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  79 kalkeiaRvLkpgGllvi 96 
                                        al+e+aRvL  gG+++i
  gi|344210014|ref|YP_004786190.1| 117 GALNEVARVLNSGGTFAI 134
                                       **************9986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   5.7e-18     1e-14       1      97 []      41     130 ..      41     130 .. 0.93

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 5.7e-18
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       v dlG GtG +t ++a ++  ++v++vDi+e+m ++ re+     + nv++v+  ++dlpf+ gs D  +s++++h 
  gi|344210014|ref|YP_004786190.1|  41 VADLGSGTGFYTDDIAPAV--ESVYAVDIQEAMHDYYREKGV---PdNVDLVTSAVDDLPFDTGSLDGAFSTMTYHE 112
                                       78****************9..9******************94...369***********************877777 PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                       +     + al+e+arvL+ gG
  gi|344210014|ref|YP_004786190.1| 113 FA---SDGALNEVARVLNSGG 130
                                       76...4589***********9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   7.3e-11   1.3e-07       2     113 ..      36     138 ..      35     161 .. 0.88
   2 ?   -2.6   0.0       2.3   4.2e+03      43      60 ..     157     173 ..     149     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 7.3e-11
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       +++ +v DlG+GtG++t  +a  + +   v+ +Di+e +  + re   k   dnv +  + + +l+  +   + D  
  gi|344210014|ref|YP_004786190.1|  36 ESDETVADLGSGTGFYTDDIAPAVES---VYAVDIQEAMHDYYRE---KGVPDNVDLVTSAVDDLP--FDTGSLDGA 104
                                       68999****************65443...**********999999...67788*************..777888887 PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedpr 113
                                       +s    ++  ++d +l+e+ rvl++gg ++i+d  
  gi|344210014|ref|YP_004786190.1| 105 FST-MTYHEFASDGALNEVARVLNSGGTFAIADWA 138
                                       774.3389999*******************99865 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.3
                   Methyltransf_31  43 lArenaqklgldnveFeq 60 
                                        A+  ++++g++ +eFe+
  gi|344210014|ref|YP_004786190.1| 157 EATDTLRQHGFT-IEFEA 173
                                       577788999997.88875 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   3.4e-09     6e-06      46     152 ..      36     135 ..      19     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.4e-09
                                       --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEEE CS
                   Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvvt 121
                                        + ++v D+ +Gtg ++ +++ +v++   v  +Di+e m +  ++    +g+  n++++++   +Lpf+ +s D   
  gi|344210014|ref|YP_004786190.1|  36 ESDETVADLGSGTGFYTDDIAPAVES---VYAVDIQEAMHDYYRE----KGVPdNVDLVTSAVDDLPFDTGSLDGAF 105
                                       4566899*************999986...7889******877655....566559*******************887 PP

                                       EES-GGG-S-HHHHHHHHHHHEEEEEEEEEE CS
                   Ubie_methyltran 122 vsfGlrnvtDklkaLkeayrvlkpGGrlvvl 152
                                        +     ++  + aL+e+ rvl  GG++ + 
  gi|344210014|ref|YP_004786190.1| 106 STMTYHEFA-SDGALNEVARVLNSGGTFAIA 135
                                       777777876.5789************99875 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   3.7e-08   6.5e-05      77     135 ..      19      78 ..      14      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.7e-08
                              DREV  77 qfrkllaiekespa.sdqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkk 135
                                       q  + l +e+ ++a s   d+++ dlG+G G  t  +ap +e vya ++ e m d  + k
  gi|344210014|ref|YP_004786190.1|  19 QRYRSLSAEELHWAlSPESDETVADLGSGTGFYTDDIAPAVESVYAVDIQEAMHDYYREK 78 
                                       555678888899985667899********************************9987766 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   7.3e-08   0.00013      20     131 ..      35     154 ..      14     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7.3e-08
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae...kakkaqkdqfdeqeaaepqgkfdlIvlrevle 93 
                                        +++  v d+G GtG  ++ +++ + sv++vD+ +++++ ++    +++   +    ++ +++ g+ d + ++++ +
  gi|344210014|ref|YP_004786190.1|  35 PESDETVADLGSGTGFYTDDIAPAVESVYAVDIQEAMHDYYRekgVPDNVDLVTSAVDDLPFDTGSLDGAFSTMTYH 111
                                       68889999*********************************999866777777777778999*************** PP

                   Methyltransf_23  94 hvpdppellrqiatllkpgGylllseplasl......kedrlll 131
                                        + +   +l+ +a+ l+ gG + + +++as       + d+++ 
  gi|344210014|ref|YP_004786190.1| 112 EFAS-DGALNEVARVLNSGGTFAIADWAASGsgrngpPVDERFS 154
                                       **98.9*********************99986666664555554 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.8e-06    0.0068       2      98 ..      43     131 ..      42     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.8e-06
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhh 78 
                                       ++G+GtG +++ ++++    ++++vDi++++ +  +ek      +n++ v+  ++dl  +   +s D  ++  + h 
  gi|344210014|ref|YP_004786190.1|  43 DLGSGTGFYTDDIAPA--VESVYAVDIQEAMHDYYREK-GVP--DNVDLVTSAVDDLPFDT--GSLDGAFSTMTYHE 112
                                       89**************..88888*********333333.332..33444555444443333..37777777777777 PP

                   Methyltransf_12  79 lkdirevldnirklLkpgGr 98 
                                       +   + +l++++++L+ gG 
  gi|344210014|ref|YP_004786190.1| 113 F-ASDGALNEVARVLNSGGT 131
                                       5.7889***********997 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   8.9e-06     0.016       6      58 ..      11      76 ..       8     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.9e-06
                                      HHHHHHHHHHHT-S-TT...........-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.....H CS
                              FtsJ  6 ayKLleidekfklfkpg...........ktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.....a 58
                                      a KL++++++++ ++ +           +tv Dlg+++G +++ ++  ++    v+avD+q+      +
  gi|344210014|ref|YP_004786190.1| 11 ADKLEDAQQRYRSLSAEelhwalspesdETVADLGSGTGFYTDDIAPAVE---SVYAVDIQEAmhdyyR 76
                                      56999999***9886444566666666677******************85...6******987544330 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.8e-05     0.086      27      72 ..      34      79 ..      24     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.8e-05
                                      -GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHT CS
                            RrnaAD 27 nleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkl 72
                                       +e + tv ++g+G+G+ T  +a  +++v ++ + e++   +++k 
  gi|344210014|ref|YP_004786190.1| 34 SPESDETVADLGSGTGFYTDDIAPAVESVYAVDIQEAMHDYYREKG 79
                                      4567899*********************************999964 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00014      0.24     104     159 ..      82     137 ..      27     183 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                                       SSTTEEES-TTS-S--TT-EEEEEEES---SS-HHHHHHHHHHHEEEEEEEEEEEE CS
                    Methyltransf_8 104 vnervvacdlakvPledesvdvavfclslmgtnladflkeanrvlkvGGllkvaev 159
                                        n ++v+  +  +P + +s d a   ++         l+e+ rvl  GG + +a+ 
  gi|344210014|ref|YP_004786190.1|  82 DNVDLVTSAVDDLPFDTGSLDGAFSTMTYHEFASDGALNEVARVLNSGGTFAIADW 137
                                       4556677788999********9999999888888999****************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); 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:                        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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1363.23
//
Query:       gi|344210015|ref|YP_004786191.1|  [L=229]
Description: urease accessory protein UreF [Haloarcula hispanica ATCC 33960]
Scores for complete 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-29  102.2   8.0    4.5e-29  101.7   8.0    1.2  1  UreF      UreF


Domain annotation for each model (and alignments):
>> UreF  UreF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.7   8.0   2.5e-33   4.5e-29       1     132 []      37     187 ..      37     187 .. 0.94

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 2.5e-33
                                       S-SHHHHHHHHHHHHTTHHHHTHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHH-. CS
                              UreF   1 vtdeaslaawledqLllglarldlavlarayraaragdaaalrelddwllatretaelrlaseqmGrsllrllrkl. 76 
                                       v+d+a+l+a l+++L+++++ ++l++l++a++aa++g+++a+ + d++l+a +++ae+r+  +q G +ll l  +l 
  gi|344210015|ref|YP_004786191.1|  37 VEDAADLEALLSTYLRQQVGPAELVALRAAHAAAADGNFEAVCRADRRLSAVTLAAEFRESAQQSGDRLLSLQTELc 113
                                       789*************************************************************************8 PP

                                       ...................-HHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHTH CS
                              UreF  77 ...........t.......hypvafglaaaalgipleeallaylfswaenlvsAavklvplGqtagqrilarla 132
                                                  +       +y+v++g+a+a +++ +++a+l+++++++++l+ Aa +l+ lG+t++qril +l+
  gi|344210015|ref|YP_004786191.1| 114 eealldryaerVdadeapgNYAVVLGVATALADVAVRDACLLCCHGFVTGLLGAAQRLLSLGHTDAQRILDDLQ 187
                                       88887777665156677889**************************************************8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1754.00
//
Query:       gi|344210016|ref|YP_004786192.1|  [L=187]
Description: urease accessory protein UreE [Haloarcula hispanica ATCC 33960]
Scores for complete 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   42.5   2.2    3.5e-11   42.5   2.2    1.8  2  UreE_N    UreE urease accessory protein, N-terminal domain
    1.7e-05   25.2   0.6    3.1e-05   24.4   0.6    1.4  1  UreE_C    UreE urease accessory protein, C-terminal domain


Domain annotation for each model (and alignments):
>> UreE_N  UreE urease accessory protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   2.2   3.9e-15   3.5e-11       6      62 .]      18      72 ..      14      72 .. 0.92
   2 ?   -2.3   0.0      0.38   3.4e+03      11      22 ..      77      88 ..      74      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 3.9e-15
                                      ..GGGSEEEEEEE-GGGTT-SEEEEE-TTS-EEEEE-SS-T---TTBEEEEETTEEE CS
                            UreE_N  6 aqadaapadtvtLtweerqkrRlrvttdsGrevglrLprgtvLrdGDiLvaddgrlv 62
                                      + +d+    tv+L+  erq++R r +t++G ++g+   r   L+dGD+L+a+dg+lv
  gi|344210016|ref|YP_004786192.1| 18 EDIDTSDHATVVLSDTERQRSRVRTETTDGCDLGIVVARD--LADGDVLEAEDGTLV 72
                                      556667778******************************9..************998 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.38
                                      SEEEEEEE-GGG CS
                            UreE_N 11 apadtvtLtwee 22
                                      a+++ ++L++++
  gi|344210016|ref|YP_004786192.1| 77 AAIEALVLDFAD 88
                                      678999999986 PP

>> UreE_C  UreE urease accessory protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.6   3.4e-09   3.1e-05      14      87 .]      96     177 ..      75     178 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.4e-09
                            UreE_C  14 laraayhLGNrHvpleikedelrie...ddhvledmlrtl.gaeveevlapfepe....ggAyeaakghgh.....h 77 
                                        +++   +GNrH++l+++++e +++   +++ +e ++ +l  a+v    +   p     +g +     h h      
  gi|344210016|ref|YP_004786192.1|  96 ALELGHAVGNRHWNLAVRDRETLFPvtdSKERMETTVAELlPADVPTRYEHVPPTtfddEGVD-----HTHrdgtgM 167
                                       44555555*****************98877888888888657777666555555544333444.....333334332 PP

                            UreE_C  78 ehehghehsH 87 
                                       +++ gh+h+H
  gi|344210016|ref|YP_004786192.1| 168 HDGGGHAHDH 177
                                       2223366666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); 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 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1394.64
//
Query:       gi|344210017|ref|YP_004786193.1|  [L=299]
Description: urease accessory protein UreD [Haloarcula hispanica ATCC 33960]
Scores for 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-47  161.3   0.7    3.7e-47  161.0   0.7    1.1  1  UreD      UreD urease accessory protein


Domain annotation for each model (and alignments):
>> UreD  UreD urease accessory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.0   0.7     2e-51   3.7e-47       1     212 [.      71     274 ..      71     275 .. 0.91

  Alignments for each domain:
  == domain 1  score: 161.0 bits;  conditional E-value: 2e-51
                                       EEEEE-SS-B-TT-EEEEEEEE-TT-EEEEEE-S-EEE---T.TS-EEEEEEEEE-TT-EEEE----EEE-TT-EEE CS
                              UreD   1 vyllsygGGlvgGDrldldvevgpgarlllttqgatkiyksraekvsrqtlrvrvaagatLellPdpvipfagsrye 77 
                                       v++ s++GG+++GDr d++++vg++a ++++tq++tk+  ++  +++  +++++v+ag+ L+++P+p+i++a+sry 
  gi|344210017|ref|YP_004786193.1|  71 VFVQSPTGGVAQGDRHDVSITVGDEAVAHVSTQSSTKVQTMTC-NYAAADTTLSVGAGGHLDYVPEPTILHADSRYV 146
                                       6899************************************954.78******************************* PP

                                       EEEEEEE-TT-EEEEEEEEE-S-CCCT--S-SSEEEEEEEE.EETTEEEEEEEEEE-T-TTST....TTTTT--EEE CS
                              UreD  78 qtqrfeLapgasllllDwvtsGrtargErwafdryrsrnevwvgdgrlllrDrlllepedesatslaerlagygvvg 154
                                       q+++++L+pga+ +++D+v++Gr argEr++f+ry sr++ +   + ll+ D+++l+p ++++ ++ + l++++v+g
  gi|344210017|ref|YP_004786193.1| 147 QEMTVDLSPGATAVVSDVVVPGRLARGERFEFERYLSRVRGTG-PDGLLFEDATHLTP-EDRDPTVPGVLGEFTVYG 221
                                       *****************************************87.689**********8.55788************* PP

                                       EEEEES......--HHHHHHTEEE..............EEEE-S.-.E.EEEEEESSHHHHH CS
                              UreD 155 tlilvgpefe..ellealreefaalprigaeeaeevlwsasrlr.g.lvvvrvlakdaeavr 212
                                       t ++++p+ +  el++al++ ++          +e  ++a++l  g  v vr+l+++ae+v+
  gi|344210017|ref|YP_004786193.1| 222 TTFVLAPDHDesELSDALHAAVTD---------DEARAGATALPnGaGVAVRALGDRAETVQ 274
                                       ******999557999999994444.........33448*****534479**********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1804.80
//
Query:       gi|344210018|ref|YP_004786194.1|  [L=207]
Description: urease accessory protein UreG [Haloarcula hispanica ATCC 33960]
Scores for complete 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   0.0    1.3e-31  109.6   0.0    1.1  1  cobW           CobW/HypB/UreG, nucleotide-binding domain
    5.2e-09   36.1   0.0    8.5e-09   35.4   0.0    1.3  1  MobB           Molybdopterin guanine dinucleotide synthesis p
    4.7e-07   29.1   1.0    2.1e-06   26.9   1.0    1.8  1  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
     0.0022   18.5   0.0     0.0022   18.5   0.0    1.4  1  ABC_tran       ABC transporter
     0.0026   17.7   0.1        1.4    8.8   0.0    2.5  3  RsgA_GTPase    RsgA GTPase
     0.0079   16.7   0.0      0.012   16.2   0.0    1.4  1  AAA_18         AAA domain
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.015   15.1   0.0    1.2  1  AAA_30         AAA domain
      0.031   14.2   0.0      0.053   13.4   0.0    1.4  1  NTPase_1       NTPase
      0.049   12.5   0.0      0.066   12.1   0.0    1.1  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
      0.051   12.7   0.1      0.088   11.9   0.1    1.3  1  LpxK           Tetraacyldisaccharide-1-P 4'-kinase
      0.081   13.3   0.0        0.1   13.0   0.0    1.3  1  AAA_16         AAA ATPase domain
      0.089   12.6   0.0       0.14   11.9   0.0    1.3  1  AAA_26         AAA domain
       0.13   11.9   0.0       0.26   10.9   0.0    1.5  1  SRP54          SRP54-type protein, GTPase domain
       0.13   12.2   0.1       0.21   11.5   0.1    1.3  1  NACHT          NACHT domain
       0.14   11.3   0.0       0.14   11.3   0.0    1.1  1  KAP_NTPase     KAP family P-loop domain
       0.19   10.7   0.0       0.26   10.3   0.0    1.2  1  T2SSE          Type II/IV secretion system protein


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 !  109.6   0.0   1.1e-34   1.3e-31       3     172 ..      11     180 ..       9     185 .. 0.91

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 1.1e-34
                                       EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.......EEEETTTTECCH.CTT-HH CS
                              cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgve......ivelenGciCct.lredll 70 
                                       ++++G++GsGKT+Ll++l+   +++gl++ vi N++  +++Da++lre+ +       +  +e+G +++t +red +
  gi|344210018|ref|YP_004786194.1|  11 VGIGGPVGSGKTSLLTALVpeLREQGLDVGVIANDIL-TQEDADVLRERFAGvvpedlVAGVETGACPHTgIREDPS 86 
                                       789*****************9899*************.*********99444457888******************* PP

                                       HHHHHHHHHH...TT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSS CS
                              cobW  71 kelealeere...erldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaad 143
                                       ++l+++ +      +ld++l+E++G ++++++          +  +d  ++v+++    ae+e+i++k + ++  +d
  gi|344210018|ref|YP_004786194.1|  87 MNLQQIDSFLadhPELDLVLVESGGdNLAATFN---------PELADYSLYVISV----AEGEDIPRKRGPGVVDCD 150
                                       ****98765555589**********88888877.........99***********....9***************** PP

                                       EEEEE-HHHHCHC...HHHHHHHHHHHHTT CS
                              cobW 144 llvlnKtDlldee.allekleerlrqlnpe 172
                                       llv+nKtDl++++  +l+++e+++++++++
  gi|344210018|ref|YP_004786194.1| 151 LLVINKTDLAPHVgVDLDVMERDADEVRDG 180
                                       **************99********999875 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 !   35.4   0.0   7.6e-12   8.5e-09       2      97 ..      11     108 ..      10     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 7.6e-12
                              MobB   2 lgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyrhrkAGAk.evlvaskerlalikel..e 75 
                                       +gi g  gsGKT+Ll+ l+pel+++gl vg+i  +     + +++ D  r r AG   e lva+ e  a  +    e
  gi|344210018|ref|YP_004786194.1|  11 VGIGGPVGSGKTSLLTALVPELREQGLDVGVIANDI----LTQEDADVLRERFAGVVpEDLVAGVETGACPHTGirE 83 
                                       6788999*************************7664....67899**********9735677777777776665777 PP

                              MobB  76 eaelsleellarlse...vDlvlvE 97 
                                       +++++l+++ + l++   +DlvlvE
  gi|344210018|ref|YP_004786194.1|  84 DPSMNLQQIDSFLADhpeLDLVLVE 108
                                       889999999999955578******9 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 !   26.9   1.0   1.9e-09   2.1e-06      31     180 ..      10     160 ..       3     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.9e-09
                                       EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----------------.--HCCCTSTTEEEEEE-----HHHH CS
                              MeaB  31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDkl.RleelavdegvfiRslpsrGalGGl 106
                                        vG+ G  G+Gk  l+ al+ elr++G  v+v+a D   +     +l ++   +   +  +gv   + p +G+    
  gi|344210018|ref|YP_004786194.1|  10 TVGIGGPVGSGKTSLLTALVPELREQGLDVGVIANDILTQEDA-DVLRERFaGVVPEDLVAGVETGACPHTGIREDP 85 
                                       79**********************************9887765.5665554135556688999999*********99 PP

                                       HHHHHHHHH.HHHHTT-SEEEEEEESSTTHHHHHHTT-SEEEEEEESSTTTTTTT--.CCCHHH-SEEEEE---HH CS
                              MeaB 107 aaktrevvl.lleaaGfDvvlietvGvGqsevdvaevvdtfvvlllpeaGDelqgik.kGileiaDiivvnkaDkk 180
                                       +++ +++   l +    D vl+e  G   + +   e++d ++ ++  + G+++   +  G+++  D++v+nk+D++
  gi|344210018|ref|YP_004786194.1|  86 SMNLQQIDSfLADHPELDLVLVESGGDNLAATFNPELADYSLYVISVAEGEDIPRKRgPGVVD-CDLLVINKTDLA 160
                                       9999988652779999****************************9999999997655257887.6*********54 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     2e-06    0.0022       5      67 ..       2      66 ..       1     203 [. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2e-06
                                      EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCE.EEE-SS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxx RF
                          ABC_tran  5 slklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkei.gvlpqe 67
                                      sl+ +   +v+i G+ G+GK++Ll +l  +l+ +  ++ +  +d+ + ++  +lr+++ gv+p++
  gi|344210018|ref|YP_004786194.1|  2 SLTHRDVATVGIGGPVGSGKTSLLTALVPELREQGLDVGVIANDILTqEDADVLRERFaGVVPED 66
                                      666677789*********************99876666555444444366666666542455555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0013       1.4     101     125 ..      10      34 ..       3      51 .. 0.80
   2 ?   -2.9   0.0       4.9   5.5e+03      27      41 ..      84      98 ..      82     106 .. 0.74
   3 !    6.2   0.0     0.008       8.9      50     100 ..     151     203 ..     149     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                                       EEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinallpelel 125
                                       t+ + G+ G GK++L+ al+pel+ 
  gi|344210018|ref|YP_004786194.1|  10 TVGIGGPVGSGKTSLLTALVPELRE 34 
                                       555779***************8644 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.9
                                      TTT--HHHHHHHHHH CS
                       RsgA_GTPase 27 epelslnlldrfLvl 41
                                      +p+++l+++d fL+ 
  gi|344210018|ref|YP_004786194.1| 84 DPSMNLQQIDSFLAD 98
                                      678888888888864 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.008
                                       EEEEE-GGG--HHH.HHHHHHHHHHHT.TSEEEE--TTTHTTHHHHHHHCTTS CS
                       RsgA_GTPase  50 vivlnKiDlleeee.eleelkeeleal.gyevllvsaktkegleelkellkdk 100
                                       ++v+nK+Dl+ +   +l+ ++ +  ++ + +v++++ k++++++e+ +++++ 
  gi|344210018|ref|YP_004786194.1| 151 LLVINKTDLAPHVGvDLDVMERDADEVrDGPVVFTNCKDETNIDEVLSHVREG 203
                                       689*******99987666666666554257999************99998875 PP

>> AAA_18  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     0.012       1      37 [.      11      52 ..      11     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrl.gf....gvnlrdvakengl 37
                                      +++ G+ G+GKt+l  +L  +l +     gv+ +d++++++ 
  gi|344210018|ref|YP_004786194.1| 11 VGIGGPVGSGKTSLLTALVPELrEQgldvGVIANDILTQEDA 52
                                      689***************777644466889999999998875 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   1.3e-05     0.015      20      66 ..      10      59 ..       2     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrviglAp...tgkaAkvLaeel 66
                                      ++ + Gp G+GKt +l+al+  ++++g +v ++A    t++ A+vL+e +
  gi|344210018|ref|YP_004786194.1| 10 TVGIGGPVGSGKTSLLTALVPELREQGLDVGVIANdilTQEDADVLRERF 59
                                      44567888*************************96444788888888754 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   4.8e-05     0.053       2      38 ..      11      46 ..      10      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.8e-05
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteev 38
                                      v i Gp G+GKt l+  ++ +l+++g+ v G++++++
  gi|344210018|ref|YP_004786194.1| 11 VGIGGPVGSGKTSLLTALVPELREQGLDV-GVIANDI 46
                                      7899***********************99.5666655 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 ?   12.1   0.0   5.8e-05     0.066      13      44 ..       6      37 ..       2      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.8e-05
                     TrwB_AAD_bind 13 retqhilivGttGsGKtqalekllrairargd 44
                                      r+++ + i G +GsGKt  l++l+ ++r++g 
  gi|344210018|ref|YP_004786194.1|  6 RDVATVGIGGPVGSGKTSLLTALVPELREQGL 37
                                      566778999********************993 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   7.9e-05     0.088      47      72 ..      18      43 ..       7      44 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.9e-05
                                      -HSHHHHHHHHHHHTTTS..-EEEEE CS
                              LpxK 47 GtGKTPlvialvkllqarglkvgvlS 72
                                      G+GKT+l  alv  l+++gl vgv++
  gi|344210018|ref|YP_004786194.1| 18 GSGKTSLLTALVPELREQGLDVGVIA 43
                                      89**********************95 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.9e-05       0.1      27      55 ..      11      41 ..       3     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.9e-05
                            AAA_16 27 vllsGesGvGKsslvrellralekd..ggif 55
                                      v + G+ G+GK+sl+++l  +l+++  ++ +
  gi|344210018|ref|YP_004786194.1| 11 VGIGGPVGSGKTSLLTALVPELREQglDVGV 41
                                      5588*************99999999662333 PP

>> AAA_26  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      11     115 ..      18     118 ..      13     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                            AAA_26  11 gvGKTvvslgLvralkrkgvkvgyfKPiqtgieededselikellgldqtyelpeplalsaplspelaarqegedid 87 
                                       g+GKT++ ++Lv  l+++g  vg+   i+++i ++ed+++++e +    +++l   +  ++ + p+   r+++ +  
  gi|344210018|ref|YP_004786194.1|  18 GSGKTSLLTALVPELREQGLDVGV---IANDILTQEDADVLRERFAGVVPEDLVAGV--ETGACPHTGIREDP-SMN 88 
                                       79*********************9...899***********9988766666655555..45567888888777.666 PP

                            AAA_26  88 lekiv..kelekdadivvVEGagglgvpit 115
                                       l++i    +   + d+v+VE  g  +  ++
  gi|344210018|ref|YP_004786194.1|  89 LQQIDsfLADHPELDLVLVESGGDNLAATF 118
                                       888854333344669999998877765555 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   0.00023      0.26       7      39 ..      14      46 ..       8      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                                      EESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  7 vGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                       G+ G+GKT+ l+ L   l+++g +v ++a D+
  gi|344210018|ref|YP_004786194.1| 14 GGPVGSGKTSLLTALVPELREQGLDVGVIANDI 46
                                      5889***************************97 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00018      0.21       2      29 ..      10      37 ..       9      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaegkl 29
                                      +v + G+ GsGKT Ll  l+ +++e+ l
  gi|344210018|ref|YP_004786194.1| 10 TVGIGGPVGSGKTSLLTALVPELREQGL 37
                                      56788****************9999876 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 ?   11.3   0.0   0.00013      0.14      19      47 ..       7      35 ..       2     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                        KAP_NTPase 19 tpivvgLygkWGsGKssllnkledelkef 47
                                      +  +vg+ g+ GsGK+sll+ l  el+e+
  gi|344210018|ref|YP_004786194.1|  7 DVATVGIGGPVGSGKTSLLTALVPELREQ 35
                                      5679******************9999998 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 ?   10.3   0.0   0.00023      0.26     134     157 ..      13      43 ..       4      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00023
                             T2SSE 134 vsGgTgsGKttllyallkeinks.......d 157
                                       + G+ gsGKt ll al+ e+ ++        
  gi|344210018|ref|YP_004786194.1|  13 IGGPVGSGKTSLLTALVPELREQgldvgviA 43 
                                       78*****************999854333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1402.26
//
Query:       gi|344210019|ref|YP_004786195.1|  [L=128]
Description: urease subunit gamma [Haloarcula hispanica ATCC 33960]
Scores for complete 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-42  142.3   0.0    5.5e-42  142.1   0.0    1.0  1  Urease_gamma  Urease, gamma subunit


Domain annotation for each model (and alignments):
>> Urease_gamma  Urease, gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.1   0.0   3.1e-46   5.5e-42       1      99 []       1      99 [.       1      99 [. 1.00

  Alignments for each domain:
  == domain 1  score: 142.1 bits;  conditional E-value: 3.1e-46
                                      ----HHHHHHHHHHHHHHHHHHHHHTT--B-HHHHHHHHHHHHHHHHHCTS-HHHHHHHHCCSS-CCCB-TTCHHH-SE CS
                      Urease_gamma  1 mkLtpreldkLllfaaaelAqkrlarGlkLnhpEavaliasevlelardgksvaelmelgkklLtredvldgvaellee 79
                                      mkLt +e+++L++f+aae+A++r++rG+ LnhpEava+i+++++e+ rdg+svae+ + ++klL+redv+dgv+e++++
  gi|344210019|ref|YP_004786195.1|  1 MKLTAKEQERLTVFTAAEVARRRKERGVPLNHPEAVAYISDWCIERGRDGQSVAEIRSGASKLLGREDVMDGVPEMIDM 79
                                      9****************************************************************************** PP

                                      EEEEEEETTEEEEEEEES-S CS
                      Urease_gamma 80 vqveatfpdgtkLvtvhdpi 99
                                      +qve +fpdgtkLvtvhdpi
  gi|344210019|ref|YP_004786195.1| 80 IQVEPVFPDGTKLVTVHDPI 99
                                      *******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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: 0.45u 0.33s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 768.51
//
Query:       gi|344210020|ref|YP_004786196.1|  [L=568]
Description: urease subunit alpha [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-64  218.3   0.3    2.3e-64  217.9   0.3    1.1  1  Amidohydro_1  Amidohydrolase family
    1.9e-49  167.0   2.7    2.3e-49  166.7   1.5    1.8  2  Urease_alpha  Urease alpha-subunit, N-terminal domain
    3.9e-10   39.8   3.6    3.1e-07   30.2   0.2    2.6  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 !  217.9   0.3   3.9e-68   2.3e-64       1     337 [.     129     452 ..     129     455 .. 0.97

  Alignments for each domain:
  == domain 1  score: 217.9 bits;  conditional E-value: 3.9e-68
                                       EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEE CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaeelplgl 77 
                                       i ++G+ D+H+H+               + +  ++al  gi+t+l++G +  a + +t ++++++ l+aae+ p+++
  gi|344210020|ref|YP_004786196.1| 129 IATAGGLDIHIHF--------------NSAQLHEHALSGGITTMLGGGYGGGATTTTTGPENVKRFLQAAEAWPVNV 191
                                       5799*********..............799*********************************************** PP

                                       EEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE.. CS
                      Amidohydro_1  78 rilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHa.. 152
                                       +++g+      g+a+ +  +re+++aga              +l+ he+++ ++e++  +l++a+++d++v++H+  
  gi|344210020|ref|YP_004786196.1| 192 GFYGK------GNASDPGPLREQVEAGA-------------CGLKLHEDWGSTPETINTCLEVAEDEDVQVCMHTdt 249
                                       *****......*****************.............8*********************************** PP

                                       TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE...HH...HHHHHHHHHHHHCEE....... CS
                      Amidohydro_1 153 letkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt...pt...eaellkerlkeagva....... 216
                                       l++ g+ve++  a +++++h +h e+a++++++d++ ++ + +++++   p+   + ++ +e+l++++v+       
  gi|344210020|ref|YP_004786196.1| 250 LNEAGFVENTFGAVDGRTMHLFHIEGAGGGHAPDIMEMVGEPNMLPSstnPSmpyTDNTFDEHLDMVMVChhlnpdv 326
                                       ***********************************************65533888889******************* PP

                                       ..HHHHHHHHSEHHHHHHHHHHHH.TSCEEEEEECTTSSCCGGHHHH...HHHHHHHHHHCCTT...TTHCHCHHHH CS
                      Amidohydro_1 217 ..hcpfsnsilrsgrealrkalde.GvkvglgtDgaasgnslnllee...lrlalklqrgllye...deegglslke 284
                                         +++f++s++r +++a++++l++ G+++++++D++a+g+ ++++ +   ++ ++k+qrg l e    ++++ ++k+
  gi|344210020|ref|YP_004786196.1| 327 peDVAFAESRVRAETIAAEDVLHDmGAISMMTSDSQAMGRMAEVIPRtwqTASKMKSQRGPLPEdegTGADNHRIKR 403
                                       ****************************************************************9998899****** PP

                                       HHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEE CS
                      Amidohydro_1 285 alrmaTingAkalglddkvGsievGkdADlvvvdldilaafvglkkdgnvkkv 337
                                       +++++T n+A++ g++d+vG++e+Gk AD+ ++     +af+g+k++++ k++
  gi|344210020|ref|YP_004786196.1| 404 YIAKYTVNPAISAGIEDHVGTLEPGKLADICLW----DPAFFGVKPAMTFKGG 452
                                       *********************************....*******998876654 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 !  166.7   1.5   3.8e-53   2.3e-49       2     120 ..       4     122 ..       3     123 .. 0.97
   2 ?   -2.8   0.0       1.3   7.7e+03      92     113 ..     272     293 ..     250     299 .. 0.74

  Alignments for each domain:
  == domain 1  score: 166.7 bits;  conditional E-value: 3.8e-53
                      Urease_alpha   2 klsreeyaelyGptvgDrvrLadtellievekDltvyGeevkfGggkviRdgmgqssaakeee.alDlvitnavilD 77 
                                       +++re+yaelyGpt+gD+vrL+dtel++eve+Dl+++G+e++fGggk++Rdg+g++  ++++e alD+v+tna+i+D
  gi|344210020|ref|YP_004786196.1|   4 DIDRENYAELYGPTTGDKVRLGDTELFAEVEDDLRTHGDEAVFGGGKTLRDGLGMAPGVTQAEgALDWVLTNATIID 80 
                                       599*****************************************************99988777************* PP

                      Urease_alpha  78 a.tgivkadigikdgrivaiGkagnpdvmdgvdeelvigastev 120
                                          giv adigi++g+i++iGkagnpd+mdgvd  +v+g+st+v
  gi|344210020|ref|YP_004786196.1|  81 PiLGIVAADIGIRNGEIAGIGKAGNPDTMDGVD--MVVGPSTDV 122
                                       989******************************..*******98 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.3
                      Urease_alpha  92 rivaiGkagnpdvmdgvdeelv 113
                                       +i + G    pd+m+ v e  +
  gi|344210020|ref|YP_004786196.1| 272 HIEGAGGGHAPDIMEMVGEPNM 293
                                       5677788889999998876444 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.4   7.3e-05      0.44       5      35 ..     125     148 ..     121     192 .. 0.73
   2 !   30.2   0.2   5.2e-11   3.1e-07     353     455 ..     338     446 ..     222     456 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 7.3e-05
                      Amidohydro_3   5 akGrlvlPGFvDsHtHlagggvnlrllrlpd 35 
                                       a+G++ ++G+ D+H+H  +++       l +
  gi|344210020|ref|YP_004786196.1| 125 AEGKIATAGGLDIHIHFNSAQ-------LHE 148
                                       9***************66655.......333 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 5.2e-11
                      Amidohydro_3 353 rargstpvkellnagvkvalgsD..apvgpfdpwprigaavmrktrrgg....evlrpdeelsleealalyTrgpAk 423
                                       ra+++++   l ++g   +++sD  a + +   +pr + +  + +   g    +  +    + +   +a yT +pA 
  gi|344210020|ref|YP_004786196.1| 338 RAETIAAEDVLHDMGAISMMTSDsqAMGRMAEVIPRTWQTASKMKSQRGplpeDEGTGADNHRIKRYIAKYTVNPAI 414
                                       5555566666777888888888887777777888888877766665555888844444557899999********** PP

                      Amidohydro_3 424 algledrkGtLevGadADlvvldadpldvdpp 455
                                         g ed+ GtLe+G+ AD++++d + + v+p+
  gi|344210020|ref|YP_004786196.1| 415 SAGIEDHVGTLEPGKLADICLWDPAFFGVKPA 446
                                       ***************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); 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:                         3  (0.000167327); expected 0.2 (1e-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: 3936.74
//
Query:       gi|344210021|ref|YP_004786197.1|  [L=134]
Description: urease subunit beta [Haloarcula hispanica ATCC 33960]
Scores for 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-45  151.0   0.1      1e-44  150.5   0.1    1.2  1  Urease_beta  Urease beta subunit


Domain annotation for each model (and alignments):
>> Urease_beta  Urease beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.5   0.1   5.7e-49     1e-44       1      97 [.       7     103 ..       7     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 150.5 bits;  conditional E-value: 5.7e-49
                                       TT-EE-SSSEEETTTT---EEEEEEE-SSS-EEEETTS-GGGS-TTEES-HHHHTTEEE-SSTT-EEEE-TT-EEEE CS
                       Urease_beta   1 pgeiiteegeielnagretiklkvantgdrpiqvgshyhflevnkaLefdRekalGlrldipagtavrfepgeekev 77 
                                       pge+i  eg+++ln+gret++++v ntgdrp qvgsh+hf+e+n+aLefdRe+a+G+rl+ipagtavrfepg+e++v
  gi|344210021|ref|YP_004786197.1|   7 PGEVIPGEGTVTLNEGRETTEVTVGNTGDRPSQVGSHFHFFEANAALEFDREAAMGMRLNIPAGTAVRFEPGDEQTV 83 
                                       8**************************************************************************** PP

                                       EEEE-STT-EE-STTSS--E CS
                       Urease_beta  78 elvelaGerkvyGlnglvng 97 
                                       elve++G+r+ +G+nglvng
  gi|344210021|ref|YP_004786197.1|  84 ELVEIGGKRRAHGMNGLVNG 103
                                       ******************98 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:                      175  (0.00976072); 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 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 915.11
//
Query:       gi|344210022|ref|YP_004786198.1|  [L=435]
Description: urea/short chain-amides ABC transporter periplasmic substrate-binding protein 1 [Haloarcula hispanica ATCC 33960]
Scores for 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-68  230.0   0.6    7.4e-68  229.7   0.6    1.1  1  Peripla_BP_6  Periplasmic binding protein
    3.3e-66  223.8   0.1    4.1e-66  223.4   0.1    1.0  1  Peripla_BP_5  Periplasmic binding protein domain
     0.0047   16.7   4.1     0.0093   15.8   4.1    1.5  1  TAT_signal    TAT (twin-arginine translocation) pathway signa


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 !  229.7   0.6   1.2e-71   7.4e-68       1     339 [.      43     390 ..      43     394 .. 0.92

  Alignments for each domain:
  == domain 1  score: 229.7 bits;  conditional E-value: 1.2e-71
                                       EEEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEETTEEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-B CS
                      Peripla_BP_6   1 pikiGlltplsGpyassgksllagaqaafeeiNaaGGinGrkielverDdaydpdraaeaarrlvdqdgvdalvgpl 77 
                                       ++kiG+l + sG +a +g + +++  +a+eeiNa+GGi+G++ie   rD ++d +r +e +r ++++++vdal+++ 
  gi|344210022|ref|YP_004786198.1|  43 TLKIGVLEDQSGNFALVGDPKAKASMLAIEEINANGGIDGKQIETFQRDPQSDNQRYQELTRTAINEENVDALWAGY 119
                                       689************************************************************************** PP

                                       SHHHHHHHHHHHHHHT-EEEESS-HHCCTTSTTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEEESSHHHHHHHHH CS
                      Peripla_BP_6  78 ssavaaavaevlakdgvpvigpagltgekcspyvfslgpsysaqasalveylakelggkkvalvyadyafgregiaa 154
                                       ssa+++a++++++++  +++++++++g+ c + +f +gp++++q+  ++ yl++e+g   +++++ady fg+ +++ 
  gi|344210022|ref|YP_004786198.1| 120 SSATREAIRPIIDRNEQLYFYTTQYEGGVCDEFTFAVGPTARQQLGIVLPYLVEEFG-PDIYTIAADYNFGQLSADW 195
                                       ******************************************************998.9****************** PP

                                       HHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEEECCC....- CS
                      Peripla_BP_6 155 lkaaakaaGgevvgeepvplgttdfsaqvlqikaagadavllagtgadlaallkaaaeaGldakrillvsws....g 227
                                       +k +a +++ +v+gee++pl++++f + +++i++a +d+v+ + +ga+ ++++ + a+aGld   i++++++    g
  gi|344210022|ref|YP_004786198.1| 196 VKVLANENDANVLGEEFIPLSESSFGSTINRIQEADPDFVMSMLVGANHTSFYEQKASAGLD---IPIGTSTamaqG 269
                                       **************************************************************...444433312125 PP

                                       CHHHHHHHHHHHHTTEEEEESCSTC...CCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHHHHHCCTHCCH CS
                      Peripla_BP_6 228 seedlkalggeaaegvlavtpyfpd...ldnpavrafvaayeaayggapppsqfaaggyiaadlllealkaagsltr 301
                                       +e+  ++l ++a+++++a ++y ++    +n     fv++y + y++ap+ ++ a   y ++ ++++a+++ag++++
  gi|344210022|ref|YP_004786198.1| 270 YEH--RRLDAPAMANIYAGVNYMEEvptESNTGDGGFVDRYFEMYPDAPYLNEEAETNYFSTYMYKKAVEQAGTTEQ 344
                                       555..899999************996656788899****************************************** PP

                                       HHHHHHHHH...S-BE....CCCTC.CBEECTTSBEE--EEEEEE- CS
                      Peripla_BP_6 302 eavraales...lgfd....gllgp.lkftaedhqasrpvyvvqvd 339
                                        +v++ales   lg++    ++ g+ +  + ++h++ + ++++++d
  gi|344210022|ref|YP_004786198.1| 345 PEVIDALESgieLGTEeapeAPEGEtIRLDGATHHVDHHMWIMRAD 390
                                       *********76655443333587862445599***********987 PP

>> Peripla_BP_5  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.4   0.1   6.8e-70   4.1e-66       1     349 [.      44     401 ..      44     408 .. 0.93

  Alignments for each domain:
  == domain 1  score: 223.4 bits;  conditional E-value: 6.8e-70
                      Peripla_BP_5   1 ikvGvLhSlsGtmaisekslkdaallaieeinaagGvlgrkieavvvdpasdwelfaekaeklieedkvevvfGcwt 77 
                                       +k+GvL  +sG  a++     +a +laieeina+gG++g++ie+   dp+sd ++++e ++  i+e++v+++  ++ 
  gi|344210022|ref|YP_004786198.1|  44 LKIGVLEDQSGNFALVGDPKAKASMLAIEEINANGGIDGKQIETFQRDPQSDNQRYQELTRTAINEENVDALWAGYS 120
                                       59*************************************************************************** PP

                      Peripla_BP_5  78 SasRkavlpvveelnalLfYpvqYEGeEssknviYtGaapnqqaipavdyllselgakrvflvGsdyvypretnril 154
                                       Sa+R+a+ p+++++++l+fY +qYEG  + +  +  G ++ qq+  ++ yl++e+g   ++ + +dy + + ++  +
  gi|344210022|ref|YP_004786198.1| 121 SATREAIRPIIDRNEQLYFYTTQYEGGVCDEFTFAVGPTARQQLGIVLPYLVEEFG-PDIYTIAADYNFGQLSADWV 196
                                       ********************************************************.******************** PP

                      Peripla_BP_5 155 kallkakggevvgeeYlplgssdvqkivakikkakpdvvlstinGdsnvafykelkeagikaekipv.vslsvae.e 229
                                       k l ++++ +v+gee++pl +s + + +++i++a pd+v+s ++G + ++fy++ ++ag++   ip+ +s+ +a+  
  gi|344210022|ref|YP_004786198.1| 197 KVLANENDANVLGEEFIPLSESSFGSTINRIQEADPDFVMSMLVGANHTSFYEQKASAGLD---IPIgTSTAMAQgY 270
                                       ***********************************************************97...6762333444325 PP

                      Peripla_BP_5 230 elaaidaealvGhlaawnYfqsvdtpenk...afvakfkarvgedrvtndpmeaayiqvklwaqAvekagstdvekv 303
                                       e +++da a++  +a +nY++ v t++n+    fv+++ +++ +   +n+ +e+ y++++++++Ave+ag+t+  +v
  gi|344210022|ref|YP_004786198.1| 271 EHRRLDAPAMANIYAGVNYMEEVPTESNTgdgGFVDRYFEMYPDAPYLNEEAETNYFSTYMYKKAVEQAGTTEQPEV 347
                                       889*************************84446****************************************9999 PP

                      Peripla_BP_5 304 real.......lgqelkapeGe.vkidpenhhlsktvrigkikadGqfeivwet 349
                                        +al       +++  +apeGe +++d ++hh+ + + i +++++ ++e v++ 
  gi|344210022|ref|YP_004786198.1| 348 IDALesgielgTEEAPEAPEGEtIRLDGATHHVDHHMWIMRADEEHNVEAVENR 401
                                       998743333223455689***99********************99999988765 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 !   15.8   4.1   1.6e-06    0.0093       2      25 ..       6      28 ..       5      29 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-06
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      +SRR+FL +s+Aa   ++l+gc+a
  gi|344210022|ref|YP_004786198.1|  6 VSRRQFLGASGAA-LVTGLAGCSA 28
                                      8*******99998.5777888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2887.72
//
Query:       gi|344210023|ref|YP_004786199.1|  [L=312]
Description: branched-chain/neutral amino acids ABC transporter permease [Haloarcula hispanica ATCC 33960]
Scores for 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-36  124.0  35.6    8.9e-36  123.4  35.6    1.2  1  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
       0.95    9.6   0.0       0.95    9.6   0.0    5.4  7  DUF2613       Protein of unknown function (DUF2613)


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 !  123.4  35.6   9.9e-40   8.9e-36       3     251 ..       9     279 ..       7     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 123.4 bits;  conditional E-value: 9.9e-40
                      BPD_transp_2   3 lnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlr 79 
                                       l++l ++a +++aA Gla++fgi+Gvinl+hg+f+++Gay+a+l++++l+ +l +a++++ lv +++g l+++ ++ 
  gi|344210023|ref|YP_004786199.1|   9 LQFLDSFAFIVLAAAGLAIIFGIMGVINLAHGEFILIGAYTATLAVTQLGLPLVVAMVAGGLVTGLFGILTERVIIS 85 
                                       578999********************************************999999999999999999999999999 PP

                      BPD_transp_2  80 lkvdelii..tll.............llsvlvgltlllltgitsgvkgqs.....svkellgfagallsflsavivl 136
                                          ++ ++  tl+              +++ +gl l +lt++t+  +g+s     ++ ++++    + s+   v++ 
  gi|344210023|ref|YP_004786199.1|  86 GAWPNWVSqrTLGrdiieplydrladSMVATFGLSL-ILTQGTRIAYGNSidglsTPFGPIEYGAFSYSTYRIVLAG 161
                                       999999884455599999999****99999999999.999999999999888877888888888888888888888* PP

                      BPD_transp_2 137 lalllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvglg 213
                                       + + l++a ++l++rt fG++ ra+ +++e+a+a+G+n++r+ +ltf i++alAgl Gal+a   +  p   g ++ 
  gi|344210023|ref|YP_004786199.1| 162 VSIGLLVATYYLFTRTDFGMRARATIQDKETAQAMGVNTERMYMLTFGIGSALAGLTGALFAPVVTMRP-TLGDQFL 237
                                       ****************************************************************99999.******* PP

                      BPD_transp_2 214 fnaiaavvlGga.....gsllgtviGaliigvvksllltllgi 251
                                        ++++avv+Gg        l g v+Ga++ ++++   +t++g 
  gi|344210023|ref|YP_004786199.1| 238 VESFVAVVVGGPsvvlgTALSGGVLGAILAVFSNL-YGTFIGR 279
                                       ************77774334444555544444444.5555443 PP

>> DUF2613  Protein of unknown function (DUF2613)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   1.9       1.3   1.1e+04      15      25 ..      22      32 ..      16      37 .. 0.60
   2 ?    0.2   0.8      0.09   8.1e+02       4      16 ..      59      71 ..      57      82 .. 0.74
   3 ?    9.6   0.0   0.00011      0.95      18      53 ..     113     148 ..     112     149 .. 0.96
   4 ?   -2.2   0.1      0.51   4.6e+03      11      20 ..     159     168 ..     158     177 .. 0.73
   5 ?   -1.7   0.5      0.36   3.2e+03       6      15 ..     209     218 ..     206     228 .. 0.74
   6 ?   -4.0   5.5       1.9   1.7e+04       9      17 ..     250     258 ..     236     272 .. 0.55
   7 ?   -1.5   1.4      0.33   2.9e+03       6      27 ..     267     288 ..     261     291 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.3
                           DUF2613 15 vlGvvavfgvt 25
                                      + G++ +fg+ 
  gi|344210023|ref|YP_004786199.1| 22 AAGLAIIFGIM 32
                                      45556666654 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.09
                           DUF2613  4 gPaaaSaVaGivl 16
                                      +P +++ VaG ++
  gi|344210023|ref|YP_004786199.1| 59 LPLVVAMVAGGLV 71
                                      5999999998444 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00011
                           DUF2613  18 vvavfgvtavvqqdsrPstdravnadsalLgsveYG 53 
                                       +va+fg++++++q +r +  ++++  s+  g +eYG
  gi|344210023|ref|YP_004786199.1| 113 MVATFGLSLILTQGTRIAYGNSIDGLSTPFGPIEYG 148
                                       69********************************** PP

  == domain 4  score: -2.2 bits;  conditional E-value: 0.51
                           DUF2613  11 VaGivlGvva 20 
                                        aG+ +G+ +
  gi|344210023|ref|YP_004786199.1| 159 LAGVSIGLLV 168
                                       6788888755 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 0.36
                           DUF2613   6 aaaSaVaGiv 15 
                                       ++ Sa aG++
  gi|344210023|ref|YP_004786199.1| 209 GIGSALAGLT 218
                                       6889999986 PP

  == domain 6  score: -4.0 bits;  conditional E-value: 1.9
                           DUF2613   9 SaVaGivlG 17 
                                       S+V G +l 
  gi|344210023|ref|YP_004786199.1| 250 SVVLGTALS 258
                                       344444442 PP

  == domain 7  score: -1.5 bits;  conditional E-value: 0.33
                           DUF2613   6 aaaSaVaGivlGvvavfgvtav 27 
                                       a+ S   G  +G +a + +++v
  gi|344210023|ref|YP_004786199.1| 267 AVFSNLYGTFIGRIALLVAALV 288
                                       6778888999999888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1814.11
//
Query:       gi|344210024|ref|YP_004786200.1|  [L=384]
Description: urea/short chain-amides ABC transporter permease [Haloarcula hispanica ATCC 33960]
Scores for 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-33  113.7  39.6    8.2e-33  113.7  39.6    1.4  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 ?   -4.2   0.1       0.4   7.3e+03      61      72 ..      36      47 ..      30      49 .. 0.60
   2 !  113.7  39.6   4.6e-37   8.2e-33       6     266 ..      57     343 ..      55     347 .. 0.91

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 0.4
                      BPD_transp_2 61 vallvgaavgll 72
                                      v++lv++a+ ++
  gi|344210024|ref|YP_004786200.1| 36 VGFLVAVAALAV 47
                                      556666655554 PP

  == domain 2  score: 113.7 bits;  conditional E-value: 4.6e-37
                      BPD_transp_2   6 ltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl..lllallvallvgaavglllgllvlrl 80 
                                       l+l+++la+++l+l++v+g++Gv+++g+  f+++Gay++++++ ++  +  + +a+++++++g++ +++lg+   + 
  gi|344210024|ref|YP_004786200.1|  57 LSLFMVLALLGLSLSVVWGYSGVLSFGQVVFFGIGAYTFGVVSINYATPggITAAVIAGIVGGGVSAAILGYFMFYG 133
                                       7899*************************************9988888889************************** PP

                      BPD_transp_2  81 kvdeliitllllsvlvgltlllltgitsgvkgqs....svkellgfagallsflsaviv.................. 135
                                       +v+ +++t+++l+  ++l  ++ +++ s ++  +    +++++ +++   l  ++a ++                  
  gi|344210024|ref|YP_004786200.1| 134 GVRDVYVTIITLVSTIVLHTFMAQTAGSEWAIGEaalgGFNGMPDIPLLTLGVGGASYQfiynpfpmriigigavei 210
                                       **********9998888888888887776665553444777777777777777777777****************** PP

                      BPD_transp_2 136 .......llalllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsip 205
                                              l++l+ +++ l  l+++ +Gr + av+e+e+  +++G+nv+rvk+++f ++galAgl+G+l+a++ + i+
  gi|344210024|ref|YP_004786200.1| 211 spfyylvLTLLVGAYLGLRALVNSDYGRVMVAVREDEDRTEMFGYNVTRVKFVVFTLGGALAGLSGVLYAARNVYID 287
                                       ******9999999**************************************************************** PP

                      BPD_transp_2 206 p.nigvglgfnaiaavvlGgagsllgtviGaliigvvksllltllgiptelarvllgallil 266
                                       p  +++ +   ++++v lGg  sllg+v+++l + ++ +  ++    + ela vllg ll++
  gi|344210024|ref|YP_004786200.1| 288 PtVFSLLFATLPVIWVSLGGRKSLLGAVVATLGVEYLRI--SM----AGELALVLLGTLLLV 343
                                       ********************************9999999..22....357889999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); 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 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 2306.40
//
Query:       gi|344210025|ref|YP_004786201.1|  [L=268]
Description: urea ABC transporter ATP-binding protein [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-31  108.3   0.0      6e-31  107.8   0.0    1.3  1  ABC_tran      ABC transporter
    7.2e-09   35.9   1.9     0.0011   18.9   0.4    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    7.9e-07   28.7   0.3    0.00034   20.1   0.3    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    2.6e-05   24.8   0.1    4.2e-05   24.1   0.1    1.3  1  AAA_23        AAA domain
    0.00011   21.9   0.0    0.00018   21.2   0.0    1.2  1  AAA_27        AAA domain
    0.00024   21.1   0.0    0.00051   20.0   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
    0.00053   19.7   0.0    0.00098   18.8   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0039   17.1   0.2     0.0088   15.9   0.2    1.6  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
     0.0053   17.2   0.1       0.01   16.3   0.1    1.4  1  AAA_16        AAA ATPase domain
     0.0057   16.7   0.0      0.026   14.6   0.0    1.9  2  MMR_HSR1      50S ribosome-binding GTPase
     0.0061   16.3   0.0     0.0081   15.9   0.0    1.2  1  AAA_15        AAA ATPase domain
     0.0064   16.2   0.0      0.011   15.4   0.0    1.7  1  AAA_30        AAA domain
     0.0066   16.7   0.1      0.019   15.2   0.1    1.7  1  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.019   14.5   0.0       0.03   13.9   0.0    1.3  1  GTP_EFTU      Elongation factor Tu GTP binding domain
       0.22   11.8   1.7        2.6    8.3   0.1    2.5  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 !  107.8   0.0     5e-34     6e-31       2     137 .]      50     194 ..      49     194 .. 0.95

  Alignments for each domain:
  == domain 1  score: 107.8 bits;  conditional E-value: 5e-34
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                       ++v++++ ege+  ++G+nGaGKStLl+l++g ++ t G+i ++g+d+++ +++e+ ++ i++ +q p++  +l+vr
  gi|344210025|ref|YP_004786201.1|  50 DDVDFSVAEGELRCLIGPNGAGKSTLLNLITGSYEATDGSIYYNGHDITDlDPHERISRGISMKFQVPSVYGDLSVR 126
                                       79*************************************************************************** PP

                                       HH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       en            e+++ +++a++  gl++ +d  +     +LS+Gq+q +++ +a + +p+llllDEp a
  gi|344210025|ref|YP_004786201.1| 127 ENvrlpvqqfadgeERRRLVAEAIEAAGLTGYEDVDA----GQLSHGQQQQLEIGMAAALEPDLLLLDEPVA 194
                                       *********9987444455************888888....*****************************75 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.4   9.2e-07    0.0011       3      22 ..      63      82 ..      62     142 .. 0.76
   2 !   16.5   0.0   4.8e-06    0.0057     228     295 ..     157     222 ..     132     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.2e-07
                            AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                      +liGpNg+GKS+LL ++ + 
  gi|344210025|ref|YP_004786201.1| 63 CLIGPNGAGKSTLLNLITGS 82
                                      59*************99653 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 4.8e-06
                            AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQvilt 295
                                       ++ +++a +lS G+++ l +  a +  +   +lll+DEp +gL+ +  + ++e + +++++ g+ +++ 
  gi|344210025|ref|YP_004786201.1| 157 GYEDVDAGQLSHGQQQQLEIGMAAALEP---DLLLLDEPVAGLDVAEREAIAERItRLNEEQGIAFVVI 222
                                       56789999*********98888888777...9********************99954444467777765 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 !   20.1   0.3   2.9e-07   0.00034      24     213 ..      59     240 ..      39     245 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.9e-07
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TT.TTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESS.SSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersa.kklrseklsdlihkskekasvkkaeveitfdnedkklk.iekeevs 98 
                                        ++ +++GpNG+GKs ll+ i      ++       ++++dl  +    ++  +  +++ f+ ++       +e+v 
  gi|344210025|ref|YP_004786201.1|  59 GELRCLIGPNGAGKSTLLNLITGSYEATDGsIYYNGHDITDLDPH----ER-ISRGISMKFQVPSVYGDlSVRENVR 130
                                       457899999999999999999433322222013334444444333....22.2333555555555443202346799 PP

                                       EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                       + ++ + +ge + ++  + +   e + l   ++++  +LS G+++ + + +  A++   p  l llDe  a LD ++
  gi|344210025|ref|YP_004786201.1| 131 LPVQQFADGEERRRLVAEAI---EAAGLTGYEDVDAGQLSHGQQQQLEIGMAAALE---P-DLLLLDEPVAGLDVAE 200
                                       99999999997777755554...55666778999999********99999986654...4.4899************ PP

                                       HHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEEE CS
                                       xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 176 vkkvaellkekskn..aQfivislreemlekadklvgvtk 213
                                       ++++ae++ + +++    f+vi ++++++++  + v v +
  gi|344210025|ref|YP_004786201.1| 201 REAIAERITRLNEEqgIAFVVIEHDTDFVANIAEEVTVLH 240
                                       ********97665545899********9999877777665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   3.5e-08   4.2e-05       5      40 ..      41      80 ..      39     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.5e-08
                            AAA_23  5 enfrsfrdqe.idF...skgltlItGpNGaGKTTildAik 40
                                      + f+ f  ++ +dF   +  l +++GpNGaGK+T+l+ i+
  gi|344210025|ref|YP_004786201.1| 41 KQFGGFTATDdVDFsvaEGELRCLIGPNGAGKSTLLNLIT 80
                                      67999966656999999999*****************997 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.5e-07   0.00018       9      46 ..      41      79 ..      38      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.5e-07
                            AAA_27  9 eryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAi 46
                                      +++G ft +  +dfs +e +l  ++GpN AGKst+l+ i
  gi|344210025|ref|YP_004786201.1| 41 KQFGGFTATdDVDFSVAEGELRCLIGPNGAGKSTLLNLI 79
                                      78****98758************************9865 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   4.3e-07   0.00051      93     127 ..      52      87 ..      35      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.3e-07
                                       HHHHCTT.SEEEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase  93 lkellkd.ktsvlvGqSGvGKStLinallpelelkt 127
                                       +   +++ ++ +l+G+ G+GKStL+n ++++ e+  
  gi|344210025|ref|YP_004786201.1|  52 VDFSVAEgELRCLIGPNGAGKSTLLNLITGSYEATD 87 
                                       55555555999*****************99877655 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   8.2e-07   0.00098      12      39 ..      46      76 ..      40      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.2e-07
                            AAA_29 12 fdg.htieidlkg..atlltGpsGsGKSTll 39
                                      f+   ++++++++     l+Gp+G+GKSTll
  gi|344210025|ref|YP_004786201.1| 46 FTAtDDVDFSVAEgeLRCLIGPNGAGKSTLL 76
                                      555556666665546899************9 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   7.4e-06    0.0088       5      23 .]     247     265 ..     247     265 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.4e-06
                      BCA_ABC_TP_C   5 eGtPaEvrndPrVieAYLG 23 
                                       eG+ +E+ +dP+V++ YLG
  gi|344210025|ref|YP_004786201.1| 247 EGPIEEIESDPEVQRIYLG 265
                                       67779*************9 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   8.4e-06      0.01      26     126 ..      61     211 ..      51     224 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.4e-06
                            AAA_16  26 lvllsGesGvGKsslvrellralekd..........................ggif..lrgkcdqlesa...ipysa 71 
                                       l  l+G+ G GKs+l++ +  ++e++                          ++ +  ++g+      +   +p ++
  gi|344210025|ref|YP_004786201.1|  61 LRCLIGPNGAGKSTLLNLITGSYEATdgsiyynghditdldpherisrgismKFQVpsVYGDLSVR--EnvrLPVQQ 135
                                       44579****************999998777777766666666666665554433443333333333..145677788 PP

                            AAA_16  72 laqalareellrqllde........aesaeleawrekleeala..............avpelagaeasrllellkrl 126
                                       +a+  +r++l+++  ++         ++ +l++ +++ +e  +              +v+ l+ ae+++++e ++rl
  gi|344210025|ref|YP_004786201.1| 136 FADGEERRRLVAEAIEAagltgyedVDAGQLSHGQQQQLEI-GmaaalepdlllldePVAGLDVAEREAIAERITRL 211
                                       99999998888888888777777763333333333333332.23566667777777777777777777777766665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.1e-05     0.026       3      24 ..      63      85 ..      62     114 .. 0.87
   2 ?   -0.4   0.0      0.97   1.2e+03      54      83 ..     194     221 ..     135     246 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                                      EEEESTTSSHHHHHHHHHTS.TE CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltge.ka 24
                                      +++G   +GKStL+n +tg+ +a
  gi|344210025|ref|YP_004786201.1| 63 CLIGPNGAGKSTLLNLITGSyEA 85
                                      689***************98443 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.97
                                       GGCSSHHHHHHHHHHHHHHHHCTSEEEEEE CS
                          MMR_HSR1  54 pGliegaseekglgkaflaleeadlillvv 83 
                                       +G ++   e++ +++++ +l+e + i++vv
  gi|344210025|ref|YP_004786201.1| 194 AG-LD-VAEREAIAERITRLNEEQGIAFVV 221
                                       34.33.223334444444444444444444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   6.8e-06    0.0081      24      43 ..      57      79 ..      40     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.8e-06
                            AAA_15 24 e...ltvliGkNnsGKSsileal 43
                                          l +liG+N++GKS++l+++
  gi|344210025|ref|YP_004786201.1| 57 AegeLRCLIGPNGAGKSTLLNLI 79
                                      333499**************998 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   9.5e-06     0.011      17      49 ..      59      90 ..      52     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.5e-06
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrv 49
                                      g  + +l Gp G+GK+t+l+ ++  +ea  g++
  gi|344210025|ref|YP_004786201.1| 59 G-ELRCLIGPNGAGKSTLLNLITGSYEATDGSI 90
                                      3.4899*********************995333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.6e-05     0.019       9     128 ..      63     222 ..      58     228 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaee......................................erpevvfvtl 47 
                                       +++G+ G+GK+tll+ ++ ++++                                            e      v l
  gi|344210025|ref|YP_004786201.1|  63 CLIGPNGAGKSTLLNLITGSYEATD---GsiyynghditdldpherisrgismkfqvpsvygdlsvrE-----NVRL 131
                                       69******************96544...1445888888888888888888877775555554442222.....2222 PP

                            AAA_22  48 psst.....sskdllrellralglelkaerlsseellealeqalrarav....ielliiDEaqh.lr...seealee 111
                                       p++      +++ l  e  +a gl + +   +  +l +  +q+l+  ++    + ll++DE    l+   +e++ e 
  gi|344210025|ref|YP_004786201.1| 132 PVQQfadgeERRRLVAEAIEAAGLTGYE-DVDAGQLSHGQQQQLEIGMAaalePDLLLLDEPVAgLDvaeREAIAER 207
                                       2222221124444444444444444444.444444444444444444445667899999997666877633444444 PP

                            AAA_22 112 LrsllnlsrkgvqliLv 128
                                       + ++ln +++g++++++
  gi|344210025|ref|YP_004786201.1| 208 I-TRLN-EEQGIAFVVI 222
                                       4.4444.4777777765 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 ?   13.9   0.0   2.5e-05      0.03       7      64 ..      63     120 ..      61     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                                       EEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHH.HHTSCSSCEEEEEE CS
                          GTP_EFTU   7 giighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeEr.ergiTiksaaisle 64 
                                       ++ig   +GK+TL+  ++ + +a++ +    +++ ++D  ++Er  rgi++k ++ s++
  gi|344210025|ref|YP_004786201.1|  63 CLIGPNGAGKSTLLNLITGSYEATDGSIYY-NGHDITDLDPHERiSRGISMKFQVPSVY 120
                                       6799999*******9999877777774444.45889*******868******9998888 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0022       2.6       3      19 ..      63      79 ..      62      91 .. 0.88
   2 ?   -2.1   0.0       3.4     4e+03      51      79 ..     162     190 ..     134     196 .. 0.52
   3 ?    1.8   0.1      0.21   2.5e+02     130     156 ..     197     223 ..     190     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0022
                            AAA_28  3 vitGgestGKTtlleaL 19
                                      +++G+ ++GK+tll+ +
  gi|344210025|ref|YP_004786201.1| 63 CLIGPNGAGKSTLLNLI 79
                                      79************976 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.4
                            AAA_28  51 dllafaervleeqleeeaaaaankvlfcD 79 
                                       d+ ++ +++ ++     aaa ++++l++D
  gi|344210025|ref|YP_004786201.1| 162 DAGQLSHGQQQQLEIGMAAALEPDLLLLD 190
                                       33333333222222234555677777777 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.21
                            AAA_28 130 dleereaiderlrealrelgipviivp 156
                                       d++ereai+er+  + +e gi +++++
  gi|344210025|ref|YP_004786201.1| 197 DVAEREAIAERITRLNEEQGIAFVVIE 223
                                       6799********************994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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 0.31s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1528.47
//
Query:       gi|344210026|ref|YP_004786202.1|  [L=232]
Description: urea ABC transporter ATP-binding protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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  119.7   0.0    2.2e-34  118.9   0.0    1.4  1  ABC_tran      ABC transporter
    3.1e-08   33.8   0.6     0.0017   18.3   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    9.6e-05   22.0   0.0    0.00018   21.1   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0056   17.1   0.0     0.0076   16.6   0.0    1.4  1  AAA_16        AAA ATPase domain
     0.0086   16.0   0.0      0.015   15.2   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
     0.0091   16.3   0.4      0.029   14.6   0.4    1.9  1  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.013   14.7   0.2       0.03   13.5   0.1    1.5  2  NB-ARC        NB-ARC domain
      0.021   15.2   0.2      0.036   14.5   0.2    1.7  1  AAA           ATPase family associated with various cellular 
      0.022   14.7   1.1       0.05   13.5   0.2    2.0  3  NTPase_1      NTPase
      0.025   14.5   0.3      0.047   13.6   0.3    1.4  1  NACHT         NACHT domain
      0.065   12.6   0.1        5.6    6.3   0.0    2.1  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.091   12.7   0.1       0.16   11.9   0.1    1.4  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
      0.096   12.7   0.0       0.21   11.6   0.0    1.6  2  AAA_14        AAA domain
       0.12   12.1   0.0       0.17   11.6   0.0    1.4  1  AAA_24        AAA domain
       0.14   12.0   0.0       0.17   11.8   0.0    1.2  1  ATPase_2      ATPase domain predominantly from Archaea
       0.15   12.2   0.3       0.33   11.1   0.2    1.6  2  MMR_HSR1      50S ribosome-binding GTPase
       0.17   11.3   0.5       0.62    9.5   0.4    1.8  1  SMC_N         RecF/RecN/SMC N terminal domain
       0.18   10.6   0.0       0.25   10.1   0.0    1.1  1  DLIC          Dynein light intermediate chain (DLIC)
       0.33   10.6   2.0       0.28   10.9   0.6    1.8  2  AAA_30        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.0   2.3e-37   2.2e-34       1     136 [.      17     160 ..      17     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 2.3e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                       l++v+l+++ege+v+++G+nG GK+tLlk+++gll+p +G i+++g+dl++    e++r+ ig++pq   +fp+ltv
  gi|344210026|ref|YP_004786202.1|  17 LRDVDLSVEEGEIVGVMGKNGVGKTTLLKTVMGLLEPSNGAIRYNGTDLTTtSADERARAGIGYIPQGRDVFPKLTV 93 
                                       689***********************************************988899********************* PP

                                       HHH.........HHHTC.HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx.........xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.........esdee.iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++n         +sde   +++ + +      ++++++++ +LSgGq+q++a+ ral+++p+llllDEp+
  gi|344210026|ref|YP_004786202.1|  94 EQNikmgetirsDSDETlYDQIYEYFPVL---EERASQEAGTLSGGQQQMLAIGRALVSNPDLLLLDEPS 160
                                       ****9999986533333455566666644...57778899*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2     7e-06    0.0066       3      83 ..      31      98 ..      29     128 .. 0.49
   2 !   18.3   0.0   1.8e-06    0.0017     181     279 ..      72     172 ..      59     189 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlers 81
                                      ++ G+Ng+GK++LL++  +l               ++g ir     l++++ +++++ +i     qg +    l++e++
  gi|344210026|ref|YP_004786202.1| 31 GVMGKNGVGKTTLLKTVMGLLEP------------SNGAIRYNGTDLTTTSADERARAGIG-YIPQGRDVFPKLTVEQN 96
                                      678**************888544............33333333333333333333333333.33333333333333333 PP

                            AAA_21 82 qv 83
                                      + 
  gi|344210026|ref|YP_004786202.1| 97 IK 98
                                      33 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.8e-06
                            AAA_21 181 ekrllqrlvrslklveielsdlgegeeliasvderlrer..gvvflengdgqelparel...SdGtkrllalltall 252
                                       e+ +++  + +  ++ ++  + +  +++ +++  +++e   +++++  +   e+ + e+   S G++++la+  al 
  gi|344210026|ref|YP_004786202.1|  72 ERARAGIGYIPQGRDVFPKLTVEQNIKMGETIRSDSDETlyDQIYEYFPVLEERASQEAgtlSGGQQQMLAIGRALV 148
                                       55555566666666666666666666666666666666678666677777777777776777*******88888888 PP

                            AAA_21 253 ralkkgsllliDEpEngLHPkllrrll 279
                                       + +   +lll+DEp  g+ P+++  + 
  gi|344210026|ref|YP_004786202.1| 149 SNP---DLLLLDEPSEGIQPSIVDQIS 172
                                       777...9**************999887 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 !   21.1   0.0     2e-07   0.00018      17      56 ..      22      62 ..      16      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2e-07
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfNk 56
                                      +++++ +++ ++G++G+GK+Tll  ++ lL p++  +r+N 
  gi|344210026|ref|YP_004786202.1| 22 LSVEEGEIVGVMGKNGVGKTTLLKTVMGLLEPSNgAIRYNG 62
                                      45554448889***********************99***95 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   8.1e-06    0.0076      23      55 ..      26      58 ..      14     190 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.1e-06
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekdggif 55
                                      ++e+v + G  GvGK++l+++++  le ++g  
  gi|344210026|ref|YP_004786202.1| 26 EGEIVGVMGKNGVGKTTLLKTVMGLLEPSNGAI 58
                                      33899******************8888884333 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   1.6e-05     0.015      96     132 ..      23      60 ..       2      77 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                                       HCTT.SEEEEECSTTSSHHHHHHHHCTT-----S---- CS
                       RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpelelktgevse 132
                                        +++ +++ ++G+ GvGK+tL++++++ le + g+++ 
  gi|344210026|ref|YP_004786202.1|  23 SVEEgEIVGVMGKNGVGKTTLLKTVMGLLEPSNGAIRY 60 
                                       555558999***************99988888887775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.4   3.1e-05     0.029       7      52 ..      29      68 ..      24     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.s 52
                                      i+ v+G  G+GKTtll++++  l+        + + ++++ + +t +
  gi|344210026|ref|YP_004786202.1| 29 IVGVMGKNGVGKTTLLKTVMGLLEP-------SNGAIRYNGTDLTtT 68
                                      66799***************99964.......666777777777633 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.2e-05      0.03      17      41 ..      26      48 ..      18      62 .. 0.86
   2 ?   -1.9   0.0       1.6   1.5e+03     120     120 ..     170     170 ..     105     207 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
                                      TSCSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqil 41
                                      e +  +v+++G+ GvGKttl+k ++
  gi|344210026|ref|YP_004786202.1| 26 EGE--IVGVMGKNGVGKTTLLKTVM 48
                                      444..9***************9986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.6
                                       . CS
                            NB-ARC 120 k 120
                                       +
  gi|344210026|ref|YP_004786202.1| 170 Q 170
                                       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 ?   14.5   0.2   3.8e-05     0.036       3      42 ..      32      73 ..      30     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.8e-05
                                      EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHH CS
                               AAA  3 lyGppGtGKTllakavakelg..vefleisgsellskyvges 42
                                      ++G  G+GKT+l k v+  l+     ++ +g++l+     e+
  gi|344210026|ref|YP_004786202.1| 32 VMGKNGVGKTTLLKTVMGLLEpsNGAIRYNGTDLTTTSADER 73
                                      68*****************96436689999999996544444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   5.3e-05      0.05       3      27 ..      31      55 ..      29      79 .. 0.84
   2 ?   -1.5   0.0       2.2   2.1e+03      90     103 ..     144     158 ..     132     207 .. 0.72
   3 ?   -2.7   0.0       5.1   4.8e+03      96     106 ..     207     217 ..     169     217 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.3e-05
                                      EEE--TTSSHHHHHHHHHHHH...G CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkssg 27
                                       + G+ GvGKtTl+k v+ ll+ s+
  gi|344210026|ref|YP_004786202.1| 31 GVMGKNGVGKTTLLKTVMGLLEPSN 55
                                      678*****************99776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
                                       HHHH.HHH-EEEE-- CS
                          NTPase_1  90 rkal.seadviviDE 103
                                        +al s++d++++DE
  gi|344210026|ref|YP_004786202.1| 144 GRALvSNPDLLLLDE 158
                                       344447888888887 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 5.1
                                       H-EEEE---ST CS
                          NTPase_1  96 adviviDEiGk 106
                                       +   v+DE G+
  gi|344210026|ref|YP_004786202.1| 207 ERGTVVDELGP 217
                                       33467888886 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   4.9e-05     0.047       3      24 ..      30      51 ..      28      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.9e-05
                                      EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqklalaw 24
                                      v + G++G+GKTtLl+ ++ ++
  gi|344210026|ref|YP_004786202.1| 30 VGVMGKNGVGKTTLLKTVMGLL 51
                                      5689*************99776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.006       5.6      27      51 ..      32      56 ..      18      79 .. 0.82
   2 ?    4.4   0.0     0.022        21      45     130 ..      87     175 ..      83     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.006
                      Mg_chelatase 27 lvGppGsGKtmlakrlpsllpplse 51
                                      ++G  G GKt l k +++ll p + 
  gi|344210026|ref|YP_004786202.1| 32 VMGKNGVGKTTLLKTVMGLLEPSNG 56
                                      689*****************98765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.022
                      Mg_chelatase  45 llpplseeealev.akiasvagkkeeekllkrrpfraphhsaskaalvGggs.kpkpGeislahnGvLfLDElpe.f 118
                                       ++p+l+ e+ +++ ++i+s ++++  +++++  p  + + s  + +l Gg++     G    ++  +L+LDE +e +
  gi|344210026|ref|YP_004786202.1|  87 VFPKLTVEQNIKMgETIRSDSDETLYDQIYEYFPVLEERASQEAGTLSGGQQqMLAIGRALVSNPDLLLLDEPSEgI 163
                                       6788888888877346788888889999999999999999999999****88567889999999********98857 PP

                      Mg_chelatase 119 krkvlevLRePl 130
                                       + ++++ + + +
  gi|344210026|ref|YP_004786202.1| 164 QPSIVDQISQDM 175
                                       778888776665 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 ?   11.9   0.1   0.00017      0.16       1      25 [.      29      53 ..      29      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                              MobB  1 vlgivgksgsGKTtLleklipelka 25
                                      ++g++gk+g GKTtLl+ ++  l+ 
  gi|344210026|ref|YP_004786202.1| 29 IVGVMGKNGVGKTTLLKTVMGLLEP 53
                                      689***************9998875 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   0.00022      0.21       3      42 ..      28      66 ..      26      85 .. 0.77
   2 ?   -3.0   0.0       7.3   6.9e+03      63      72 ..     149     158 ..     110     161 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldder 42
                                      +i+ ++G   vGKTtllk+++  l  +++  + +n  d +
  gi|344210026|ref|YP_004786202.1| 28 EIVGVMGKNGVGKTTLLKTVMGLLE-PSNGAIRYNGTDLT 66
                                      7999***************995554.77777777666655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.3
                            AAA_14  63 ekktylflDE 72 
                                       ++  +l+lDE
  gi|344210026|ref|YP_004786202.1| 149 SNPDLLLLDE 158
                                       3566777777 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018      0.17       5      22 ..      30      47 ..      27     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      + ++G++g+GKTtl+k+ 
  gi|344210026|ref|YP_004786202.1| 30 VGVMGKNGVGKTTLLKTV 47
                                      679************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 ?   11.8   0.0   0.00018      0.17      18      47 ..      25      54 ..      17     119 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                          ATPase_2 18 epneiyfiYGpegsGKtaLlkeiienledk 47
                                      e+ ei+ + G  g+GKt+Llk ++  le +
  gi|344210026|ref|YP_004786202.1| 25 EEGEIVGVMGKNGVGKTTLLKTVMGLLEPS 54
                                      6689999**************999887655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00035      0.33       2      21 ..      30      49 ..      29      81 .. 0.74
   2 ?   -2.5   0.0       5.7   5.4e+03      97      97 ..     175     175 ..     136     202 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00035
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      v+++G+  vGK+tL+++ +g
  gi|344210026|ref|YP_004786202.1| 30 VGVMGKNGVGKTTLLKTVMG 49
                                      89**************9987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.7
                                       H CS
                          MMR_HSR1  97 l 97 
                                       +
  gi|344210026|ref|YP_004786202.1| 175 M 175
                                       2 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 ?    9.5   0.4   0.00065      0.62      26     147 ..      29     143 ..      18     158 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00065
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrr 102
                                       +  ++G+NG GK+ ll  ++ +L   s+ ++r +  +dl +   + ++  +a +  +   ++++     ++++++++
  gi|344210026|ref|YP_004786202.1|  29 IVGVMGKNGVGKTTLLKTVMGLLEP-SNGAIRYNG-TDLTTT--SADERARAGIGYI--PQGRD---VFPKLTVEQN 96 
                                       6679*************99777764.444788765.455554..2222233333332..33333...2234444444 PP

                                       EETTSEEEEEETTEEE-H.HHHHHHHH.CTT-STTCS-HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 103 vkrkgeseykingkevtk.kevselle.sagiskelLSgGektLval 147
                                       +k +++ +   +++   +  e+  +le +a  +  +LSgG+++++a+
  gi|344210026|ref|YP_004786202.1|  97 IKMGETIRSDSDETLYDQiYEYFPVLEeRASQEAGTLSGGQQQMLAI 143
                                       44443322222222222222333333312333445677777777665 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00026      0.25      26      77 ..      28      78 ..      21      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00026
                              DLIC 26 ksvlvlGedgsGkttliaklqGveeekkGrGleylyldvkdedrddltrlnv 77
                                        v v+G++g Gkttl+  + G+ e+  G  + y   d+     d+ +r ++
  gi|344210026|ref|YP_004786202.1| 28 EIVGVMGKNGVGKTTLLKTVMGLLEPSNGA-IRYNGTDLTTTSADERARAGI 78
                                      55779*********************9995.888888888888888888765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.6    0.0003      0.28      18      49 ..      27      58 ..      20     160 .. 0.84
   2 ?   -2.1   0.0       2.8   2.6e+03      88     104 ..     206     222 ..     170     230 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrv 49
                                        ++ + G  G GKtt+lk++  ++e ++g +
  gi|344210026|ref|YP_004786202.1| 27 GEIVGVMGKNGVGKTTLLKTVMGLLEPSNGAI 58
                                      4588999**************99999885444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.8
                            AAA_30  88 pgtllivDEagmvdtkq 104
                                        ++  +vDE g   +++
  gi|344210026|ref|YP_004786202.1| 206 MERGTVVDELGPSTIAD 222
                                       34677888888665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1343.30
//
Query:       gi|344210027|ref|YP_004786203.1|  [L=471]
Description: sodium-dependent transporter [Haloarcula hispanica ATCC 33960]
Scores for complete 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-46  159.4  28.0    4.5e-26   91.6  13.0    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 !   73.7   7.1   6.7e-25   1.2e-20       1     112 [.       4     117 ..       4     121 .. 0.94
   2 !   91.6  13.0   2.5e-30   4.5e-26     184     483 ..     147     434 ..     131     441 .. 0.83

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 6.7e-25
                               SNF   1 RetwskkldfilsvvGfavgLgnvWRFPYlcyknGGGafliPYlilllvaGiPlfflelalGqytreGaitvwrkic 77 
                                       R++w + l f+l++vG a gLgn+WRFP+l+  nGG afli Yl++++ +G+P +  e+ lG+  r+   ++ r ++
  gi|344210027|ref|YP_004786203.1|   4 RDSWISNLGFVLAAVGGAAGLGNIWRFPWLTAGNGGSAFLIVYLLVVVGIGVPGLLAEFVLGRCGRQTPTAALRSLT 80 
                                       899***********************************************************************998 PP

                               SNF  78 Pllkg..iGyasivvalyvglyYnvilawalfYlfss 112
                                           g  +G   ++ +l++  +Y v+ +w l Y++ s
  gi|344210027|ref|YP_004786203.1|  81 GSRWGswLGAFNVLTTLVILSFYSVVGGWILRYTLVS 117
                                       77655448*************************9866 PP

  == domain 2  score: 91.6 bits;  conditional E-value: 2.5e-30
                               SNF 184 llvawvvvylailkGvkssgkvvyftatfPyvvllvllvrgvlLpGavkgikfyltpdlekllep..kvWidaatqi 258
                                       l  +  +v++++ +G++ ++kv+    +   ++ll l v + + pG++ g  fyl+ d e l     +v   aa q 
  gi|344210027|ref|YP_004786203.1| 147 LGSVAGIVFFGVSHGIERVSKVMLPGVV---LILLGLAVWTATQPGTAAGYAFYLSFDAEYLAANflSVIGPAAGQA 220
                                       5567789****************99999...899999************************9986458999****** PP

                               SNF 259 ffslgigfGvlialasYnkfennvyrdallvslinsltsvlaglvvFsvlGfmaeeqgekisevaeeGpgLaFiayp 335
                                       +f+l++g Gv++++asY + +  + rd+l++++ n+++ vlaglvv  +l     +qg+   +  + Gpg +F+a +
  gi|344210027|ref|YP_004786203.1| 221 LFTLSLGAGVMLTYASYLDDNASLPRDTLVIAVSNTFIGVLAGLVVIPLLF----SQGV---DPGQGGPGALFVALA 290
                                       ***********************************************9984....2333...34679********** PP

                               SNF 336 ealtklplsplwsvlFFlmlillgldsqfgtvegiitavvDefkvllrrrelltlivavlaflvglllvtegGiyvl 412
                                       +a ++lp ++l ++ FF  +++++++s ++ +e+ ++++vD+f v  rrr ++ +   ++a   gl+l++     v+
  gi|344210027|ref|YP_004786203.1| 291 TAFATLPGGELVATAFFATVLMAAVTSGISLLETPVATLVDSFGV-PRRRATVLVSALLAATGSGLALTS----PVF 362
                                       ********************************************9.566666666666666667777654....678 PP

                               SNF 413 tlldkyaaslsllvvvlleaiavawvyglkkflddi..kemlgfrpllflklcwkfvspllllvlliasivkl 483
                                       +++    a l l+v  ++ ++ v w+   + +++    +e  g+ +   + l+++ v p+++l+ll+ ++ +l
  gi|344210027|ref|YP_004786203.1| 363 QFVSGTLADLMLTVGLFAFTVIVGWLLRGEALTEFRagTESFGWLARP-WLLTVSWVLPVVVLFLLTNTLASL 434
                                       888888888888888888899999987766665543014455555544.445666778999999988887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); 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:                         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: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 2689.83
//
Query:       gi|344210028|ref|YP_004786204.1|  [L=147]
Description: MaoC domain-containing protein dehydratase [Haloarcula hispanica ATCC 33960]
Scores for 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   60.9   0.0    1.1e-16   60.5   0.0    1.1  1  MaoC_dehydratas  MaoC like domain
      6e-08   32.9   0.0    1.9e-07   31.3   0.0    1.7  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
  ------ inclusion threshold ------
      0.097   12.4   0.1       0.16   11.7   0.1    1.3  1  COE1_HLH         Transcription factor COE1 helix-loop-helix d


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 !   60.5   0.0   1.8e-20   1.1e-16      10     108 ..      12     110 ..       7     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 1.8e-20
                                       EEEEEEEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTT.EGGGEEEEEEEE CS
                   MaoC_dehydratas  10 vetekeitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdn.vvarvgeikvrF 85 
                                       v++++ +tv++++i+ +     D +p H+d+++Ak + fgg +a+G+ t+ai  +l +e   d    a vg +++r+
  gi|344210028|ref|YP_004786204.1|  12 VRQSDGYTVSKSEIVEFGE-KYDPQPFHTDADAAKDSVFGGLVASGWQTAAICMRLNVENSEDMaTQAGVGVDDLRW 87 
                                       678899*************.******************************************99999********** PP

                                       -S--BTTCEEEEEEEEEEEEEEE CS
                   MaoC_dehydratas  86 tkpVlpgdtlkvelevvgkrdvr 108
                                        +p  pgdtl+ ++e  +kr  +
  gi|344210028|ref|YP_004786204.1|  88 HQPLQPGDTLRLRTEIIDKRPSD 110
                                       ****************9999876 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 !   31.3   0.0   3.2e-11   1.9e-07       4     130 ..      10     133 ..       8     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 3.2e-11
                   MaoC_dehydrat_N   4 GaefepvkaevereavrefakavgetnpayldeeaaraagyrsliaPptflivlatkap.....ellealgidlsrl 75 
                                       G + + + ++v+++++ ef +   +++p ++d +aa+++ +++l+a  + + ++ ++ +     ++  + g+     
  gi|344210028|ref|YP_004786204.1|  10 GDVRQSDGYTVSKSEIVEFGEKY-DPQPFHTDADAAKDSVFGGLVASGWQTAAICMRLNvenseDMATQAGV----- 80 
                                       666677889**********9986.79*********************9987777774421123345544444..... PP

                   MaoC_dehydrat_N  76 lhgeqefeyhepiraGDelttesriadvydkkgvGalefivvettvtnqrGepva 130
                                         g   +++h+p+ +GD+l+ +++i d +  ++  +  +i+++++  nq++e v 
  gi|344210028|ref|YP_004786204.1|  81 --GVDDLRWHQPLQPGDTLRLRTEIIDKRPSDSDPSRGYITTRHEGLNQDDELVI 133
                                       ..45678***********************99977889**************996 PP

>> COE1_HLH  Transcription factor COE1 helix-loop-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   2.7e-05      0.16      18      38 ..      90     110 ..      81     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
                          COE1_HLH  18 PrhPGDperLpkeiILkRAAd 38 
                                       P +PGD  rL  eiI kR  d
  gi|344210028|ref|YP_004786204.1|  90 PLQPGDTLRLRTEIIDKRPSD 110
                                       889***************776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 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:                        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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 929.52
//
Query:       gi|344210029|ref|YP_004786205.1|  [L=241]
Description: creatinine amidohydrolase [Haloarcula hispanica ATCC 33960]
Scores for 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-63  212.8   0.4    5.7e-63  212.6   0.4    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 !  212.6   0.4   3.2e-67   5.7e-63       3     241 .]       1     234 [.       1     234 [. 0.90

  Alignments for each domain:
  == domain 1  score: 212.6 bits;  conditional E-value: 3.2e-67
                      Creatininase   3 ltwpeveea.lkeddvailPvGstEqHGphlplgtDtliaealaervaeklgakalvlPtlpyGvseehlgfpGTis 78 
                                       + wpe+e a ++ ++++i++vGs+EqHG hlpl++Dtl +++l++r+a+++g +al +Pt+  G+s +h++fpGTi+
  gi|344210029|ref|YP_004786205.1|   1 MVWPEIESAlDNGTRTVIIAVGSIEQHGRHLPLNMDTLDGDELSRRMAAEMG-DALAAPTIRPGCSGHHMEFPGTIT 76 
                                       67*******788889*******************************888877.58********************** PP

                      Creatininase  79 lspetliavlrdileslarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaae.aa 154
                                       + petl++v+r +++sl +hGf++ivlv  Hggn  ++k +a ++++e +a ++ + + +++++       ++  ++
  gi|344210029|ref|YP_004786205.1|  77 VPPETLMDVIRSYCRSLDTHGFEHIVLVPTHGGNFGPVKTVAPDIARELEASVIPLADLDEHMQL-----LNEGlSK 148
                                       *************************************************7776654433333333.....3333355 PP

                      Creatininase 155 eeseeeegggHAgelEtSlmlalrpelVrmdraedpeeaklakegvstaedaeelspsGvlGdpskataekGealle 231
                                          e +++ +HAg +Et+++la+++ lVr++++e+++e + +++    +e++++++++GvlGdp++at e+Gea++e
  gi|344210029|ref|YP_004786205.1| 149 AGIEYKQDVIHAGAAETAIVLAIDEGLVRTENIEPGPEGDISPA-RLLSEGFKSITENGVLGDPTAATTEAGEAIIE 224
                                       555555699**************************999988887.999***************************** PP

                      Creatininase 232 aaveelaell 241
                                        +ve+ +e++
  gi|344210029|ref|YP_004786205.1| 225 NVVEAYVEAV 234
                                       *****99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1451.92
//
Query:       gi|344210030|ref|YP_004786206.1|  [L=65]
Description: hypothetical protein HAH_5088 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   19.5   0.0      0.002   19.5   0.0    1.1  1  DUF393    Protein of unknown function, DUF393
  ------ inclusion threshold ------
      0.067   13.0   0.0      0.095   12.5   0.0    1.3  1  TraF      F plasmid transfer operon protein


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 !   19.5   0.0   2.2e-07     0.002       2      31 ..       9      38 ..       8      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.2e-07
                            DUF393  2 lyDgeCplCnravqflerrdrkgrirfadl 31
                                       yDgeCp C+ a++ le+ +  g i++   
  gi|344210030|ref|YP_004786206.1|  9 SYDGECPYCSVAAKALEQVEDIGAISWYEE 38
                                      5******************99999999765 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.1e-05     0.095     130     157 ..       3      30 ..       1      37 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.1e-05
                              TraF 130 eygLlfFyrgkcpyceaqapilqafadk 157
                                       +yg ++ y+g+cpyc  +a+ l++++d 
  gi|344210030|ref|YP_004786206.1|   3 RYGSVLSYDGECPYCSVAAKALEQVEDI 30 
                                       7888999****************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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 0.26s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 434.22
//
Query:       gi|344210031|ref|YP_004786207.1|  [L=51]
Description: hypothetical protein HAH_5089 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); 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 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 376.14
//
Query:       gi|344210032|ref|YP_004786208.1|  [L=175]
Description: hypothetical protein HAH_5090 [Haloarcula hispanica ATCC 33960]
Scores for complete 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-07   30.0   0.1    4.7e-07   29.3   0.1    1.4  1  SHOCT            Short C-terminal domain
    4.2e-05   23.5   1.1    7.3e-05   22.7   1.1    1.4  1  DUF1707          Domain of unknown function (DUF1707)
  ------ inclusion threshold ------
      0.016   13.9   0.0       0.02   13.6   0.0    1.1  1  Sulfate_transp   Sulfate permease family


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 !   29.3   0.1   7.8e-11   4.7e-07       2      28 .]     109     135 ..     108     135 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 7.8e-11
                             SHOCT   2 aLekLkeLyarGeIteEEFeakKakLL 28 
                                       a+++L++ ya G+It+EEFe +   LL
  gi|344210032|ref|YP_004786208.1| 109 AIDILRKQYATGAITDEEFEHRLNTLL 135
                                       89********************99987 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   1.1   1.2e-08   7.3e-05       5      41 ..     103     139 ..     101     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.2e-08
                           DUF1707   5 dadReravelLrealaeGrLtldEfdeRleaalaArt 41 
                                       d+d   a+++Lr+ +a G +t +Ef++Rl + l+ + 
  gi|344210032|ref|YP_004786208.1| 103 DEDTASAIDILRKQYATGAITDEEFEHRLNTLLQSED 139
                                       788899************************9998765 PP

>> Sulfate_transp  Sulfate permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.4e-06      0.02      75     127 ..      28      82 ..      14     102 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.4e-06
                    Sulfate_transp  75 eepekgieiattltllaGviqvllGllRLgflv...eflseavlsGfiaGaaivil 127
                                       e+p+k  + ++++ ++ Gvi++  +l+R+g +v   +++s ++ + f+ G+++++ 
  gi|344210032|ref|YP_004786208.1|  28 EHPRK-RANLAVSGFVIGVIFLSSWLIRVGNYVlhpSYVSASAFISFLLGSGFILS 82 
                                       44444.4455689*******************96667999999999999***9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1318.40
//
Query:       gi|344210033|ref|YP_004786209.1|  [L=432]
Description: hypothetical protein HAH_5091 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------

   [No hits detected that satisfy 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:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2915.42
//
Query:       gi|344210034|ref|YP_004786210.1|  [L=208]
Description: hypothetical protein HAH_5092 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   4.7      0.054   13.7   1.6    1.8  2  DUF5368     Family of unknown function (DUF5368)
       0.14   12.0   0.0        1.1    9.1   0.0    2.3  3  FtsK_gamma  Ftsk gamma domain
        2.9    8.2   5.3        2.2    8.6   1.5    2.5  3  DUF3267     Putative zincin peptidase


Domain annotation for each model (and alignments):
>> DUF5368  Family of unknown function (DUF5368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.6     9e-06     0.054      25      93 ..      61     129 ..      58     145 .. 0.75
   2 ?   -1.4   0.9      0.43   2.6e+03      59      77 ..     151     169 ..     118     195 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9e-06
                           DUF5368  25 lalavlvtvafvlvlirerklsskrlvraelvglv.GgvlalllvaavtqsglsDiggpvDlllllliaa 93 
                                       + + +l++v++ +vl r+ + s+ rl ra ++g + G+   +l  + +t++g +Dig  + ++l+ + a+
  gi|344210034|ref|YP_004786210.1|  61 ISANALLLVGLSTVLRRDSA-SMSRLQRAFAFGALfGTGGCVLGTLLFTTAGTNDIGREITAFLIWALAI 129
                                       56778999******999976.788999999988651555666668899*************999876542 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.43
                           DUF5368  59 vGgvlalllvaavtqsgls 77 
                                       +G++l++  v+av+  gls
  gi|344210034|ref|YP_004786210.1| 151 LGAALTVPPVLAVAYIGLS 169
                                       4444444444444444444 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.57   3.4e+03      20      30 ..      46      56 ..      39      58 .. 0.76
   2 ?    9.1   0.0   0.00019       1.1      12      32 ..      72      92 ..      63      92 .. 0.88
   3 ?   -1.0   0.0      0.27   1.6e+03      30      37 ..     140     147 ..     139     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.57
                        FtsK_gamma 20 aStSllQRrlr 30
                                       S+ ++QR lr
  gi|344210034|ref|YP_004786210.1| 46 FSAIWVQRTLR 56
                                      578899**998 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00019
                        FtsK_gamma 12 elvveegkaStSllQRrlriG 32
                                        v++ + aS+S lQR +  G
  gi|344210034|ref|YP_004786210.1| 72 STVLRRDSASMSRLQRAFAFG 92
                                      67999************9866 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.27
                        FtsK_gamma  30 riGYnRAa 37 
                                        iGY RA 
  gi|344210034|ref|YP_004786210.1| 140 GIGYLRAD 147
                                       59****95 PP

>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       0.2   1.2e+03      55      71 ..       9      25 ..       2      41 .. 0.79
   2 ?   -1.4   0.0      0.48   2.9e+03      77      91 ..      80     101 ..      54     110 .. 0.54
   3 ?    8.6   1.5   0.00037       2.2      51      94 ..     124     175 ..     105     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.2
                           DUF3267 55 laPfvllgilllllall 71
                                        P++ l++++ll+ ++
  gi|344210034|ref|YP_004786210.1|  9 AGPILGLSAVCLLITAV 25
                                      67889999999888776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.48
                           DUF3267  77 l.......llllllalnaagsa 91 
                                               ++++ +++ ++g++
  gi|344210034|ref|YP_004786210.1|  80 AsmsrlqrAFAFGALFGTGGCV 101
                                       0444445566666677777776 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00037
                           DUF3267  51 iiillaPfvllgilllllalllpsstl........llllllalnaagsagDl 94 
                                       i++l  Pfv+lg++++ +++l ++st          +l ++ + ++++ +D+
  gi|344210034|ref|YP_004786210.1| 124 IWALAIPFVILGLVGWGIGYLRADSTRlgaaltvpPVLAVAYIGLSMAGVDF 175
                                       788889***************9988777887777666666677777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1531.19
//
Query:       gi|344210035|ref|YP_004786211.1|  [L=396]
Description: quinohemoprotein alcohol dehydrogenase [Haloarcula hispanica ATCC 33960]
Scores for complete 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  116.8  29.0    9.5e-22   77.7   8.4    3.0  3  PQQ_2     PQQ-like domain
    4.1e-13   49.4  39.1      0.015   15.8   0.8    8.0  7  PQQ_3     PQQ-like domain
    2.7e-06   27.1   2.4        6.7    6.8   0.1    6.1  5  PQQ       PQQ enzyme repeat


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 !   48.2   6.5   1.7e-16     1e-12      94     236 ..      66     206 ..      56     207 .. 0.82
   2 !   77.7   8.4   1.6e-25   9.5e-22       5     228 ..     106     314 ..     103     318 .. 0.84
   3 !   16.2   0.3     1e-06     0.006      25      91 ..     330     393 ..     312     396 .] 0.85

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 1.7e-16
                             PQQ_2  94 edGkrlWstqqrseepae.lrssaspavagdtvvvgessgklvaldpkdGkvlWerelaaprgtselsrvgdisgrp 169
                                       ++  + W+ + ++++     +++++ +va++tvv+ +   ++val+++dG + W r l+ ++  s +  +gd  + p
  gi|344210035|ref|YP_004786211.1|  66 TTPSVRWHADISTSSGGGeTAGASAGVVADGTVVLTT-ATGVVALSLRDGTEQWRRDLTPATVPSVV-DIGDEPAPP 140
                                       5556677744444322223555666666777777777.999*****************777877766.6******** PP

                             PQQ_2 170 vvaegtVyassgqgrllaldlatgrrlwskeissinglpildgdllyvvsagelialdratGavlWk 236
                                       v+++ +V+ ++ +  ++al+++ g++ w ++ ++  g p +++d l+v +++++ ++   +G+++W+
  gi|344210035|ref|YP_004786211.1| 141 VISNSRVFLATADS-VTALEIGDGSVAWRNTDTAGAGVPTVTDDALFVPTTDGVARFATDDGRRQWT 206
                                       ***99******999.8999******99*9998888888****************************8 PP

  == domain 2  score: 77.7 bits;  conditional E-value: 1.6e-25
                             PQQ_2   5 vsaldaatGaelWrvdlar.......plgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplv 74 
                                       v+al+ ++G+e Wr dl++       ++g +++ +v s++++f a + + ++al+  +G+v W++t ++   g p+v
  gi|344210035|ref|YP_004786211.1| 106 VVALSLRDGTEQWRRDLTPatvpsvvDIGDEPAPPVISNSRVFLA-TADSVTALEIGDGSVAWRNTDTAG-AGVPTV 180
                                       56***************88556555549999999**********9.9*******************6665.8889** PP

                             PQQ_2  75 aegrvvvvasdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerela 151
                                       +++ ++v + dg ++++ ++dG+r+W+   ++        ++  a ++ +v++ge   k++a+d++ G+v We+ + 
  gi|344210035|ref|YP_004786211.1| 181 TDDALFVPTTDG-VARFATDDGRRQWTATADG--------TRLAAADSTVVIAGE---KITAVDAAAGEVQWEH-S- 243
                                       ********9776.6677779*******55554........444455555566666...****************.2. PP

                             PQQ_2 152 aprgtselsrvgdisgrpvvaegtVyassgqgrllaldlatgrrlwskeissinglpildgdllyvvsa.....gel 223
                                                  +++sg pvv++gtVy+s+ +g l+   l+ g ++w  +      +p+++ d++y  ++     +  
  gi|344210035|ref|YP_004786211.1| 244 -----------DRPSGYPVVSDGTVYVSGTYGDLIGRSLTDGTEQWRLDDRRSLEFPVVTPDSVYAIERpgessSAT 309
                                       ...........3467****************************99*8887777888*********999668888777 PP

                             PQQ_2 224 ialdr 228
                                       +a+dr
  gi|344210035|ref|YP_004786211.1| 310 FAFDR 314
                                       88877 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1e-06
                             PQQ_2  25 lgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvvasdgqlial 91 
                                       +gg v  +  +++ +f+ +  + l+a+ +  G+ +W++ +e ++v+   v +g +v v++dg+++al
  gi|344210035|ref|YP_004786211.1| 330 IGGAV--TAAADDAVFTFQSDDGLTAFTTRLGEAVWQYPAEYQAVSL-AVLDGGIVSVSPDGTVVAL 393
                                       66777..55599999999*************************9999.99999999******99987 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   2.0   0.00055       3.3       3      39 ..      70     112 ..      69     113 .. 0.63
   2 !   11.6   0.0     5e-05       0.3       1      38 [.     114     160 ..     114     162 .. 0.76
   3 !   10.4   1.0   0.00012      0.71       1      32 [.     163     193 ..     163     196 .. 0.83
   4 !    7.8   0.6   0.00079       4.7       1      39 [.     201     234 ..     201     234 .. 0.85
   5 !   14.2   2.1     8e-06     0.048       1      29 [.     236     262 ..     236     300 .. 0.85
   6 ?    3.0   0.0     0.026   1.6e+02       8      36 ..     329     354 ..     321     357 .. 0.70
   7 !   15.8   0.8   2.5e-06     0.015       1      36 [.     359     393 ..     359     396 .] 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00055
                             PQQ_3   3 vlWsvql....pgpvnssp...avdgglvyvgtgdGtlyAlDae 39 
                                       v+W  ++    +g  ++++   +v++g+v+ +t   +++Al  +
  gi|344210035|ref|YP_004786211.1|  70 VRWHADIstssGGGETAGAsagVVADGTVVLTTA-TGVVALSLR 112
                                       6788855222222222223668***********9.888888665 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5e-05
                             PQQ_3   1 GevlWsvqlpgpvnssp..........avdgglvyvgtgdGtlyAlDa 38 
                                       G+++W+++l  +++ s+          ++++ +v+ +t   +++Al+ 
  gi|344210035|ref|YP_004786211.1| 114 GTEQWRRDLTPATVPSVvdigdepappVISNSRVFLATA-DSVTALEI 160
                                       99*****77543333334777777888***********9.99999986 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00012
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGt 32 
                                       G v W+ +  + + + p+v ++ ++v t+dG 
  gi|344210035|ref|YP_004786211.1| 163 GSVAWRNTDTAGA-GVPTVTDDALFVPTTDGV 193
                                       7899**9665544.67**************96 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.00079
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDae 39 
                                       G+++W+ + +g     +a+++ +v+++++  +++A+Da+
  gi|344210035|ref|YP_004786211.1| 201 GRRQWTATADGT---RLAAADSTVVIAGE--KITAVDAA 234
                                       788999998763...48**********96..*****995 PP

  == domain 5  score: 14.2 bits;  conditional E-value: 8e-06
                             PQQ_3   1 GevlWsv.qlpgpvnsspavdgglvyvgtg 29 
                                       Gev+W++ + p+ +   p+v++g+vyv+++
  gi|344210035|ref|YP_004786211.1| 236 GEVQWEHsDRPSGY---PVVSDGTVYVSGT 262
                                       9******5556544...**********998 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.026
                             PQQ_3   8 qlpgpvnsspavdgglvyvgtgdGtlyAl 36 
                                       +++g+v   +a++++ v++  +d +l+A+
  gi|344210035|ref|YP_004786211.1| 329 NIGGAV---TAAADDAVFTFQSDDGLTAF 354
                                       335555...59999999999999999998 PP

  == domain 7  score: 15.8 bits;  conditional E-value: 2.5e-06
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAl 36 
                                       Ge +W+++  ++++s +++dgg+v v ++dGt++Al
  gi|344210035|ref|YP_004786211.1| 359 GEAVWQYPAEYQAVSLAVLDGGIVSV-SPDGTVVAL 393
                                       7889*******998766667776655.99******9 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.1    0.0011       6.7       2      35 ..      97     129 ..      96     132 .. 0.78
   2 !    4.1   0.1    0.0082        49       3      25 ..     147     168 ..     146     170 .. 0.93
   3 !    5.2   0.0    0.0037        22      10      26 ..     226     242 ..     220     246 .. 0.84
   4 ?    2.7   0.0     0.023   1.4e+02      20      37 ..     359     376 ..     347     377 .. 0.86
   5 ?    1.9   0.0     0.041   2.5e+02       1      15 [.     379     393 ..     379     396 .] 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0011
                                       EEEEEETTSEEEEEETTTCCEEEEEESSSCGSSE CS
                               PQQ   2 vvylgsadGylyAlDadTGkvlWrfktggpvlsl 35 
                                       +v+l++a   ++Al +++G++ Wr ++ ++ + +
  gi|344210035|ref|YP_004786211.1|  97 TVVLTTAT-GVVALSLRDGTEQWRRDLTPATVPS 129
                                       55555555.899*************999887765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0082
                                       EEEEETTSEEEEEETTTCCEEEE CS
                               PQQ   3 vylgsadGylyAlDadTGkvlWr 25 
                                       v+l++ad  + Al + +G v Wr
  gi|344210035|ref|YP_004786211.1| 147 VFLATAD-SVTALEIGDGSVAWR 168
                                       8999999.9*************7 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0037
                                       SEEEEEETTTCCEEEEE CS
                               PQQ  10 GylyAlDadTGkvlWrf 26 
                                        ++ A+Da+ G+v W++
  gi|344210035|ref|YP_004786211.1| 226 EKITAVDAAAGEVQWEH 242
                                       579**********9985 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.023
                                       CCEEEEEESSSCGSSESE CS
                               PQQ  20 GkvlWrfktggpvlslpi 37 
                                       G+ +W++++++  +sl +
  gi|344210035|ref|YP_004786211.1| 359 GEAVWQYPAEYQAVSLAV 376
                                       7889******99998765 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.041
                                       TEEEEEETTSEEEEE CS
                               PQQ   1 gvvylgsadGylyAl 15 
                                       g+++  s+dG+++Al
  gi|344210035|ref|YP_004786211.1| 379 GGIVSVSPDGTVVAL 393
                                       567888********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2632.81
//
Query:       gi|344210036|ref|YP_004786212.1|  [L=70]
Description: hypothetical protein HAH_5094 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); 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: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 453.61
//
Query:       gi|344210037|ref|YP_004786213.1|  [L=87]
Description: hypothetical protein HAH_5095 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   85.4   0.1    1.9e-24   85.2   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 !   85.2   0.1   1.1e-28   1.9e-24       1      69 [.       8      77 ..       8      78 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 1.1e-28
                                      HHHHHHHHHHTTSSSTTBHHHHHHHH-TTSS-----BTTB---TTTTGGGS.-GGGSB-SHHHHHHHHHH CS
                            MTH865  1 elkeqivealegadFPikspeeLlaalPkGaettceagdvevtagelgkkl.kdsdFPyksaedladdiv 69
                                      +l++++  ++++a++P+++p+eL+++lP+G++tt+eagdv+v ++++g+++ + +d+Py++a +l+dd++
  gi|344210037|ref|YP_004786213.1|  8 QLRAELEAVFTSAEYPVEEPMELVPVLPDGPSTTFEAGDVSVGVMDFGTEYaEYQDYPYETAAALIDDLM 77
                                      699************************************************99***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 636.78
//
Query:       gi|344210038|ref|YP_004786214.1|  [L=65]
Description: heavy-metal-associated protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   0.4    1.2e-16   60.9   0.4    1.0  1  HMA       Heavy-metal-associated domain
  ------ inclusion threshold ------
       0.13   12.3   0.1       0.89    9.6   0.0    1.9  2  BOFC_N    Bypass of Forespore C, N terminal


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 !   60.9   0.4   1.3e-20   1.2e-16       1      62 []       4      62 ..       4      62 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 1.3e-20
                               HMA  1 tvrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                      t+ v+gm C++C+++ve+++++l gV+ ++ d ++ +v V+gd++    +++i+a+e+agy+
  gi|344210038|ref|YP_004786214.1|  4 TLTVEGMSCGHCEQTVEEAIEALAGVQGAEADKDAEQVSVDGDVST---EQLIAAVEDAGYD 62
                                      689*******************************************...************7 PP

>> BOFC_N  Bypass of Forespore C, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.066   5.9e+02      16      27 ..      16      27 ..      15      32 .. 0.79
   2 ?    9.6   0.0    0.0001      0.89       6      25 ..      39      58 ..      38      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.066
                                      EEEEEEEEEEHH CS
                            BOFC_N 16 eekveEtiwsme 27
                                      e++veE+i+++ 
  gi|344210038|ref|YP_004786214.1| 16 EQTVEEAIEALA 27
                                      67899***9986 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0001
                                      EEE-SSS-EEEEEEEEEEEE CS
                            BOFC_N  6 ervYlDGevseekveEtiws 25
                                      e+v +DG+vs+e+   ++++
  gi|344210038|ref|YP_004786214.1| 39 EQVSVDGDVSTEQLIAAVED 58
                                      7888********99888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 452.34
//
Query:       gi|344210039|ref|YP_004786215.1|  [L=144]
Description: UspA domain-containing protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   93.8   1.5    1.4e-26   93.7   1.5    1.0  1  Usp             Universal stress protein family
  ------ inclusion threshold ------
      0.014   15.4   0.1      0.025   14.6   0.1    1.4  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 !   93.7   1.5   1.6e-30   1.4e-26       1     140 [.       1     138 [.       1     139 [. 0.98

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 1.6e-30
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my  IlV++Dgs + k++le+ ++ a  r+ ++++l+v+d+ra+ + +d ++++  e l  e++e+     ++ +e+
  gi|344210039|ref|YP_004786215.1|   1 MYSDILVPTDGSASMKQVLEHTIDIADGRDVTVHALYVVDDRAFLSMDDKMQDEVLENLRTEGEEATSVV-RDTLEQ 76 
                                       999*************************************************************999886.****** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       +g++v + +  g+pa+ i+ ++ + d+dl+ +G+   ++ ++ +lGS++++v+ ++++pVl V
  gi|344210039|ref|YP_004786215.1|  77 EGIEVSTAIQRGKPADRIVSYVADADIDLVTMGTQA-DKYEKNMLGSTAQKVVTKSSVPVLTV 138
                                       ************************************.9***********************87 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.8e-06     0.025      23     120 ..      29     135 ..      19     141 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-06
                                       TTSEEEEEEEE-HHHHTCGS-CHHHHHHHHHHHHH........HHHHHHHTT..--EEEEESSHHHHHHHHHHHCTE CS
                    DNA_photolyase  23 sgepvipvfvldpekahklrvgaarvdfllesLad........LdeeLrelg..irLvvrrgdpadvlpelakelga 89 
                                       ++ +v++++v+d++++ ++   ++ +d +le+L+          +++L++ g  ++  + rg+pad ++++++++++
  gi|344210039|ref|YP_004786215.1|  29 RDVTVHALYVVDDRAFLSM--DDKMQDEVLENLRTegeeatsvVRDTLEQEGieVSTAIQRGKPADRIVSYVADADI 103
                                       5667999999999966666..5555555555555422222222777889999334457899**************** PP

                                       CEEEEE---SHHHHHHHHHHHHHHH.HCTSEE CS
                    DNA_photolyase  90 savvanreyepdererdeavkealr.kagiev 120
                                       + v++ ++ + +e+++    ++ +  k++++v
  gi|344210039|ref|YP_004786215.1| 104 DLVTMGTQADKYEKNMLGSTAQKVVtKSSVPV 135
                                       **************997665544332556665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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 0.22s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1201.51
//
Query:       gi|344210040|ref|YP_004786216.1|  [L=451]
Description: sulfatase [Haloarcula hispanica ATCC 33960]
Scores for 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-32  111.0   0.0    1.1e-31  110.4   0.0    1.2  1  Sulfatase        Sulfatase
    1.5e-07   31.3   0.1      0.015   14.9   0.2    2.3  2  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
     0.0024   17.1   0.0       0.19   10.9   0.0    2.2  2  Phosphoesterase  Phosphoesterase family
     0.0031   16.2   0.0     0.0045   15.7   0.0    1.2  1  DUF229           Protein of unknown function (DUF229)
     0.0036   16.4   0.0     0.0059   15.7   0.0    1.2  1  DUF1501          Protein of unknown function (DUF1501)
  ------ inclusion threshold ------
       0.15   11.4   0.0       0.29   10.4   0.0    1.4  1  Metalloenzyme    Metalloenzyme superfamily
        0.2   10.6   0.1         11    4.9   0.0    2.3  2  Alk_phosphatase  Alkaline phosphatase


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 !  110.4   0.0   4.2e-35   1.1e-31       1     307 [.       4     312 ..       4     314 .. 0.83

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 4.2e-35
                                       EEEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTTHH CS
                         Sulfatase   1 pnvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgggg 77 
                                       pnv+l+++d ++a++ +l g+ ++ttp+l++  +e +++t++ ++a+ + p+  +l+tg +++ +    +      +
  gi|344210040|ref|YP_004786216.1|   4 PNVLLVVLDCVRAANTSLLGHRRRTTPFLEAFGREATVYTQARTTASWSLPAHTSLFTGVPAEGHT-LKI-----TE 74 
                                       9*****************************999****************************98866.333.....67 PP

                                       CTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC...CTTTSEEEETSSSCHHTCCCCCCCCCECTCCCTTTTC CS
                         Sulfatase  78 lpqteatLpellkeaGYntaaigkwhlgwssrqsvyk...nrgfdrflgfptgsaalkdpekseyngevlrvppegg 151
                                       + q  +t+ ++l++ GY+t+++           +  +   ++ f++++   + s++++dp+ ++           +g
  gi|344210040|ref|YP_004786216.1|  75 RLQPGQTIFDFLHKEGYETGVFTENPYLTV---H--PsglSDSFETVVTERPDSTDVDDPS-ETR----------NG 135
                                       899999*************55543333222...2..2345778888888777777777766.332..........35 PP

                                       SHHHHHHHHHHHHHHCCCTSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCH.................... CS
                         Sulfatase 152 ysddrlldealefllarndkpfflylatlapHappeapdeyakkyatffddgseaar.................... 208
                                       ++   ++de+ e+  +++++ + + l ++  H p+ a+++  ++        + a+                     
  gi|344210040|ref|YP_004786216.1| 136 VDGFWYADELTEW-VDEQTESWAACLNLMDAHMPY-ATRDAYDE--------WGADLywgmhdelpikwewsvygeq 202
                                       7788889999999.6888**************754.44444343........2221123555567778889999999 PP

                                       .......HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCG....HHTTSSSCTTCSSSHHHHB CS
                         Sulfatase 209 .......qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgaslee....sngplrggkganayeggtr 274
                                               l   y+++++++D  +++v+ +Le  g+ld+tlvv+t+Dhg+  +e    ++ p     g+ + e+ ++
  gi|344210040|ref|YP_004786216.1| 203 lppgvgqLLEPLYDGAIRQTDAILEQVIGDLEARGVLDDTLVVITADHGDGFGEppqaATEPPAVMHGMGTQEELFH 279
                                       *****9556679*********************************************98888899999999****** PP

                                       EEEEEEETTTSHCEEECSEEEGGGHHHHHHHHT CS
                         Sulfatase 275 vPllvwwpgekaprvseelvshiDlfptildla 307
                                       vPl+v++pg+ ++r+ e l++++ +   +l+++
  gi|344210040|ref|YP_004786216.1| 280 VPLVVRGPGQTESRRIESLATLSRFPDAVLAAF 312
                                       ********************9999999999887 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2     6e-06     0.015       1      61 [.       6      68 ..       6      70 .. 0.88
   2 !   14.1   0.0     1e-05     0.027     198     233 ..     216     251 ..     200     266 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6e-06
                                      EEEEEETT-B...TTHHHHHGSTSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHH CS
                      Phosphodiest  1 vlvislDGlr...adlldrlaellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeH 61
                                      vl+++lD++r    +ll + ++++p+l+a+ +e + ++    +  + + p+h+sl TG   + H
  gi|344210040|ref|YP_004786216.1|  6 VLLVVLDCVRaanTSLLGHRRRTTPFLEAFGREATVYT-QARTTASWSLPAHTSLFTGVPAEGH 68
                                      799*******777777877557****************.6667789*************99988 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES-- CS
                      Phosphodiest 198 edalrrvDkaigdLlealderglsaetniilvSDHG 233
                                         a+r+ D+ +++ +  l+ rg+ ++t +++++DHG
  gi|344210040|ref|YP_004786216.1| 216 DGAIRQTDAILEQVIGDLEARGVLDDTLVVITADHG 251
                                       5789*******************************9 PP

>> Phosphoesterase  Phosphoesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.0    0.0087        22      97     188 ..      19     100 ..      12     166 .. 0.80
   2 !   10.9   0.0   7.5e-05      0.19     258     330 ..     219     289 ..     215     302 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0087
                   Phosphoesterase  97 lvmgyfkredipvlwelaqeftlcDryFssvlggtepNrlflisgtsdpsGteggpsladpkktvlkgftqktiger 173
                                       +++ + +r+++p+l +  +e t+  +   ++ + + p +  l++g      +eg +      k +++ ++ +ti++ 
  gi|344210040|ref|YP_004786216.1|  19 TSLLGHRRRTTPFLEAFGREATVYTQA-RTTASWSLPAHTSLFTGVP----AEGHTL-----KITERLQPGQTIFDF 85 
                                       677888999999999999999999999.6999999999999999998....566655.....667889999****** PP

                   Phosphoesterase 174 LsekgvswaiYqeal 188
                                       L+++g+  +++ e+ 
  gi|344210040|ref|YP_004786216.1|  86 LHKEGYETGVFTENP 100
                                       *******99999986 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7.5e-05
                   Phosphoesterase 258 vaagdklikevlealtsspqwaktllivtyDEngGfyDhVappvapvsdpdglkGd.pyglgvrvPllviSpya 330
                                       + + d ++++v+  l++     +tl+++t D  +Gf     pp a ++ p  ++G   +   ++vPl+v +p+ 
  gi|344210040|ref|YP_004786216.1| 219 IRQTDAILEQVIGDLEARGVLDDTLVVITADHGDGF---GEPPQAATEPPAVMHGMgTQEELFHVPLVVRGPGQ 289
                                       7788999*****************************...78887777777777777666777899999988875 PP

>> DUF229  Protein of unknown function (DUF229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.8e-06    0.0045     312     348 ..     220     256 ..     197     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-06
                            DUF229 312 ealDedllkylkklekkgllentlvlllsDHGlrfgk 348
                                       +++D  l +++ +le++g+l++tlv++ +DHG  fg+
  gi|344210040|ref|YP_004786216.1| 220 RQTDAILEQVIGDLEARGVLDDTLVVITADHGDGFGE 256
                                       5789999999**********************98886 PP

>> DUF1501  Protein of unknown function (DUF1501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.3e-06    0.0059     269     302 ..     218     251 ..     210     258 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-06
                           DUF1501 269 lakelDqalaaLlkdLkqrGllddTlVvwagEFG 302
                                        ++++D  l++ + dL++rG lddTlVv +++ G
  gi|344210040|ref|YP_004786216.1| 218 AIRQTDAILEQVIGDLEARGVLDDTLVVITADHG 251
                                       5699**************************9977 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00011      0.29     157     218 ..     218     291 ..     214     315 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHTTS-T....TTEEEEEE-SSB-....-TTTSS..............-----EEEEEESTT--- CS
                                       xxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxx....xxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 157 aieaaDeavkeildaieq....vdgilvvtADHgn....aedmvkrdk......qplTsHtlepVPilivgkglap 218
                                       ai + D+++++++ ++e+    +d+++v+tADHg     +++  +  +         T+  l +VP+++ g+g+++
  gi|344210040|ref|YP_004786216.1| 218 AIRQTDAILEQVIGDLEArgvlDDTLVVITADHGDgfgePPQAAT--EppavmhGMGTQEELFHVPLVVRGPGQTE 291
                                       789999999999999997333357899******852211344444..23354444455555667777777777655 PP

>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.011        28      45     118 ..      35     109 ..      15     146 .. 0.74
   2 ?    4.9   0.0    0.0042        11     296     313 ..     240     255 ..     221     382 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.011
                                       EEEEESSECSTTSSGH..HHHHHHHHHSSBTBTT-BSB-TTST-B---HHHHHHHTT-EEEEEEEEETTSHHHHTT CS
                   Alk_phosphatase  45 vglsktyavdkqvtDS..aataTAyacgvktyngaigvdaaagkevksvleaAkkaGkstGlVtTtritdAtPaal 118
                                        g++ t  ++++ t S    + T + +gv +  +++ +++   ++ +++ +  +k+G++tG+ t        P++l
  gi|344210040|ref|YP_004786216.1|  35 FGREATVYTQARTTASwsLPAHTSLFTGVPAEGHTLKITER-LQPGQTIFDFLHKEGYETGVFTENPYLTVHPSGL 109
                                       466666666666554411457899*****************.9******************998776666666654 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0042
                                       TTEEEEEEESSEESEEEE CS
                   Alk_phosphatase 296 ketlvvvTaDHshvfsfg 313
                                       ++tlvv TaDH     fg
  gi|344210040|ref|YP_004786216.1| 240 DDTLVVITADHGD--GFG 255
                                       69*********98..444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); 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:                         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 0.29s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3022.31
//
Query:       gi|344210041|ref|YP_004786217.1|  [L=141]
Description: hypothetical protein HAH_5099 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   13.1   0.1        0.1   12.8   0.1    1.4  1  PIN_2     PIN domain
       0.11   12.7   0.0          1    9.5   0.0    2.0  2  RHH_8     Ribbon-Helix-Helix transcriptional regulator family


Domain annotation for each model (and alignments):
>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.1e-05       0.1      21      60 ..      34      73 ..       6     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                             PIN_2 21 ilvekaleliapeeaveeiekhkealvkksklseeeleel 60
                                         +++ + +a+e++++eie +++++v+  +l++e +++ 
  gi|344210041|ref|YP_004786217.1| 34 FSNKSEFQRFAVEYVLSEIEDYEPEMVDFDELQKEVFQHQ 73
                                      455678899*********************9999998865 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 ?    9.5   0.0   0.00011         1      18      48 ..      25      55 ..       9      75 .. 0.82
   2 ?    1.1   0.0     0.048   4.3e+02      22      51 ..      85     114 ..      83     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00011
                             RHH_8 18 iDlLveeGfYsnRtDlirtairaqLakhdda 48
                                      ++ +v eG +sn++++ r a+   L++ +d 
  gi|344210041|ref|YP_004786217.1| 25 VEEMVAEGVFSNKSEFQRFAVEYVLSEIEDY 55
                                      6679*****************9999887775 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.048
                             RHH_8  22 veeGfYsnRtDlirtairaqLakhddalkq 51 
                                       ++e fY n + + + air  +++ ++ +  
  gi|344210041|ref|YP_004786217.1|  85 INENFYENAARVRQFAIRGDIETAEEYIDT 114
                                       5789****9999999***999999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 928.80
//
Query:       gi|344210042|ref|YP_004786218.1|  [L=357]
Description: thioredoxin reductase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-27   95.8   0.0    3.4e-27   95.4   0.0    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.2e-14   54.3   0.0    3.3e-09   36.4   0.0    2.8  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    4.1e-06   27.3   0.0      0.048   14.2   0.2    2.5  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    5.6e-06   25.7   4.0    0.00023   20.4   0.7    2.7  3  FAD_binding_2  FAD binding domain
    2.5e-05   24.0   3.4     0.0094   15.6   1.9    2.3  2  DAO            FAD dependent oxidoreductase
    4.6e-05   22.7   0.0    0.00022   20.5   0.0    1.8  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
    7.1e-05   22.2   0.6    0.00012   21.5   0.6    1.3  1  FAD_binding_3  FAD binding domain
    0.00014   20.7   0.2      0.016   13.9   0.5    2.2  2  HI0933_like    HI0933-like protein
    0.00023   20.7   1.8    0.00051   19.5   0.6    1.9  2  FAD_oxidored   FAD dependent oxidoreductase
    0.00055   19.1   0.3     0.0013   17.9   0.2    1.7  2  GIDA           Glucose inhibited division protein A
     0.0037   16.6   0.1      0.007   15.6   0.1    1.4  1  Thi4           Thi4 family
  ------ inclusion threshold ------
      0.011   15.7   0.7       0.44   10.5   0.0    2.3  2  NAD_binding_9  FAD-NAD(P)-binding
      0.014   15.7   0.3      0.034   14.4   0.3    1.8  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      0.051   12.6   0.4       0.29   10.2   0.3    1.9  2  Lycopene_cycl  Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   0.0   2.7e-30   3.4e-27       1     294 []       9     291 ..       9     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 2.7e-30
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.........HHHHCHHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.........evvkklnqgie 68 
                                       +dv+v+GgGpAGl+ al+  + g+++++++++g    g+  + +  ++v + +e +s         e+v+ ++  +e
  gi|344210042|ref|YP_004786218.1|   9 YDVAVVGGGPAGLTSALYTTRLGMDTIVINRGG----GRAAMMTDTHNVIGVTEDVSgnefletarEQVQDYGGTYE 81 
                                       69***************************6555....4444444444444444444445578889999999999999 PP

                                       CCHCCTCEEEEESC.EEEEETEEECTCEEEEEESEEEE---EEE-BC..TCTTC.TTBEECCSECHHHHHHCCSS-T CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  69 lllgeevvkidpgk.kkvklekkkegdeekiaydklvlAtGssprdl..gipGvaenvgklvrtldsaealklkllp 142
                                       +   e+v  +  ++   +++++++     ++a +++vlAtG+   ++  ++p     +gk+++ + +++a+     p
  gi|344210042|ref|YP_004786218.1|  82 RGFVESVEPLADDNeDGFTVTTSD----DELAVKRVVLATGFADERPdpPLP----RTGKGLHWCLHCDAFMFVGEP 150
                                       988878877776664566664333....48***********98888833555....44777789********99999 PP

                                       SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE..EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                       Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge..kle 217
                                         + v G G  +  +A+ + ++ ++v ++ ++d++      e+s++ +  l ++ v+++  t+    + +++    +
  gi|344210042|ref|YP_004786218.1| 151 --VFVMGTGEAAAHVAMIMLNYTDDVDILTRGDEP------EWSDETQTMLDNHPVDIV-DTELSGKRTDDDgwL-S 217
                                       ..************************999999988......6****************9.777776666666544.4 PP

                                       .EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHH CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 218 .vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqq 293
                                        ++ edg++ +++  +   G     el+ ++lgl  +++g + vd++++t++ g+ya+GD +    g ++++ A+ +
  gi|344210042|ref|YP_004786218.1| 218 aYEFEDGSVREYKGGFPMLGSDYHAELA-DELGLDRNDDGTVAVDDHGETSISGVYAVGDLT---PGHNQIPIAMGE 290
                                       5***************************.*********************************...777777777666 PP

                                       H CS
                                       x RF
                       Pyr_redox_2 294 G 294
                                       G
  gi|344210042|ref|YP_004786218.1| 291 G 291
                                       5 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 !   14.7   0.1   1.1e-05     0.014       2      30 ..      13      40 ..      12      49 .. 0.89
   2 !   36.4   0.0   2.6e-12   3.3e-09     102     305 .]      86     275 ..      45     275 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkg 30
                                      ++G+GPaGl++a+   ++g+ d +++ +g
  gi|344210042|ref|YP_004786218.1| 13 VVGGGPAGLTSALYTTRLGM-DTIVINRG 40
                                      8*******************.67899987 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 2.6e-12
                       Pyr_redox_3 102 eeVesvkk.edegfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkyagqkvvViGgknSav 177
                                       e+Ve ++  +++gf+v+ts +++  k+v++AtG+ d    +  p    +  h     ++  + g+ v V G ++ a+
  gi|344210042|ref|YP_004786218.1|  86 ESVEPLADdNEDGFTVTTSDDELAVKRVVLATGFADERPDPPLPRTG-KGLHWCLHCDAFMFVGEPVFVMGTGEAAA 161
                                       5555555556899*********************9999999999998.677776666666899************** PP

                       Pyr_redox_3 178 DaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeey.kvktedgk 253
                                        +A+ + +++ +V ++trg+e             p   ++ +++++++ +++++++   + ++++      ++edg 
  gi|344210042|ref|YP_004786218.1| 162 HVAMIMLNYTDDVDILTRGDE-------------PEWSDETQTMLDNHPVDIVDTELSGKRTDDDGWLsAYEFEDG- 224
                                       *******************84.............333333344444444555555433333333333314456775. PP

                       Pyr_redox_3 254 kvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                       +v++++  + ++G + ++++ ++ ++++++dg+++++++  et ++g++ +G
  gi|344210042|ref|YP_004786218.1| 225 SVREYKGGFPMLGSDYHAELADELGLDRNDDGTVAVDDHG-ETSISGVYAVG 275
                                       6788888888888888888888888888888888887765.57788888877 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   0.2   3.7e-05     0.048       2      31 ..      11      40 ..      10      51 .. 0.92
   2 !   10.6   0.0    0.0005      0.64       2      57 ..     151     200 ..     150     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                      v+vvGgG  gl  A + ++lg ++ v+ r+
  gi|344210042|ref|YP_004786218.1| 11 VAVVGGGPAGLTSALYTTRLGMDTIVINRG 40
                                      89*************************997 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0005
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngiev 57 
                                       v v+G G  +  +A ++ ++ ++V ++ r+d++        s+++q+ l ++ +++
  gi|344210042|ref|YP_004786218.1| 151 VFVMGTGEAAAHVAMIMLNYTDDVDILTRGDEPE------WSDETQTMLDNHPVDI 200
                                       789*****************************99......6666677776666665 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.7   1.8e-07   0.00023       1      32 [.      10      41 ..      10      49 .. 0.93
   2 ?   -1.1   0.0      0.58   7.4e+02     186     233 ..     104     161 ..      47     172 .. 0.63
   3 !    5.2   0.1    0.0075       9.6     376     402 ..     258     278 ..     248     289 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.8e-07
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                      Dv V+G+G AGL++Al  ++ G +++v++ ++
  gi|344210042|ref|YP_004786218.1| 10 DVAVVGGGPAGLTSALYTTRLGMDTIVINRGG 41
                                      9***************************9986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.58
                                       CEEEEEESEEEE-----GG.......................GSSSBSSGT.T-S-HHHHHH CS
                     FAD_binding_2 186 revrirakavvlatgGfgr.............allkellgaaaeaettnap.avtGdglala 233
                                       ++ +++ k+vvlatg +               +++     +  +++ ++ p  v+G+g a+a
  gi|344210042|ref|YP_004786218.1| 104 SDDELAVKRVVLATGFADErpdpplprtgkglHWC----LHCDAFMFVGEPvFVMGTGEAAA 161
                                       33345567899999888866666666666666565....34666666666666777776665 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0075
                                       EEBETTSBESTTEEESSBTEEE-STCE CS
                     FAD_binding_2 376 vetdengrvldadgqpipGLYAaGeva 402
                                       v++      +d++++ i+G YA+G  +
  gi|344210042|ref|YP_004786218.1| 258 VAV------DDHGETSISGVYAVGDLT 278
                                       334......666666*********877 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.9   7.4e-06    0.0094       1      29 [.      10      40 ..      10      52 .. 0.90
   2 !    7.6   0.0     0.002       2.5     147     230 ..      64     141 ..      56     200 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.4e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                      dv+++GGG +Gl+ A++ +r g  ++++ +g
  gi|344210042|ref|YP_004786218.1| 10 DVAVVGGGPAGLTSALYTTRLGmdTIVINRG 40
                                      8*****************9999999998887 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHHHTT-EEEESECEEEEEE...EETCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTTCTTTSEE.E CS
                               DAO 147 kltaalaraaealGveilegtevtglee...edgkvwgverttp.gendaadavVnaaGawsdllgllkeldlpi.s 218
                                       +++   ++++++ G++  +g  v+++e    +++++ +v  tt+  e  a++ vV+a+G ++d+    +  d+p+ +
  gi|344210042|ref|YP_004786218.1|  64 EFLETAREQVQDYGGTYERG-FVESVEPladDNEDGFTV--TTSdDEL-AVKRVVLATG-FADER---P--DPPLpR 130
                                       56667777888899999999.777775554344778999..6664543.7899******.44432...3..344337 PP

                                       EEEEEEEEEEEC CS
                               DAO 219 pvrgqvlvlkpl 230
                                         +g ++ l + 
  gi|344210042|ref|YP_004786218.1| 131 TGKGLHWCL-HC 141
                                       777777776.43 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   0.0      0.41   5.3e+02       3      22 ..       9      28 ..       7      40 .. 0.71
   2 !   20.5   0.0   1.7e-07   0.00022     118     239 ..      84     194 ..      62     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.41
                       K_oxygenase  3 lDligiGiGpsnLsLaille 22
                                      +D++ +G Gp+ L+ a+ + 
  gi|344210042|ref|YP_004786218.1|  9 YDVAVVGGGPAGLTSALYTT 28
                                      78888888888887776655 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 1.7e-07
                       K_oxygenase 118 eveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepkiPevlekle..gkervvHsseylerkeellakk 192
                                        ve+vep ++++e+ +tv++     + +el  +++vl++G   + P+   + +  g + ++H + ++         +
  gi|344210042|ref|YP_004786218.1|  84 FVESVEPLADDNEDGFTVTT-----SDDELAVKRVVLATGFADERPDPPLPRTgkGLHWCLHCDAFMFVG------E 149
                                       49999999999999*****9.....567899*********877777654444311456788888888875......8 PP

                       K_oxygenase 193 riaVvGsGqSaaeifedllrrqkkvelklvtrsealeplddspfvne 239
                                        + V+G G  aa++++ +l+  +  +++++tr+++ e +d+++ +++
  gi|344210042|ref|YP_004786218.1| 150 PVFVMGTGEAAAHVAMIMLNYTD--DVDILTRGDEPEWSDETQTMLD 194
                                       9******************9988..8999***********9987665 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.6   9.2e-08   0.00012       2      33 ..       9      40 ..       8      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9.2e-08
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      +dV++VG+GpaGl++al  ++ G +++++++ 
  gi|344210042|ref|YP_004786218.1|  9 YDVAVVGGGPAGLTSALYTTRLGMDTIVINRG 40
                                      79***************************995 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.5   1.3e-05     0.016       1      32 [.       9      40 ..       9      48 .. 0.91
   2 ?    4.3   0.0      0.01        13     130     163 ..      86     118 ..      57     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllleka 32
                                      +dv+v+GgG+AGl  A+   + g ++++++++
  gi|344210042|ref|YP_004786218.1|  9 YDVAVVGGGPAGLTSALYTTRLGMDTIVINRG 40
                                      59*************************99876 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.01
                                       --EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 130 tevksvekeedgkfrvktkseeeleadklvlAtG 163
                                       ++v+ ++ +++  f+v+t s++el+ +++vlAtG
  gi|344210042|ref|YP_004786218.1|  86 ESVEPLADDNEDGFTVTT-SDDELAVKRVVLATG 118
                                       5677777888888*****.9*************9 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.6     4e-07   0.00051       1      32 [.      10      41 ..      10      92 .. 0.83
   2 ?   -0.2   0.0      0.38   4.8e+02     400     415 ..     153     168 ..     149     177 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4e-07
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveerg 32
                                      Dv VvGGgpaG++ A+   r G  ++++++ g
  gi|344210042|ref|YP_004786218.1| 10 DVAVVGGGPAGLTSALYTTRLGMDTIVINRGG 41
                                      9***************************9864 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.38
                      FAD_oxidored 400 cmalGqAaGvaAalal 415
                                       +m +G+Aa+++A + l
  gi|344210042|ref|YP_004786218.1| 153 VMGTGEAAAHVAMIML 168
                                       799*********9876 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2     1e-06    0.0013       1      39 [.      10      48 ..      10      75 .. 0.80
   2 ?   -2.3   0.0       1.4   1.8e+03     131     149 ..     100     118 ..      82     121 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--S CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaels 39
                                      dv V+GgG AG+  Al + rlG++++ i    ++ a + 
  gi|344210042|ref|YP_004786218.1| 10 DVAVVGGGPAGLTSALYTTRLGMDTIVINRGGGRAAMMT 48
                                      79*************************955555544443 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.4
                                       EEETTS-EEEECEEEE--T CS
                              GIDA 131 vvtedgetikakavviatG 149
                                        vt+++ ++  k vv+atG
  gi|344210042|ref|YP_004786218.1| 100 TVTTSDDELAVKRVVLATG 118
                                       4566677788899*****9 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   5.5e-06     0.007      18      49 ..       9      39 ..       4      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.5e-06
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailer 49
                                       Dv++vG+G++GLt+a y ++  ++ +++++r
  gi|344210042|ref|YP_004786218.1|  9 YDVAVVGGGPAGLTSALYTTRL-GMDTIVINR 39
                                      6*****************9999.999999986 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 ?    3.3   0.2     0.058        74       1      13 [.      12      24 ..      12      34 .. 0.86
   2 ?   10.5   0.0   0.00034      0.44     121     154 ..      85     118 ..      63     120 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.058
                     NAD_binding_9  1 aivGaGprGlavl 13
                                      a+vG+Gp+Gl+ +
  gi|344210042|ref|YP_004786218.1| 12 AVVGGGPAGLTSA 24
                                      89*******9876 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00034
                     NAD_binding_9 121 raevvdleeradgqavlladgaslaadaVvLAlG 154
                                        ++v+ l+++++    +++++++la+++VvLA+G
  gi|344210042|ref|YP_004786218.1|  85 VESVEPLADDNEDGFTVTTSDDELAVKRVVLATG 118
                                       345555555665567779999************9 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   2.7e-05     0.034       1      39 [.      13      48 ..      13      84 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.7e-05
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EEC CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasye 39
                                      +vG+G +Gl+ A + ++ g d  ++ ++   GGraa  +
  gi|344210042|ref|YP_004786218.1| 13 VVGGGPAGLTSALYTTRLGMDTIVINRG---GGRAAMMT 48
                                      8*********************999777...66655443 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   0.00022      0.29       1      32 [.      10      39 ..      10      69 .. 0.79
   2 ?    0.5   0.0      0.19   2.4e+02      84     145 ..      60     123 ..      43     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00022
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                      Dv+v+G+GpAgl  A      + g+  ++i+ 
  gi|344210042|ref|YP_004786218.1| 10 DVAVVGGGPAGLTSALYT--TRLGMDTIVINR 39
                                      9************99998..666666666654 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.19
                     Lycopene_cycl  84 vsskrlkeellerlvengvklleakvesveeeea..geslvvleggrkirarlvvdarglaslk 145
                                       vs +++ e   e++ + g ++ ++ vesve+  +   +   v+  + ++  + vv a+g a ++
  gi|344210042|ref|YP_004786218.1|  60 VSGNEFLETAREQVQDYGGTYERGFVESVEPLADdnEDGFTVTTSDDELAVKRVVLATGFADER 123
                                       66677777778888888999999999999975553245677788888999999******55544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); 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 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2176.39
//
Query:       gi|344210043|ref|YP_004786219.1|  [L=224]
Description: RNaseH [Haloarcula hispanica ATCC 33960]
Scores for 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   38.9   0.0    8.5e-10   38.5   0.0    1.2  1  RVT_3     Reverse transcriptase-like
    1.5e-08   34.9   0.0    2.5e-08   34.2   0.0    1.3  1  RNase_H   RNase H
  ------ inclusion threshold ------
      0.048   13.4   0.1       0.16   11.7   0.0    1.9  2  SCP_3     Bacterial SCP ortholog
        1.4    9.5   5.4        5.3    7.7   0.4    3.2  3  LRV       Leucine rich repeat variant


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 !   38.5   0.0   1.9e-13   8.5e-10       2     122 ..      95     213 ..      94     215 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.9e-13
                             RVT_3   2 fdgafkkksgaggagvvirdsnGevllagaeklqgkasveeAElqALlrGLq.lalklgirrlvvegDsktvvqlln 77 
                                       +dg+  +++g +gag+vi  ++  +   g+ ++++++++ +AE++AL  GL+ la+++  + +++ +Ds+tv++ + 
  gi|344210043|ref|YP_004786219.1|  95 VDGSA-HSNGPAGAGAVIQADETPIARLGR-PVGSRTNNNVAEYAALHLGLRaLAARCDPETVEIRIDSMTVINHIW 169
                                       68843.8999*********99998888888.77******************8469999******************* PP

                             RVT_3  78 grekvksselanlldeirkllksfesvsvehipReqNrvAdalAk 122
                                       g+++  + ++  + + i ++l+++   +++h   +   +Ada A+
  gi|344210043|ref|YP_004786219.1| 170 GNKE-STVKATPYSTAITDHLSALPAHEWTHLADSDPNPADAQAT 213
                                       ***9.***************************9999999998875 PP

>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   5.5e-12   2.5e-08       3      78 ..      90     169 ..      88     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 5.5e-12
                                       SEEEEEEEEEECTTTCEEEEEEECTT..E..EEEEEECCCCHHHHHHHHHHHHHHHTT.SC...SEEEEEES-HHHH CS
                           RNase_H   3 avvvYtDGsclgnpgeggagavlykegar..nisapleeaqtnnraELsAvieaLkalksd...ekvniytDSkYvv 74 
                                       +vv+Y+DGs+   +g++gagav++ +++    + +p+  ++ nn aE  A++  L+al +    e+v+i+ DS  v+
  gi|344210043|ref|YP_004786219.1|  90 QVVLYVDGSAH-SNGPAGAGAVIQADETPiaRLGRPVGSRTNNNVAEYAALHLGLRALAARcdpETVEIRIDSMTVI 165
                                       79*******77.6688899999987754444666788899****************997666669999*****8888 PP

                                       HHHH CS
                           RNase_H  75 kgit 78 
                                       + i 
  gi|344210043|ref|YP_004786219.1| 166 NHIW 169
                                       8443 PP

>> SCP_3  Bacterial SCP ortholog
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.53   2.4e+03      34      56 ..      91     115 ..      87     123 .. 0.70
   2 ?   11.7   0.0   3.6e-05      0.16       7      51 ..     137     183 ..     127     220 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.53
                             SCP_3  34 avqcveGprhtrg..tPpnvvetdp 56 
                                       +v  v+G++h+ g     +v+++d 
  gi|344210043|ref|YP_004786219.1|  91 VVLYVDGSAHSNGpaGAGAVIQADE 115
                                       5677899999998444456777665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.6e-05
                             SCP_3   7 aavrltleelaekapGksvEvRvpPfaavqcveGprht..rgtPpnv 51 
                                       aa++l l++la++ + ++vE+R+  +++++ + G + +  + tP + 
  gi|344210043|ref|YP_004786219.1| 137 AALHLGLRALAARCDPETVEIRIDSMTVINHIWGNKEStvKATPYST 183
                                       6788999**************************98765124577554 PP

>> LRV  Leucine rich repeat variant
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.4    0.0012       5.3      10      23 ..      11      24 ..       8      28 .. 0.81
   2 ?    2.1   0.6     0.069   3.1e+02       7      25 ..     133     152 ..     132     153 .. 0.55
   3 ?    1.2   0.2      0.13     6e+02       5      19 ..     144     156 ..     141     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0012
                               LRV 10 rPdlPpeaLerLah 23
                                      r +lP+e+L  La+
  gi|344210043|ref|YP_004786219.1| 11 RERLPAETLSPLAT 24
                                      666**********8 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.069
                               LRV   7 VArrPdlPpeaLerLah.DP 25 
                                       VA++ +l+++ +   a+ DP
  gi|344210043|ref|YP_004786219.1| 133 VAEYAALHLGLRALAARcDP 152
                                       56666666665555555666 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.13
                               LRV   5 aaVArrPdlPpeaLe 19 
                                       +a+A+r  ++pe++e
  gi|344210043|ref|YP_004786219.1| 144 RALAAR--CDPETVE 156
                                       578888..8888765 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:                      230  (0.0128284); 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 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 1348.92
//
Query:       gi|344210044|ref|YP_004786220.1|  [L=400]
Description: quinoprotein glucose dehydrogenase [Haloarcula hispanica ATCC 33960]
Scores for 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-114  380.2   0.0   1.1e-113  380.0   0.0    1.0  1  GSDH            Glucose / Sorbosone dehydrogenase
      0.004   16.9   2.5      0.004   16.9   2.5    1.8  2  TAT_signal      TAT (twin-arginine translocation) pathway sig
  ------ inclusion threshold ------
       0.63   10.4   4.6        3.3    8.2   0.1    2.6  2  Glucodextran_B  Glucodextranase, domain B


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 !  380.0   0.0  1.8e-117  1.1e-113       1     332 []      55     396 ..      55     396 .. 0.95

  Alignments for each domain:
  == domain 1  score: 380.0 bits;  conditional E-value: 1.8e-117
                                       -S-EEEEEE-TTS.-EEEEETTTEEEEEE..TTEE.EEEEE-.----STT-SEEEEEE-TTTTTS-EEEEEEEE-.. CS
                              GSDH   1 lehPwslaflpdg.rlLvtersGrlrlvk.adgklkepiagvpevvakgqgGlldvalhpdfaenrlvYltyaeaee 75 
                                       le+Pws++ lpdg +lLvter Gr+ +v+ adg++ +p++g p+v+a+gqgG+ld alhpdf++  +vYlty++a +
  gi|344210044|ref|YP_004786220.1|  55 LESPWSVTPLPDGsQLLVTERVGRVVVVDsADGTI-TPVTGAPSVYASGQGGMLDAALHPDFPDPAWVYLTYSKA-N 129
                                       689*********6589*************555565.*************************************87.9 PP

                                       .TTSSEEEEEEEEE-SS..-EEEEEEEEEEE---TT-------EEE-TTS-EEEE---TT-.....GGGGG-TT-SS CS
                              GSDH  76 ekggagtavararlsedeaaledlevifrqepkvesgahfGsrlafgpdgtLfvtvGdrsk.....reeaqdlssel 147
                                       ++g++ t+++r+rl++++a++e +e+++ +ep  +s+ hfGsr++fgpdg ++vtvGdr+       + aqd+++el
  gi|344210044|ref|YP_004786220.1| 130 DSGASATHLGRGRLNAADAQFETFEQLHVAEPFIDSDGHFGSRVVFGPDGLVYVTVGDRQFkdfgpDHVAQDRTNEL 206
                                       99999*******************************************************95565555********* PP

                                       SEEEEE-TTSSB-TT-TTTT-TTS-TTEEEE--SCE---EE-TTT--EEEEEE--SSSEEEEEE-TT-B--TTT-S. CS
                              GSDH 148 GkilrlnkdGsvpadnpfvgkagakpeiwsyGhRnpqGlaldpdtgeLwesEhGprggDelnlieaGknYGWplvsy 224
                                       G++lrl++ G +p+ npf+++++a ++i+syGhRn+qG++++pdtg++w++E+G+++gDe+n++e+G+nYGWp++ +
  gi|344210044|ref|YP_004786220.1| 207 GTTLRLTPSGGIPDANPFTDDPDAVDSIFSYGHRNAQGMTVHPDTGDIWQTEFGEQDGDEINIVERGANYGWPVADE 283
                                       ***************************************************************************** PP

                                       ......S-......-S-TTS---SEEETT-...--EEEEEEE........TTEEEEEETTTTEEEEEEEEEEEEEEE CS
                              GSDH 225 geeYs.gkkiges.etreglekpvlvwtps...iapsglafytgdafpewkgdllvggLksqsllrleldegekvve 296
                                       g++Y  g++ig s  +r+++ +pv++w+++   ++psg +fytgdaf+ew gdllvggL+sq+l+r+++d g++v+e
  gi|344210044|ref|YP_004786220.1| 284 GCTYGsGDPIGVShAERDDVVAPVYSWDCGsggFPPSGTTFYTGDAFTEWTGDLLVGGLASQYLARFTVD-GRTVEE 359
                                       ****8577999887999************98999************************************.889*** PP

                                       EEEEEESS-.-EEEEEE-TT.S-EEEEE-TTTTT... CS
                              GSDH 297 eerlleelgeriRdVeqgpd.Galyvltdeedgkllr 332
                                       ++ ll+++g+riRdV ++p+ G++  + d++d+ ++r
  gi|344210044|ref|YP_004786220.1| 360 ATPLLADRGWRIRDVVVEPEtGHVLAAIDSSDAPIVR 396
                                       *******************99********99998876 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 !   16.9   2.5   6.7e-07     0.004       2      24 ..       1      23 [.       1      25 [. 0.83
   2 ?   -4.6   1.5         3   1.8e+04      17      21 ..      33      37 ..      32      39 .. 0.30

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.7e-07
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                      ++RR+FL  s+ +aA++++g  a
  gi|344210044|ref|YP_004786220.1|  1 MDRRTFLAVSGLTAAGTLAGCSA 23
                                      79***********9999766555 PP

  == domain 2  score: -4.6 bits;  conditional E-value: 3
                        TAT_signal 17 Aaalg 21
                                      A+a++
  gi|344210044|ref|YP_004786220.1| 33 ATATA 37
                                      22222 PP

>> Glucodextran_B  Glucodextranase, domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.7      0.02   1.2e+02       6      50 ..      22      68 ..      18      75 .. 0.85
   2 ?    8.2   0.1   0.00055       3.3      12      45 ..      80     113 ..      70     120 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.02
                                      EES-SEEE-SSSEEEEEEEE-SSEEEEEETTEEEEE-..-B...TT. CS
                    Glucodextran_B  6 tapealstadsatavvsGttaaakvyvsvnGtiteap..ltpagdGt 50
                                      +ap +    d ata+ sG ++ +   v    + +e+p  +tp  dG+
  gi|344210044|ref|YP_004786220.1| 22 SAPSDDQQGDGATATASGQADGSETAVETVADGLESPwsVTPLPDGS 68
                                      578888889************99999999999999987789999994 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00055
                                       EE-SSSEEEEEEEE-SSEEEEEETTEEEEE--B. CS
                    Glucodextran_B  12 stadsatavvsGttaaakvyvsvnGtiteapltp 45 
                                          dsa+ +++  t a  vy s  G +++a l p
  gi|344210044|ref|YP_004786220.1|  80 VVVDSADGTITPVTGAPSVYASGQGGMLDAALHP 113
                                       568***************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 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:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2398.01
//
Query:       gi|344210045|ref|YP_004786221.1|  [L=57]
Description: hypothetical protein HAH_5103 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   10.7   2.7       0.69   10.4   2.7    1.1  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 ?   10.4   2.7   3.8e-05      0.69      16      54 ..       4      43 ..       2      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.8e-05
                            DUF202 16 tslalialglallrffltgepsalg.kilglilivlgilt 54
                                      t+++ +a+g+++++ fl + p ++g   lg++++++gil+
  gi|344210045|ref|YP_004786221.1|  4 TAILHAAFGVLIVAGFLVSAPLSYGlYGLGAACFIAGILL 43
                                      99************99988888887677899999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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 0.29s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 345.36
//
Query:       gi|344210046|ref|YP_004786222.1|  [L=43]
Description: hypothetical protein HAH_5104 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                        79  (0.00440627); expected 358.6 (0.02)
Passed bias filter:                       60  (0.00334653); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 283.42
//
Query:       gi|344210047|ref|YP_004786223.1|  [L=475]
Description: trk active potasium channel [Haloarcula hispanica ATCC 33960]
Scores for complete 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  148.1   2.7    1.4e-22   80.1   0.4    2.7  2  TrkA_N         TrkA-N domain
    6.7e-25   86.7   0.2      1e-11   44.5   0.1    3.4  3  TrkA_C         TrkA-C domain
     0.0029   17.0   0.0     0.0075   15.6   0.0    1.7  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
  ------ inclusion threshold ------
      0.014   15.8   0.7      0.076   13.5   0.1    2.5  2  NAD_binding_7  Putative NAD(P)-binding
      0.061   13.8   0.3        0.8   10.2   0.0    2.4  2  XdhC_C         XdhC Rossmann domain
        0.1   11.1   0.0       0.15   10.5   0.0    1.2  1  DUF2193        Uncharacterized protein conserved in archaea (
       0.26   10.8   1.8        2.7    7.5   0.0    3.1  3  NmrA           NmrA-like family
       0.35   10.4   3.3        1.9    8.0   0.1    3.3  4  PGM1_C         PGM1 C-terminal domain


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.1   5.2e-22   1.2e-18       1     116 []      47     161 ..      47     161 .. 0.96
   2 !   80.1   0.4   6.3e-26   1.4e-22       1     115 [.     274     380 ..     274     381 .. 0.93

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 5.2e-22
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       ++++ +G   + l++eL+++g ++v+i +d+e+++el + g++v+ gd+ ++++L++a +e+ada+ia + dde+n 
  gi|344210047|ref|YP_004786223.1|  47 VVLCNYGPREEVLIDELTARGVQYVIIKQDREAADELHAAGYTVMSGDPESDAALKRARLEHADALIANV-DDETNP 122
                                       578888888899*******7768**********************************************9.99**** PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                        ++l+a+e  ++ ++++ ++dp +a++ + +gad+v+sp
  gi|344210047|ref|YP_004786223.1| 123 SVLLSAREVDSEVRTVSLTEDPTTADYHRFAGADHVLSP 161
                                       *************************************98 PP

  == domain 2  score: 80.1 bits;  conditional E-value: 6.3e-26
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       ++i+G+G vGrs++  L+++g +++ id ++             vvgdatd++vL++a+i++a +v+ a++dd+a i
  gi|344210047|ref|YP_004786223.1| 274 VVIAGMGVVGRSVTSSLTDAGFEYTTIDPEDHPTVD--------VVGDATDRDVLRKADIMDAGTVVLALPDDTAAI 342
                                       79*****************6645*****96544444........89******************************* PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEE CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehaellkklgadvvis 115
                                       +a+ +++elnp ++iiara++ e++ +l+++gad+v+s
  gi|344210047|ref|YP_004786223.1| 343 FATFAIRELNPRIEIIARANEHENVSKLYRAGADYVLS 380
                                       ************************************87 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.9   6.5e+03       4      34 ..      88     118 ..      85     130 .. 0.69
   2 !   38.5   0.0   3.3e-13   7.4e-10       1      67 [.     193     261 ..     193     264 .. 0.94
   3 !   44.5   0.1   4.6e-15     1e-11      12      69 ..     415     474 ..     408     475 .] 0.94

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.9
                                       EEEE--GGGTTSBHHHHTHHHHS-EEEEEE- CS
                            TrkA_C   4 vtvpagsplvGktlkelnlrargvlvvairR 34 
                                       +tv +g p  +  lk ++l++ ++l++ +  
  gi|344210047|ref|YP_004786223.1|  88 YTVMSGDPESDAALKRARLEHADALIANVDD 118
                                       5677777777777888888777888887754 PP

  == domain 2  score: 38.5 bits;  conditional E-value: 3.3e-13
                                       CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEE.E-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar.gvlvvai.rRggeliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                       ++e+ + +gs l+G+t++e+++ +r g+ ++++ +Rg++   p++d ++ ++ vl+  g   +l++l+e
  gi|344210047|ref|YP_004786223.1| 193 IAEFPLQSGSELIGQTIAESGIFERtGAAIIGVwVRGNFHSPPPPDVRFDARSVLVATGRETELDQLKE 261
                                       5899*****************************99**99999999*********************997 PP

  == domain 3  score: 44.5 bits;  conditional E-value: 4.6e-15
                                       GTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                            TrkA_C  12 lvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                        vGk+l+++++r+r g++vva  R+  ++++p  ++v+e+GD+l+v+g +++++++++ +
  gi|344210047|ref|YP_004786223.1| 415 AVGKSLADADIRNRtGCTVVAAERErRVITNPAASFVIESGDELIVAGIDENISRFQSTF 474
                                       69********************99989*****************************9866 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   0.0   3.3e-06    0.0075      37     124 ..     272     358 ..     248     368 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.3e-06
                                       SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEE...EE-S--STTTTTSBS CS
                      2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDiv...slhlpltpetrhlin 110
                                         v i G+G +G++v   l+  g++ + +d+  +++   + +g   ++  ++l+++Di    +++l l ++t  ++ 
  gi|344210047|ref|YP_004786223.1| 272 GDVVIAGMGVVGRSVTSSLTDAGFEYTTIDPEDHPTV--DVVG--DATDRDVLRKADIMdagTVVLALPDDTAAIFA 344
                                       5689****************************88665..4434..46778899999998666788889999999999 PP

                                       HHHHHCSTTTEEEE CS
                      2-Hacid_dh_C 111 aeelakmkkgaili 124
                                         +++++ +   +i
  gi|344210047|ref|YP_004786223.1| 345 TFAIRELNPRIEII 358
                                       99988888776655 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 ?   -1.2   0.0       1.2   2.8e+03      58      72 ..      98     119 ..      60     140 .. 0.56
   2 ?   13.5   0.1   3.4e-05     0.076       9      73 ..     273     339 ..     269     368 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.2
                     NAD_binding_7  58 d.......legadlviaatddr 72 
                                       d       le ad +ia +dd+
  gi|344210047|ref|YP_004786223.1|  98 DaalkrarLEHADALIANVDDE 119
                                       1222222255555555555444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.4e-05
                     NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeel..ekdlegadlviaatddre 73 
                                        v+++G G v+ +  ++l +ag + t ++pe ++ ++   +++++++  ++d+ +a +v+ a +d+ 
  gi|344210047|ref|YP_004786223.1| 273 DVVIAGMGVVGRSVTSSLTDAGFEYTTIDPEDHPTVDVVGDATDRDVlrKADIMDAGTVVLALPDDT 339
                                       69*****************************777777777788888877788777777766666654 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1       0.2   4.4e+02      21      66 ..      67     107 ..      44     157 .. 0.65
   2 ?   10.2   0.0   0.00035       0.8       1      45 [.     274     330 ..     274     377 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.2
                                       TEEEEEEES-GGGG-GGG-TT-SE-EEEE--S-HHHHHHHHHHHSS CS
                            XdhC_C  21 gfrvtvvdpreefatkerfpeadetavvvlthdhklDaealeaalr 66 
                                       g++ +++++++e+a  +++    ++ + v++ d++ Da++ +a l+
  gi|344210047|ref|YP_004786223.1|  67 GVQYVIIKQDREAA--DELH---AAGYTVMSGDPESDAALKRARLE 107
                                       55555555555433..2222...24566666666666665555553 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00035
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE.............- CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade.............t 45 
                                       +vi G g v++++ + +  +gf+ t +dp+++  t++ + +a++             t
  gi|344210047|ref|YP_004786223.1| 274 VVIAGMGVVGRSVTSSLTDAGFEYTTIDPEDH-PTVDVVGDATDrdvlrkadimdagT 330
                                       68***************************996.4444444444344444444555542 PP

>> DUF2193  Uncharacterized protein conserved in archaea (DUF2193)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   6.6e-05      0.15     337     375 ..      52      90 ..      33     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.6e-05
                           DUF2193 337 dgfnaemvvdlltkrfhnyvqlyptrgaaaeLhnvDflD 375
                                        g   e+++d lt r   yv ++++r+aa+eLh + +  
  gi|344210047|ref|YP_004786223.1|  52 YGPREEVLIDELTARGVQYVIIKQDREAADELHAAGYTV 90 
                                       555678899************************988754 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0012       2.7      31      73 ..      74     117 ..      57     126 .. 0.84
   2 ?   -1.4   0.0      0.62   1.4e+03     174     218 ..     121     165 ..     115     175 .. 0.79
   3 ?    0.4   0.3      0.18     4e+02       3      24 ..     275     296 ..     274     358 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0012
                                       -S-SHHHHHHHHSTTEEEES-TT-HHHHHHH.HTT-SEEEE--- CS
                              NmrA  31 dtkselakslkeaGvelvkgdlddkeslvea.lkgvdvvfsvtg 73 
                                       ++++e+a++l +aG ++++gd ++++ l++a l+ +d+ ++++ 
  gi|344210047|ref|YP_004786223.1|  74 KQDREAADELHAAGYTVMSGDPESDAALKRArLEHADALIANVD 117
                                       56899******************999999987899999999886 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.62
                                       -TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHH CS
                              NmrA 174 npkavlldaeeDiGafvikilkdprklkgkriklagntlsgneiv 218
                                       np+  l   e D    ++++ +dp+++  +r + a  +ls++ i+
  gi|344210047|ref|YP_004786223.1| 121 NPSVLLSAREVDSEVRTVSLTEDPTTADYHRFAGADHVLSPKRIL 165
                                       554444477788888899999******************999885 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.18
                                       ESSTTSHHHHHHHHHHHHHT-E CS
                              NmrA   3 viGaTGrqGksvvrallkaghk 24 
                                       vi + G  G+sv++ l++ag++
  gi|344210047|ref|YP_004786223.1| 275 VIAGMGVVGRSVTSSLTDAGFE 296
                                       7777777888888887777775 PP

>> PGM1_C  PGM1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1   0.00087       1.9      32      51 ..      66      85 ..      47      86 .. 0.84
   2 ?   -3.6   0.0       3.6   8.1e+03      13      21 ..     177     185 ..     177     185 .. 0.93
   3 ?   -1.4   0.0      0.79   1.8e+03      21      51 ..     331     372 ..     329     373 .. 0.68
   4 ?    0.7   0.1      0.16   3.7e+02      32      45 ..     427     440 ..     411     440 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00087
                            PGM1_C 32 grveyliiAesleeAeeler 51
                                      + v y+ii  ++e+A+el++
  gi|344210047|ref|YP_004786223.1| 66 RGVQYVIIKQDREAADELHA 85
                                      7899**************86 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.6
                            PGM1_C  13 YdpetreGV 21 
                                       +dpe+ eGV
  gi|344210047|ref|YP_004786223.1| 177 FDPEAIEGV 185
                                       9****9999 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.79
                            PGM1_C  21 VVlyt.gtlpgd..........grveyliiAesleeAeeler 51 
                                       VVl   +++++            r+e ++ A ++e ++ l+r
  gi|344210047|ref|YP_004786223.1| 331 VVLALpDDTAAIfatfairelnPRIEIIARANEHENVSKLYR 372
                                       555555555555666666666667778888999999999988 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.16
                            PGM1_C  32 grveyliiAeslee 45 
                                       +r +++++A+++e+
  gi|344210047|ref|YP_004786223.1| 427 NRTGCTVVAAERER 440
                                       8899******9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2749.31
//
Query:       gi|344210048|ref|YP_004786224.1|  [L=413]
Description: putative phosphate permease [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-35  122.9  40.0    1.4e-34  119.6  38.3    2.5  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 !  119.6  38.3     8e-39   1.4e-34       1     335 [.      20     403 ..      20     405 .. 0.86

  Alignments for each domain:
  == domain 1  score: 119.6 bits;  conditional E-value: 8e-39
                              PHO4   1 iGanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselm.lgmlaallgaavw 76 
                                       iG   ++ af+++vgsk ++  +A++l ++f f+Ga+++G +V  t+++giv       ++++ ++ + +l+ +++ 
  gi|344210048|ref|YP_004786224.1|  20 IGGSSTGVAFGPAVGSKLVRKVTAAALFSVFAFIGAWTVGRNVIVTMSEGIVP-----AAQFTpVAGVGVLFFTGLS 91 
                                       68889999********************************************3.....44455588899******** PP

                              PHO4  77 lllatvlglPvStthslvGaliGaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvkeklkna 153
                                       ll+ +++g+P+St+++ vGa++G +la+    +++   +++iv +w+++Pl+g++i+a++             l++ 
  gi|344210048|ref|YP_004786224.1|  92 LLVSNIYGVPASTSMTAVGAIVGLGLAT---GSLNEALMFTIVSAWIVAPLIGLVIGAAIGRYAYPQ------LEAR 159
                                       ***************************6...4577777999*****************988766655......2222 PP

                              PHO4 154 lralpvlvlvtiailalsilfkgesk......kddeeteklf.kflqvvsaalvsfahGanDvanaiGplla..ali 221
                                       l ++ +           ++ ++ + +      + + + + l+ ++l++  a++++f+ Ga+++ana++pl+   a+ 
  gi|344210048|ref|YP_004786224.1| 160 LSFTRLE--------RQLVQIDRSGRfprlrlNRNASPRDLIgSALVLAIACYMGFSAGASNAANAVAPLVGngAV- 227
                                       2222222........1122222222233444556677777888***************************442222. PP

                              PHO4 222 siykaskevplwvlllgglaialGlllgGkrviktvGekitkkltpsrGfaaelaaaltvllasklglPvStThvlv 298
                                              ++    +ll ++ai+lG +++++r   tvG  it +l    ++ ++ ++a+++ ++s++g+P S    ++
  gi|344210048|ref|YP_004786224.1| 228 -------SID-QGVLLAVAAISLGGFTIARRTLATVGDGIT-DLPILAALIVSSVGATIITVLSYYGIPASLAVSTT 295
                                       .......122.366788899*********************.6********************************** PP

                              PHO4 299 gavvGvGlak................................................................... 308
                                        +++G G+ +                                                                   
  gi|344210048|ref|YP_004786224.1| 296 CCIIGLGWGRasravtltelatppseskpgpnlstgalaapsteeekpagptvgelaagesptpetspsvpaigeed 372
                                       **********99***************************************************************** PP

                              PHO4 309 ....kresavnwklvrnivlaWvlTlpvsal 335
                                           + e+  +   + +iv+ WvlT  +s++
  gi|344210048|ref|YP_004786224.1| 373 ieelTAENLFDPAATSRIVILWVLTPSLSVV 403
                                       *999778999999***********9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2472.50
//
Query:       gi|344210049|ref|YP_004786225.1|  [L=475]
Description: cationic amino acid transporter [Haloarcula hispanica ATCC 33960]
Scores for complete 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  41.1    1.5e-42  145.9  41.1    1.0  1  AA_permease_2   Amino acid permease
    3.1e-42  144.8  39.3    3.9e-42  144.4  39.3    1.1  1  AA_permease     Amino acid permease
    0.00029   19.8  12.2    0.00029   19.8  12.2    2.2  2  Spore_permease  Spore germination protein


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 !  145.9  41.1   2.5e-46   1.5e-42       1     402 [.      43     443 ..      43     466 .. 0.82

  Alignments for each domain:
  == domain 1  score: 145.9 bits;  conditional E-value: 2.5e-46
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       ++l++ +a+ ig++ig+gifv +  +aa++g a++l++ i+ li  l v+l   El++a+prsgG y + ++++g  
  gi|344210049|ref|YP_004786225.1|  43 IGLVGGLAIGIGTMIGAGIFVFPglAAANAGLAATLSFAIGGLIA-LLVALPTSELATAMPRSGGGYYFISRGMGTA 118
                                       6889999**************99999999***************9.89***************************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgp.dlqgntwltyliaiaililvalinirgikesakiqnilgilk 151
                                        + +++  +w++ +++ a++l+ ++ y   ++++ ++     ++++i+ ++ + +++++i g+  +akiqn+++ + 
  gi|344210049|ref|YP_004786225.1| 119 YGAIVGLGLWLGLMFASAFYLVGLGHYASAVFAElNVALPFSPVIGIGLLFGAALTALSIGGTENTAKIQNVVVGVL 195
                                       ****************************9999876544434489***************************988877 PP

                     AA_permease_2 152 illpliiliilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifig 226
                                       ++++      l + ++d+ g     t  ++ff+ g   vl + + v+ s+ Gf  +a v+ e+k+  +++p+a++ +
  gi|344210049|ref|YP_004786225.1| 196 LVVL---TGFLSYGVLDAVGVFGGGTVPEQFFSKGYLPVLTTAALVFTSYLGFAQVATVAGEIKQpgRNLPLAMVGS 269
                                       7533...33344555444333321112346787777778999999*****************998889********* PP

                     AA_permease_2 227 llivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvleala 303
                                       +liv+v+y+++ ++++ + + d + + +++  ++++  + +g + +a+++  ++ l+ + ++n+ ++++sr ++al+
  gi|344210049|ref|YP_004786225.1| 270 VLIVTVFYVVTIFVATSAFGADRLGEFGETA-MVEVARDFLGLP-GAVAILGAGLLATFSSANASILSASRAVYALS 344
                                       ************************9999976.777877777744.44444557889********************* PP

                     AA_permease_2 304 rdgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphl 379
                                       rd  lPr  + vn ++g+p +a+         l+ l++   +  + +l++v+s++++i+y+l+ i++++lr+++p++
  gi|344210049|ref|YP_004786225.1| 345 RDALLPRKASEVNlRYGTPHVALLSAGGPI--LV-LVA---TGRVELLAEVASFLHLIMYGLMCIALIVLRRRNPEW 415
                                       ***********************9999995..32.333...3579******************************99 PP

                     AA_permease_2 380 kr.....pgkilvaiigalfllfllval 402
                                              pg+++v  +gal ++ l+v++
  gi|344210049|ref|YP_004786225.1| 416 YSpsyqvPGYPVVPVVGALASFGLIVFM 443
                                       4434555555444444433333333322 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.4  39.3   6.6e-46   3.9e-42       3     430 ..      49     444 ..      47     467 .. 0.89

  Alignments for each domain:
  == domain 1  score: 144.4 bits;  conditional E-value: 6.6e-46
                       AA_permease   3 lvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviG 79 
                                       l i +g +iG+g+fv  g ++++aG++++ l+++++g++ +lv+l ++e+at++p+sgg y+++sr +g + G  +G
  gi|344210049|ref|YP_004786225.1|  49 LAIGIGTMIGAGIFVFPGLAAANAGLAAT-LSFAIGGLIALLVALPTSELATAMPRSGGGYYFISRGMGTAYGAIVG 124
                                       6799**********************555.*********************************************** PP

                       AA_permease  80 lnylfswitvlaleltaasiliq..fwelvtdlpkawvt......gavflvvlliinlvgvkvygeaefilalikii 148
                                       l +++   ++ a+ l++++++ +  f+el+ +lp    +      g++f ++l+++++ g +  ++++ ++  ++++
  gi|344210049|ref|YP_004786225.1| 125 LGLWLGLMFASAFYLVGLGHYASavFAELNVALP----FspvigiGLLFGAALTALSIGGTENTAKIQNVVVGVLLV 197
                                       ******************9998722445555555....2556699******************************** PP

                       AA_permease 149 aiiafiivg...iillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiia 222
                                        + +f+  g   +++++gg++ ++              +++++g         + ++  ++ v+ ++ G+  va++a
  gi|344210049|ref|YP_004786225.1| 198 VLTGFLSYGvldAVGVFGGGTVPE--------------QFFSKG--------YLPVLTTAALVFTSYLGFAQVATVA 252
                                       *********99999******9999..............799999........9************************ PP

                       AA_permease 223 gEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinavilta 299
                                       gE+k P +++P a+   v+++t+fYv  ++++++ ++ + lg + ++a     ++++  ++g++++  ++ a++l a
  gi|344210049|ref|YP_004786225.1| 253 GEIKQPGRNLPLAMVGSVLIVTVFYVVTIFVATSAFGADRLGEFGETA----MVEVARDFLGLPGAVAILGAGLL-A 324
                                       *********************************************999....66*************99999966.7 PP

                       AA_permease 300 alssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisali 375
                                       ++ssan+s+ sasR++y+l++d l+P k  ++  ++g P++a+l      l+++  a   +      + l  ++ + 
  gi|344210049|ref|YP_004786225.1| 325 TFSSANASILSASRAVYALSRDALLPrKASEVNLRYGTPHVALLSAGGPILVLV--ATGRV------ELLAEVASFL 393
                                       89************************99999999*******9875544444444..33333......47899999** PP

                       AA_permease 376 glivwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillila 430
                                        li+++l++++++++R+    +  ++ + +++ +++p  ++++ +a   +++++ 
  gi|344210049|ref|YP_004786225.1| 394 HLIMYGLMCIALIVLRRR---NPEWY-SPSYQVPGYPVVPVVGALASFGLIVFMQ 444
                                       *****************9...88888.8899999999999888776666665554 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8  12.2   4.9e-08   0.00029      12     238 ..      53     292 ..      48     296 .. 0.80
   2 ?   -1.5   0.1      0.15   8.8e+02     125     164 ..     375     413 ..     362     420 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.9e-08
                    Spore_permease  12 vsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpekt.liellkkilgkw......LGsll 81 
                                       + +++G+gi ++p+ +a++a+  + +s  ++g+i+l+++l +++l   +p +   + +++ ++g+       LG  l
  gi|344210049|ref|YP_004786225.1|  53 IGTMIGAGIFVFPGLAAANAGLAATLSFAIGGLIALLVALPTSELATAMPRSGgGYYFISRGMGTAygaivgLGLWL 129
                                       679**********************************************9865257777888877622223355566 PP

                    Spore_permease  82 silfi..lyFlllaafelRefseliqvflledtplwiiilllllvilYlvvkGieslar.eflfiivilliilllil 155
                                       +++f+   y + l       f+el   ++l+  p++ i ll+ +    l ++G e+ a+ +++++ v l++   +++
  gi|344210049|ref|YP_004786225.1| 130 GLMFAsaFYLVGLGHYASAVFAEL--NVALPFSPVIGIGLLFGAALTALSIGGTENTAKiQNVVVGVLLVVLTGFLS 204
                                       666651133344455556666665..5789**************9999***********967777776666666666 PP

                    Spore_permease 156 lfslklaei..knlrP..vlgngikpvlkslkttslsflgveillllvpflkdkkkvkkaallg.vlistllylltt 227
                                         +l+ + +      P   + +g+ pvl  +  +  s+lg+  +  +   +k++ + +  a++g vli+t++y++t+
  gi|344210049|ref|YP_004786225.1| 205 YGVLDAVGVfgGGTVPeqFFSKGYLPVLTTAALVFTSYLGFAQVATVAGEIKQPGRNLPLAMVGsVLIVTVFYVVTI 281
                                       666666554222233433799*********************************9999999886489********** PP

                    Spore_permease 228 livilvlsveq 238
                                       +++ ++++++ 
  gi|344210049|ref|YP_004786225.1| 282 FVATSAFGADR 292
                                       ********997 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.15
                    Spore_permease 125 ilYlvvkGieslareflfiivilliilllillfslklaei 164
                                        ++++++ +e la e++ ++  ++  l+ i l++l+  ++
  gi|344210049|ref|YP_004786225.1| 375 LVLVATGRVELLA-EVASFLHLIMYGLMCIALIVLRRRNP 413
                                       4566677777788.78888888888888888888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 2824.20
//
Query:       gi|344210050|ref|YP_004786226.1|  [L=244]
Description: universal stress protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   28.9   0.9    0.00015   22.3   0.1    2.5  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 !    4.9   0.1    0.0019        34      29     109 ..      30     103 ..       6     106 .. 0.70
   2 !   22.3   0.1   8.3e-09   0.00015       4     140 ..     112     233 ..     109     234 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0019
                                       CTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSS CS
                               Usp  29 rgaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaeeilevaeeedad 105
                                        +  l   hvi++++ +  + +  e +  e  +  ++       + + ag  +++  v  +d+  +i ++  e+d+ 
  gi|344210050|ref|YP_004786226.1|  30 AHIVLLGYHVIPEQTAPGQARMQFEDRALERLDDYEA-------MFEGAGATVERRLVFTHDGQKTIDRMIAEHDCM 99 
                                       4455555566666666655555555555555555554.......457899999999999999999999999999997 PP

                                       EEEE CS
                               Usp 106 liVv 109
                                        ++v
  gi|344210050|ref|YP_004786226.1| 100 AVLV 103
                                       7765 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 8.3e-09
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                        +lV+v g    +++++  +    + +a+++l hv d+++ +   +       ++l++ ++                
  gi|344210050|ref|YP_004786226.1| 112 DVLVPVRGAIGVDRLARVVASVFGEMDADVTLYHVADEDTTDDDIQTLLGGMADRLAEFGMDP------------LR 176
                                       589***999999************************************************965............68 PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       +++ + ++ dp ++i+++a++   d +V+G ++  +l+ +++G  +++++++   pV vV
  gi|344210050|ref|YP_004786226.1| 177 VETRIDRDQDPLDAIADIADS--FDTVVMGETD-PSLATFVFGMPADQIAERFLGPVFVV 233
                                       999*****************9..89********.************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 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:                        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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1456.29
//
Query:       gi|344210051|ref|YP_004786227.1|  [L=225]
Description: regulatory protein PrrC [Haloarcula hispanica ATCC 33960]
Scores for 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-21   74.7   0.2    8.2e-21   74.3   0.2    1.1  1  SCO1-SenC   SCO1/SenC
     0.0037   17.1   1.5     0.0059   16.4   1.5    1.3  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
  ------ inclusion threshold ------
       0.11   12.2   0.1       0.25   11.0   0.1    1.6  1  KRAB        KRAB box


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 !   74.3   0.2   1.4e-24   8.2e-21      22     133 ..      79     200 ..      68     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 1.4e-24
                         SCO1-SenC  22 kpslvffgFthCpdvCpttlanmaevldalgeea..ekvqplfiTvDPerDtpevlkeyleafdpriig.....ltG 91 
                                       +p l++f+++hC++vCp+ +++ ++++++ ++++  ++v++l +T DP+rDt e+l +y+++++ ++ +     l+ 
  gi|344210051|ref|YP_004786227.1|  79 TPALLTFFYSHCQTVCPVLISTQRNIQSHAQNNGyaDAVRFLPMTFDPARDTAERLGAYADEMNVDVDSenwqfLRP 155
                                       6899*****************************76699*****************************9999**9777 PP

                         SCO1-SenC  92 .skeeiakaake.frvyvekvedees.dytvdHsssvyLvdpdgr 133
                                        sk+  +++++e f+v+++++e e+   y++ H++ ++Lv++dg 
  gi|344210051|ref|YP_004786227.1| 156 aSKQRAKDVIQEqFGVVFQRTEPEDMdMYMFTHTALTLLVNADGF 200
                                       6999999999999****99999888889***************96 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   1.5   9.9e-07    0.0059       4      25 ..       3      24 ..       1      25 [. 0.93

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.9e-07
                        TAT_signal  4 RRdFLKgsAAaaAAaalggcaa 25
                                      RR+ LK ++A++  ++++gc++
  gi|344210051|ref|YP_004786227.1|  3 RRTVLKSTGAVGTIVGVAGCLG 24
                                      ********************97 PP

>> KRAB  KRAB box
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   4.3e-05      0.25       9      37 ..     143     171 ..     139     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.3e-05
                              KRAB   9 VdFtqeEWelLdpaQreLYrdVMlEnyrn 37 
                                       Vd   e W+ L pa ++  +dV++E ++ 
  gi|344210051|ref|YP_004786227.1| 143 VDVDSENWQFLRPASKQRAKDVIQEQFGV 171
                                       6667899******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1392.30
//
Query:       gi|344210052|ref|YP_004786228.1|  [L=175]
Description: thioredoxin [Haloarcula hispanica ATCC 33960]
Scores for complete 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   30.7   0.0    2.8e-07   30.4   0.0    1.1  1  Redoxin        Redoxin
    5.4e-06   26.3   0.0    7.2e-06   25.9   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    0.00019   21.7   0.0    0.00032   21.0   0.0    1.3  1  Thioredoxin_8  Thioredoxin-like
    0.00066   19.6   0.0     0.0014   18.6   0.0    1.4  2  Thioredoxin    Thioredoxin
  ------ inclusion threshold ------
      0.085   13.3   0.0       0.13   12.7   0.0    1.3  1  Thioredoxin_2  Thioredoxin-like domain


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 !   30.4   0.0   7.7e-11   2.8e-07      25     131 ..      56     158 ..      33     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 7.7e-11
                                       H..HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH........HHHHHHHTT-TSEEEE CS
                           Redoxin  25 e..fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf........vkefwgkeglkfpvls 91 
                                       +   +g ++v+  +++ +c +C  +++ l+  ++++   +v++v v+  n+ +         +++w+++g  ++v +
  gi|344210052|ref|YP_004786228.1|  56 AvpTPGTVTVIDLFAT-WCAPCDDQLRILNAMQPEYT--DVSFVSVT--NERPsetltradISAWWNRNGGVWTVGL 127
                                       33578999********.************99999954..56664443..333335789999**************** PP

                                       -TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEE CS
                           Redoxin  92 DgsaaftkalGlrleedaseglrtpryavidedgkvvyle 131
                                       D+++++ +alG++         ++p  a+ de g v   +
  gi|344210052|ref|YP_004786228.1| 128 DPGSELLAALGAN---------GLPYIAITDESGTVQFGH 158
                                       ***********99.........9***********998765 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0     2e-09   7.2e-06      25     122 ..      61     155 ..      41     156 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2e-09
                                       TSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCH......HHHHHHHH-H.SSEEEE-TTSHHH CS
                          AhpC-TSA  25 gkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspe......shkkfiekeslnfpllsDeegkva 95 
                                       g ++v+  +++ wc +C ++l+ l+++ +e++  +v  + v+ + p       ++ ++ ++++  +++ +D+ +++ 
  gi|344210052|ref|YP_004786228.1|  61 GTVTVIDLFAT-WCAPCDDQLRILNAMQPEYT--DVSFVSVTNERPSetltraDISAWWNRNGGVWTVGLDPGSELL 134
                                       7899*******.********************..89999999999999***************************** PP

                                       HHTT-EETTTTECSCEEEEE-TTSBEE CS
                          AhpC-TSA  96 kaygvlkeekglalratfvidkegkir 122
                                        a+g+        l+   + d+ g+++
  gi|344210052|ref|YP_004786228.1| 135 AALGAN------GLPYIAITDESGTVQ 155
                                       ******......999999999999997 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   8.9e-08   0.00032       1      95 []      61     154 ..      61     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 8.9e-08
                                       .SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS.-HHHHHHHGGGS.-TTSEE.EE-TT-HHHHT CS
                     Thioredoxin_8   1 gkvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldk.keeefekylkkn.kkpwlsvpfddkkrnklk 75 
                                       g+v+++  +a+wc+pc++ ++ l++++ ++    +v +v+v + + +e  +++ ++   +++    +++ +  ++l 
  gi|344210052|ref|YP_004786228.1|  61 GTVTVIDLFATWCAPCDDQLRILNAMQPEYT---DVSFVSVTNERpSETLTRADISAWwNRNGGVWTVGLDPGSELL 134
                                       5799**************************8...9********9736666777777766667777788888999999 PP

                                       T-S--TT-SEEEEE-TT-BE CS
                     Thioredoxin_8  76 kkynvkaiPtlvvldkngev 95 
                                         ++ +++P + + d +g+v
  gi|344210052|ref|YP_004786228.1| 135 AALGANGLPYIAITDESGTV 154
                                       99999999999999999876 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   3.8e-07    0.0014      18      71 ..      61     113 ..      50     115 .. 0.86
   2 ?   -3.3   0.0       2.5     9e+03      63      83 ..     132     152 ..     124     165 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.8e-07
                                       SSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-S CS
                       Thioredoxin  18 kklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyeve 71 
                                        +  +++ +A+wC++C      l++++ e++ +v ++ v ++  +++ ++ +++
  gi|344210052|ref|YP_004786228.1|  61 GTVTVIDLFATWCAPCDDQLRILNAMQPEYT-DVSFVSVTNERPSETLTRADIS 113
                                       56789*************999**********.9****99999988888888776 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.5
                                       HHHHHTT-SSSSEEEEEETTE CS
                       Thioredoxin  63 dlakkyevegiPtlklfkngk 83 
                                       +l + ++ +g+P + ++ ++ 
  gi|344210052|ref|YP_004786228.1| 132 ELLAALGANGLPYIAITDESG 152
                                       555666777888888877665 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.7e-05      0.13       7     100 ..      63     162 ..      59     171 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.7e-05
                     Thioredoxin_2   7 pvlvvftdpdCpyCkklkkelkel.ddvtvrvllfplkpsfepkavaiwcakekkkafkd........ieenvelar 74 
                                        ++++  +++C  C+   + l  + +++t+  +   ++++    ++ + +a+     ++         ++  +el+ 
  gi|344210052|ref|YP_004786228.1|  63 VTVIDLFATWCAPCDDQLRILNAMqPEYTDVSFVS-VTNE--RPSETLTRADIS-AWWNRnggvwtvgLDPGSELLA 135
                                       578888899******99997777777787772222.3333..555666666655.4555578888899********* PP

                     Thioredoxin_2  75 kygvrgtPtivfldgk.eivarlpGyv 100
                                       ++g +g+P+i + d++ ++++   G+ 
  gi|344210052|ref|YP_004786228.1| 136 ALGANGLPYIAITDESgTVQFGHSGLA 162
                                       ***************999988888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1111.38
//
Query:       gi|344210053|ref|YP_004786229.1|  [L=219]
Description: cytochrome C biogenesis protein transmembrane region/thiol-disulfide transporter [Haloarcula hispanica ATCC 33960]
Scores for 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-14   52.7  12.8    8.9e-14   51.9  12.8    1.3  1  DsbD      Cytochrome C biogenesis protein transmembrane regio
  ------ inclusion threshold ------
      0.098   12.4   0.4      0.098   12.4   0.4    2.5  2  DUF3188   Protein of unknown function (DUF3188)


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 !   51.9  12.8     1e-17   8.9e-14       3     209 ..      15     206 ..      13     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1e-17
                              DsbD   3 laGllsflsPCilpliPaylsyisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdvkevir 79 
                                       +aG+ +f++PC +pl+P y++y  + s  dv        +l  a   + G  l +++++l + +lgq lk+   +++
  gi|344210053|ref|YP_004786229.1|  15 GAGITTFFAPCAFPLLPGYIGYYMNESDRDVG-------MLPPATAAAGGALLALTLVALLVLALGQPLKNALPMLE 84 
                                       69********************9855444443.......5889999999999999999999**************** PP

                              DsbD  80 rvaglivillGlhflgvfkievleklklllkikkkaelsvlgalllGltFalgwsPCigPvlasvlalaaskeslak 156
                                        v+gl  i +G+ +l       l+ +  l        +sv g  ++G ++a+ ++ C+ P+++ v+  a     l +
  gi|344210053|ref|YP_004786229.1|  85 PVIGLGLIAFGVVML-------LNSEPELRVPLPARPASVTGFGVFGAVYAVAAAGCVVPLFFGVVSQALALP-LRT 153
                                       ****99999999888.......444444433333334445677789*********************999998.999 PP

                              DsbD 157 gallllvyvlGlaipfllvglllellkkklkslkkyskaveiaggvllvllGv 209
                                       ++l+l vy+lG aip++ v+ll++   +  +++  + + ++++++v+++++G 
  gi|344210053|ref|YP_004786229.1| 154 SVLVLAVYALGVAIPLVGVTLLAGAGIELWRTVGTHLQRMHQLAAVVMIVAGG 206
                                       *************************999**********************995 PP

>> DUF3188  Protein of unknown function (DUF3188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   1.1      0.55   4.9e+03       5      12 ..      62      69 ..      58      74 .. 0.54
   2 ?   12.4   0.4   1.1e-05     0.098       2      38 ..      88     124 ..      88     129 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.55
                           DUF3188  5 Lillglli 12
                                      L l++ll+
  gi|344210053|ref|YP_004786229.1| 62 LTLVALLV 69
                                      44555555 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.1e-05
                           DUF3188   2 AplLillgllillysqrqgsdr..lqslPallvGlgLiv 38 
                                       +++Li+ g+++ll  +++   r  l + Pa ++G g+ +
  gi|344210053|ref|YP_004786229.1|  88 GLGLIAFGVVMLL--NSEPELRvpLPARPASVTGFGVFG 124
                                       699**********..********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); 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):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1406.02
//
Query:       gi|344210054|ref|YP_004786230.1|  [L=519]
Description: trk system potassium uptake protein TrkH [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-66  225.4  14.4    6.3e-66  222.8  14.4    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 !  222.8  14.4   3.5e-70   6.3e-66      63     489 ..     118     505 ..     102     511 .. 0.91

  Alignments for each domain:
  == domain 1  score: 222.8 bits;  conditional E-value: 3.5e-70
                              TrkH  63 f...ldalfeavsgltttglsvivveeslprsgltlraqlqqiGglgvvvlaylslptlg..rgsaflylseaqkee 134
                                       f   lda+fe++sg+t tgl+v+ +ee+lprs  ++r++++++Gg+gv+vl++++l + g  +gs+ ly+sea    
  gi|344210054|ref|YP_004786230.1| 118 FlnpLDAVFESMSGFTGTGLTVAETEEQLPRSLHWWRSFIEWVGGVGVIVLTVAILQRGGgsSGSYTLYESEA---- 190
                                       24449***************************************************888889***********.... PP

                              TrkH 135 lggkelrslselikilvvyyvgleilafvllvvliytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSla 211
                                       +++k ++s+  +++ +++++vgl++ +++l+           +++      plw+a++h+m+++ ++Gfs++++S++
  gi|344210054|ref|YP_004786230.1| 191 RSEKIHPSIVTTVREIWKIFVGLTLGSIALF---------LLAGM------PLWDAINHGMTGIATGGFSVHSASIG 252
                                       9*************************99999.........899**......************************** PP

                              TrkH 212 sfnknivillvaiifiilGnigFpillrviiaikkkilrdlkqikeslsflldlprrcftLllasgfvwllllelav 288
                                        +++ ++i+ ++++++++G i+Fpi++ +  + ++++l+             dl++r+ ++ +  g ++l+ +    
  gi|344210054|ref|YP_004786230.1| 253 FYDS-PLIEYATVPVMVAGSIAFPIHYLI-FKGEIRNLY------------ADLQTRWVFIWFTAGSLVLTGILY-- 313
                                       ****.*********************955.556677755............8*******6666666665555443.. PP

                              TrkH 289 lnvtdnilfilldegslvvksipkgsrvlkalFqsvstrta.GFsvvdls.....nlhpaikvllvlmmyigglpgS 359
                                                    + +   + ++  + ++ alFq vs+ +  GF +++++      +++   +   l m  gg++gS
  gi|344210054|ref|YP_004786230.1| 314 -------------A-NGQYATLE--ETFRVALFQFVSATSNtGFGSASIGggteqVWSAGATLWACLGMLTGGAAGS 374
                                       .............3.34444555..88999*******99999*******73333359999999************** PP

                              TrkH 360 taggIrrtnvyeefslgkyeieqekepk.avskksidgkhlerqllvdlws....lflvlliilileglklsdvqep 431
                                       t+ g++ ++v ++++  +++i++ + p+ a++  +i+ ++l ++     +     +f++++ +l++ + +l  v  p
  gi|344210054|ref|YP_004786230.1| 375 TVSGLKLIRVVTLVKGTVWQIQDVFRPQtAIKYLQIGERRLSEEQAQREYTeatvVFILWITFLVIGVAVLLRVLSP 451
                                       **************************************************9889888889889999999******** PP

                              TrkH 432 dfsffdiLfevvSaygtvGLSlGaknaslsaqlttisklvlialmirGrlrglpvlld 489
                                          + +++f v+Sa+ +vGLS+G    ++ +++++ +k++li++m++Grl+++p++++
  gi|344210054|ref|YP_004786230.1| 452 AHPLEYVIFDVMSAQSNVGLSSG----ITGPDMPDTAKAMLILNMWVGRLEIIPIAVL 505
                                       ***********************....****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 3183.55
//
Query:       gi|344210055|ref|YP_004786231.1|  [L=236]
Description: Trk potassium uptake system protein [Haloarcula hispanica ATCC 33960]
Scores for 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-25   87.5   4.6    1.1e-24   86.9   2.5    2.0  2  TrkA_N           TrkA-N domain
      4e-14   52.2   0.5    1.5e-12   47.2   0.1    2.4  2  TrkA_C           TrkA-C domain
     0.0005   20.2   0.2    0.00081   19.5   0.2    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00097   19.5   0.9      0.002   18.5   0.3    1.7  2  NAD_binding_7    Putative NAD(P)-binding
     0.0011   19.2   0.5     0.0027   17.9   0.2    1.8  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0022   17.9   0.4     0.0078   16.2   0.5    1.7  2  ADH_zinc_N       Zinc-binding dehydrogenase
     0.0037   16.6   1.8     0.0058   15.9   1.8    1.2  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0042   17.3   0.9     0.0093   16.2   0.9    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.005   16.8   3.1     0.0073   16.2   1.8    1.9  1  NAD_binding_10   NAD(P)H-binding
     0.0069   16.9   0.1      0.013   16.0   0.1    1.5  1  XdhC_C           XdhC Rossmann domain
  ------ inclusion threshold ------
      0.011   16.3   0.4      0.043   14.4   0.2    2.1  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.012   15.9   0.1      0.017   15.4   0.1    1.2  1  Peripla_BP_3     Periplasmic binding protein-like domain
      0.022   14.5   0.0      0.055   13.2   0.0    1.7  1  PEP-utilizers    PEP-utilising enzyme, mobile domain
      0.033   15.0   0.6        0.1   13.5   0.6    1.8  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.039   13.8   0.3      0.059   13.2   0.3    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.04   13.5   1.8       0.18   11.3   0.4    2.1  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.049   14.2   1.8       0.11   13.1   1.8    1.6  1  ATPgrasp_N       ATP-grasp N-terminal domain
      0.084   13.1   0.2       0.21   11.8   0.2    1.7  1  PK_C             Pyruvate kinase, alpha/beta domain
      0.085   12.2   0.3       0.24   10.7   0.1    1.8  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.39    9.9   3.1        3.5    6.8   1.1    2.1  2  Pyr_redox_2      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 !   86.9   2.5   1.2e-27   1.1e-24       1     115 [.       3     117 ..       3     118 .. 0.94
   2 ?    0.1   0.0       1.1   9.5e+02      57      75 ..     168     186 ..     160     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 1.2e-27
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatgddea 75 
                                       ii +G+G++G+ l+e  +  g+ +vvvi++d +r++e++ e+ ++v+++dat +e+Le+ag+++ada+i++t++d++
  gi|344210055|ref|YP_004786231.1|   3 IITVGAGDIGTPLIEIATGtGN-EVVVIERDAARADEVASEFdCMVLNADATVKETLEDAGADRADAIITTTDQDAT 78 
                                       6779***************555.7******************9********************************** PP

                                       HHHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEE CS
                            TrkA_N  76 nilavllakelnpkkkiiaraqdpehaellkklgadvvis 115
                                       n++++lla+el   + i++ +++peh +l+k++g++++ +
  gi|344210055|ref|YP_004786231.1|  79 NVMVSLLAQELEI-PAIVSVVHNPEHMNLFKQIGVNTMEN 117
                                       *********9666.88*******************98765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                                       HTTGGGESEEEE-SSSHHH CS
                            TrkA_N  57 eagiekadaviaatgddea 75 
                                       e g+ +ad++++a++ ++a
  gi|344210055|ref|YP_004786231.1| 168 EEGLLDADTLVVAIERKDA 186
                                       6789999999999987654 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.09        81       3      36 ..       3      35 ..       1      54 [. 0.73
   2 !   47.2   0.1   1.6e-15   1.5e-12       1      70 []     147     221 ..     147     221 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.09
                                      EEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T..- CS
                            TrkA_C  3 evtvpagsplvGktlkelnlrar.gvlvvairRg..g 36
                                       +tv+ag   +G++l e  + +  g  vv i R+   
  gi|344210055|ref|YP_004786231.1|  3 IITVGAGD--IGTPLIE--IATGtGNEVVVIERDaaR 35
                                      56666665..9******..77777*****99998551 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 1.6e-15
                                       CEEEEEE--GGGTTSBHHHHT....HHHHS-EEEEEE-T..-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkeln....lrargvlvvairRg..geliipsgdtvLeeGDvllvvgspsdlaelrellg 70 
                                       ++e+tv++ +p++G tl e++    l a + lvvai R+  + +i p+g t++e+GD+l+v++ + ++ e+++++g
  gi|344210055|ref|YP_004786231.1| 147 VFEITVTEAAPIAGLTLIEADeeglLDA-DTLVVAIERKdaDAPITPRGQTRIEAGDLLTVYSGSGATPEVTDIFG 221
                                       79*****************887776666.*******8888********************************9996 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2     9e-07   0.00081      15      86 ..       3      76 ..       1      94 [. 0.74

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9e-07
                                      EEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EE..EEGCGHHHH.HHT-SEEEE-SSSS CS
                      Shikimate_DH 15 vlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiea..lkleelkel.laeadvvisatase 86
                                      ++ +GaG +++ +++     g + vvv+ R+ +ra+e+a+e++   ++a  +  e l+++  ++ad +i+ t   
  gi|344210055|ref|YP_004786231.1|  3 IITVGAGDIGTPLIEIATGTGNE-VVVIERDAARADEVASEFDCMVLNAdaTVKETLEDAgADRADAIITTTDQD 76
                                      6779**********988777766.******************665443310333334433267899999999765 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 !   18.5   0.3   2.2e-06     0.002      12      98 ..       5     104 ..       2     107 .. 0.73
   2 ?   -1.9   0.0       4.9   4.4e+03      59      74 ..     171     186 ..     134     197 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-06
                     NAD_binding_7  12 vvGgGevAarkvrklleagakvtvvapevkeele..........elvklaeeele.kdlegadlviaatddrelner 77 
                                        vG+G++++  ++    +g +v+v+  + +++ e          +     +e+le +  ++ad +i++td+++ n  
  gi|344210055|ref|YP_004786231.1|   5 TVGAGDIGTPLIEIATGTGNEVVVIERDAARADEvasefdcmvlNADATVKETLEdAGADRADAIITTTDQDATNVM 81 
                                       59**************************744433555553333211112344454244888**************** PP

                     NAD_binding_7  78 iaeaakarri..lvnvadkpelc 98 
                                       +  +a++ +i   v v+ +pe+ 
  gi|344210055|ref|YP_004786231.1|  82 VSLLAQELEIpaIVSVVHNPEHM 104
                                       *******9994457778888766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.9
                     NAD_binding_7  59 legadlviaatddrel 74 
                                       l +ad++++a+++++ 
  gi|344210055|ref|YP_004786231.1| 171 LLDADTLVVAIERKDA 186
                                       4456666666666555 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 !   17.9   0.2     3e-06    0.0027       4      81 ..       5      90 ..       2     102 .. 0.75
   2 ?   -0.7   0.0       1.5   1.4e+03     113     135 ..     187     210 ..      92     224 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3e-06
                                      EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........EEE-SSHHHHHHHC.....SEEEE-SSSHHHH CS
                     NAD_binding_2  4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........akaaesieelvasl.....dvvitmvkagkav 69
                                       +G G +G+++++  +  g +v+v++r++++++e+++e         a++ e++e+    +     d++it  ++++a+
  gi|344210055|ref|YP_004786231.1|  5 TVGAGDIGTPLIEIATGTGNEVVVIERDAARADEVASEFdcmvlnadATVKETLED----AgadraDAIITT-TDQDAT 78
                                      69**********************************99788885555555555555....444435777775.445556 PP

                                      HHHHHSHCCC-- CS
                     NAD_binding_2 70 deviegllealk 81
                                      + +++ l+++l+
  gi|344210055|ref|YP_004786231.1| 79 NVMVSLLAQELE 90
                                      655555666665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                                       EEEEE.SHHHHHHHT-EEEEEEE- CS
                     NAD_binding_2 113 daPVS.GGeegAekGtLsimvGGs 135
                                       daP++  G+   e+G L  + +Gs
  gi|344210055|ref|YP_004786231.1| 187 DAPITpRGQTRIEAGDLLTVYSGS 210
                                       444443455666666665555555 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.5   8.7e-06    0.0078       2     101 ..      11     108 ..      11     115 .. 0.80
   2 ?    2.1   0.0       0.2   1.8e+02       8      41 ..      84     118 ..      79     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.7e-06
                                       HHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                        ADH_zinc_N   2 vGlaavqlAkalGaeviavdsseeklelakk.lGadevinykeadlverikeltggegvdvvfecvGsgatleaalk 77 
                                       +G+ ++++A   G ev+++ +++ +++ +++ + +  v+n++  +++e ++++   + +d+++ ++  +++ +  ++
  gi|344210055|ref|YP_004786231.1|  11 IGTPLIEIATGTGNEVVVIERDAARADEVASeFDC-MVLNADA-TVKETLEDAG-ADRADAIITTTD-QDATNVMVS 83 
                                       68889*********************777765985.5667745.8999999999.78******9999.999999999 PP

                                       CEEEEEEE.EECSCTSSEEEEEHHH CS
                        ADH_zinc_N  78 llkpgGrl.vvvGggkgeeefdlrn 101
                                       ll+    + ++v +++++e+++l++
  gi|344210055|ref|YP_004786231.1|  84 LLAQELEIpAIVSVVHNPEHMNLFK 108
                                       9998866624555577777766665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.2
                                       HHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEET CS
                        ADH_zinc_N   8 qlAkalGa.eviavdsseeklelakklGadeviny 41 
                                        lA  l +  ++ v++++e   l k++G++   n+
  gi|344210055|ref|YP_004786231.1|  84 LLAQELEIpAIVSVVHNPEHMNLFKQIGVNTMENP 118
                                       5777888867777***************9887776 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   1.8   6.5e-06    0.0058      32      99 ..       4      73 ..       2      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.5e-06
                                      EEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEEHCHHHHHHHHH.HHH-SEEEE-- CS
                       AlaDh_PNT_C 32 lviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvevlksqeellaea.vkeadvvigtv 99
                                      + +G+G  G+  i++a+g g +V+v++ ++ar+ ++ s +   ++++ +  +e+l++a + +ad +i+t 
  gi|344210055|ref|YP_004786231.1|  4 ITVGAGDIGTPLIEIATGTGNEVVVIERDAARADEVASeFDCMVLNADATVKETLEDAgADRADAIITTT 73
                                      569***********************************9999999999988898887647889*****95 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 !   16.2   0.9     1e-05    0.0093       1      45 [.       3      62 ..       3     110 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-05
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..................T CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka..................l 45
                                      ++ +GaG +G +++e    +++   e++v++r+ ++++++a++                    
  gi|344210055|ref|YP_004786231.1|  3 IITVGAGDIGTPLIEIATGTGN---EVVVIERDAARADEVASEFdcmvlnadatvketledaG 62
                                      6889**************9998...5**********999996544444444444333333331 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 !   16.2   1.8   8.1e-06    0.0073       3      73 ..       8      78 ..       7     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.1e-06
                                      TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT.-SEEEES---TCC CS
                    NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkg.adaVvsalggggk 73
                                       G +G  l++ +   g  ev+++ R++++++e+++e  + v+ +d+t +e+l++a ++ ada+++++ ++++
  gi|344210055|ref|YP_004786231.1|  8 AGDIGTPLIEIATGTG-NEVVVIERDAARADEVASEFDCMVLNADATVKETLEDAGADrADAIITTTDQDAT 78
                                      699***********95.8****************999******************875168***99976665 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.5e-05     0.013       2      60 ..       4      82 ..       3     121 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-05
                                      EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG.................-GGG-TT-SE...........-EEEE--S CS
                            XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpreefa.................tkerfpeade...........tavvvlth 52
                                      + +Gag+++ +l+++a  +g +v+v++ +++ a                          +           +a++  t 
  gi|344210055|ref|YP_004786231.1|  4 ITVGAGDIGTPLIEIATGTGNEVVVIERDAARAdevasefdcmvlnadatV--------KetledagadraDAIITTTD 74
                                      569************************999766666666666665544442........03444555676555555555 PP

                                      -HHHHHHH CS
                            XdhC_C 53 dhklDaea 60
                                      + ++  ++
  gi|344210055|ref|YP_004786231.1| 75 QDATNVMV 82
                                      44444433 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   4.8e-05     0.043       2      31 ..       3      32 ..       2      59 .. 0.92
   2 ?   -1.0   0.0       3.1   2.8e+03      30      53 ..      65      88 ..      63     104 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.8e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                      ++ vG+G+ig  l ++++  g++V v+er 
  gi|344210055|ref|YP_004786231.1|  3 IITVGAGDIGTPLIEIATGTGNEVVVIERD 32
                                      689*************************96 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.1
                                      SSSSSSTTSSHHHHHHHHHHHHHT CS
                         Pyr_redox 30 rsdkllrllDeeaskilqeklekn 53
                                      r+d +    D++a +++   l ++
  gi|344210055|ref|YP_004786231.1| 65 RADAIITTTDQDATNVMVSLLAQE 88
                                      777788888999888888777554 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 ?   15.4   0.1   1.9e-05     0.017      50     107 ..      29      98 ..      20     131 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                                       S-SS-SSHHHHH...............HHH.HHCC.-SEEEEESSCCHHHHHHHHHCCTT--TTTTEEEE CS
                      Peripla_BP_3  50 aaddpaaaaaaraal.........ll.qal.klaa.lPtAviaasDelAlgvlqalreaglrvPedlsvi 107
                                        ++d+a a+++++            + + l +++a +++A+i ++D+ A  v+  l +++l++P  +sv+
  gi|344210055|ref|YP_004786231.1|  29 IERDAARADEVASEFdcmvlnadaTVkETLeDAGAdRADAIITTTDQDATNVMVSLLAQELEIPAIVSVV 98 
                                       44555555555544455434333322455574444699******************************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 ?   13.2   0.0   6.1e-05     0.055       8      55 ..      48      99 ..      42     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-05
                                      EEES---HHHHT..TS-GEEEEEES..--TTHHHHHHHHHHTT--EEE--SS CS
                     PEP-utilizers  8 Lvaeetspsdia..gldkaaGivte..rGGmtSHaAivArelgiPaVvgvge 55
                                      L a+ t ++ ++  g d+a +i+t   + + +  ++++A+el+iPa+v v +
  gi|344210055|ref|YP_004786231.1| 48 LNADATVKETLEdaGADRADAIITTtdQDATNVMVSLLAQELEIPAIVSVVH 99
                                      556666666666225569*****8744668889999************9865 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.6   0.00011       0.1       4      73 ..       4      76 ..       1     116 [. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
                                      EEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS...HHHHHTCT...TESEEEE-S-GG CS
                      GFO_IDH_MocA  4 aiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd...leelladp...eidavivatpng 73
                                        +GaG ig++ +  +     + evv ++++da+ra++va +f++ + +    ++e l+d    ++da+i +t  +
  gi|344210055|ref|YP_004786231.1|  4 ITVGAGDIGTPLI-EIATG-TGNEVV-VIERDAARADEVASEFDCMVLNAdatVKETLEDAgadRADAIITTTDQD 76
                                      569*********9.66555.455555.8*****************9655556655555554454566655444443 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 ?   13.2   0.3   6.6e-05     0.059       4      74 ..       5      76 ..       2      96 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.6e-05
                                      EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH.HHHCCTTTTSS-HHHHCCCHHCEEEES-HH CS
                           3HCDH_N  4 viGaGtmGagiaavfasagleVvlvdiseealekalekiek.sleklvekgklkeeeveaalarisfttdle 74
                                       +GaG +G+ + +++  +g eVv+++++++++++++++     l+  +  +++ e+  +++++ i +ttd +
  gi|344210055|ref|YP_004786231.1|  5 TVGAGDIGTPLIEIATGTGNEVVVIERDAARADEVASEFDCmVLNADATVKETLEDAGADRADAIITTTDQD 76
                                      69********************************99999884334333333333444455555555555544 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 ?   11.3   0.4    0.0002      0.18       1      42 [.       1      42 [.       1      86 [. 0.81
   2 ?    2.0   0.1      0.15   1.4e+02     127     157 ..      77     105 ..      47     124 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTT CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsg 42
                                      m i  +G+G +G +   +    g+ev+++  d+++ d++ s+
  gi|344210055|ref|YP_004786231.1|  1 MYIITVGAGDIGTPLIEIATGTGNEVVVIERDAARADEVASE 42
                                      56889******************************9998765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.15
                                       HHHHCHHHHHHHHCSS-TTCEEEEE------ CS
                    UDPG_MGDP_dh_N 127 taeelvkkileeaskkkgvdfdvvsnPEflr 157
                                       +++ ++ ++l+++ +   + ++vv+nPE ++
  gi|344210055|ref|YP_004786231.1|  77 ATN-VMVSLLAQELEI-PAIVSVVHNPEHMN 105
                                       333.333444444433.47899******875 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 ?   13.1   1.8   0.00012      0.11       4      81 ..      19      92 ..      16      93 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                                      HHHTT-EEEEEEETTS----S-TT.EEEEEEE-TTT-HHHHHHHHHHHHHHS--SEEE---G..GGHHHHHHHHHHTT- CS
                        ATPgrasp_N  4 AkaLGikvvlvdeedewapeelaelvekfipldlaqdpdaaleavralsrerpvdGivtftd..lavplvArlaeaLgL 80
                                      A   G +vv+++++   a e + e    f  + l++ +  + e+++ +  +++ d+i+t+td  ++ ++v+ la++L++
  gi|344210055|ref|YP_004786231.1| 19 ATGTGNEVVVIERDAARADEVASE----FDCMVLNA-DATVKETLEDA-GADRADAIITTTDqdATNVMVSLLAQELEI 91
                                      556688999999999777766666....44444443.33555666664.4567899999975227899*********** PP

                                      S CS
                        ATPgrasp_N 81 P 81
                                      P
  gi|344210055|ref|YP_004786231.1| 92 P 92
                                      9 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 ?   11.8   0.2   0.00024      0.21       2     100 ..      52     181 ..      51     191 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TSSEEEEEESHHHHHHHHHHCT..TEEHHH.HHHHH...... CS
                              PK_C   2 aiakaaveaaeelgakaIvvltesGetArliskyrpkvpiiavtpneltarqlalyr..Gvypvlvekakt...... 70 
                                       a++k + e a    a+aI++ t +  t  ++s + ++++i a+ +  +   +++l++  Gv +++    +       
  gi|344210055|ref|YP_004786231.1|  52 ATVKETLEDAGADRADAIITTTDQDATNVMVSLLAQELEIPAIVSVVHNPEHMNLFKqiGVNTMEN--PQRliaesl 126
                                       555666666666789**********************76666666444444444332113333331..122233333 PP

                                       .................TTSHHHHHHHHHHH...........TTSS-STSEEEEE CS
                              PK_C  71 ..............aestdellreavkvake...........aglvkkgdevvvt 100
                                                       ++ e+++  v  a             +gl++++ +vv++
  gi|344210055|ref|YP_004786231.1| 127 frsvdrpsivdymrVGDVAEVFEITVTEAAPiagltlieadeEGLLDADTLVVAI 181
                                       3333333333333322222222222111111233333333336666776666666 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 ?   10.7   0.1   0.00027      0.24      41      76 ..       5      40 ..       2      63 .. 0.76
   2 ?   -2.0   0.0       2.1   1.9e+03     102     147 ..     100     145 ..      93     179 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                                      EES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHH CS
                      2-Hacid_dh_C 41 iiGlGrIGqavakrlkafgmkviaydrskkkeeeee 76
                                       +G+G+IG+ +++++++ g +v++++r   + +e++
  gi|344210055|ref|YP_004786231.1|  5 TVGAGDIGTPLIEIATGTGNEVVVIERDAARADEVA 40
                                      58************************9987666222 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.1
                                       STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCC CS
                      2-Hacid_dh_C 102 tpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkia 147
                                       +pe  +l+++   + m +   li  +    vd+  +++ ++ g +a
  gi|344210055|ref|YP_004786231.1| 100 NPEHMNLFKQIGVNTMENPQRLIAESLFRSVDRPSIVDYMRVGDVA 145
                                       5666666666666666666666666666666666666666666665 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 ?    6.8   1.1    0.0039       3.5     146     176 ..       4      34 ..       2     145 .. 0.75
   2 ?    3.6   0.1     0.037        33     197     237 ..     143     183 ..     132     220 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0039
                                       EEES-SHHHHHHHHHHHHHT-EEEEEESSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 146 vvvGgGyiGvElAaalaklgkevtlveardr 176
                                       + vG+G iG+ l   ++  g ev+++e+   
  gi|344210055|ref|YP_004786231.1|   4 ITVGAGDIGTPLIEIATGTGNEVVVIERDAA 34 
                                       679*********************9997433 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.037
                                       TEEEEESCEEEEEEETTEEEE.EEETTSCEEEESEEEE-S-E CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 197 Gvevklgtsvkeidgngekle.vvledgeeidadlvvvavGv 237
                                       +v+ +++ +v+e+ +    l+  + +++  +dad++vva+ +
  gi|344210055|ref|YP_004786231.1| 143 DVAEVFEITVTEAAPIAG-LTlIEADEEGLLDADTLVVAIER 183
                                       566677888999998887.88455555555*********944 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); 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:                        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: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1365.06
//
Query:       gi|344210056|ref|YP_004786232.1|  [L=119]
Description: hypothetical protein HAH_5114 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   12.9   0.0       0.11   12.7   0.0    1.1  1  p25-alpha  p25-alpha


Domain annotation for each model (and alignments):
>> p25-alpha  p25-alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.1e-06      0.11      83     136 ..      26      82 ..       9      93 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.1e-06
                         p25-alpha  83 eel....eliekliegkgPklqgvtkatkagavdrltDtskYTGshkerfDesgkgkg 136
                                       ++l    + +++l+ +  P l+ + +a + +++ r  D+  YT +  +r De+g+g+g
  gi|344210056|ref|YP_004786232.1|  26 SQLsdivHYAQQLLREH-PPLTEAIEAREGETLVRTEDHGAYTIVVVKRPDETGEGRG 82 
                                       22223334578888888.666666999*****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 716.80
//
Query:       gi|344210057|ref|YP_004786233.1|  [L=254]
Description: transcription regulator [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-13   48.3   0.6    1.2e-12   47.5   0.6    1.4  1  TrkA_C          TrkA-C domain
      6e-12   44.9   0.2    1.2e-11   44.0   0.2    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    2.6e-11   43.2   0.4    4.9e-11   42.3   0.4    1.5  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    4.9e-06   26.4   0.0    1.1e-05   25.3   0.0    1.6  1  HTH_11          HTH domain
    1.7e-05   24.8   0.0    3.5e-05   23.8   0.0    1.6  1  HTH_20          Helix-turn-helix domain
    8.3e-05   22.3   0.0    0.00019   21.1   0.0    1.6  1  HTH_DeoR        DeoR-like helix-turn-helix domain
    0.00012   21.8   0.1    0.00062   19.6   0.0    2.1  2  MarR_2          MarR family
    0.00037   20.1   0.0    0.00063   19.3   0.0    1.4  1  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
     0.0013   18.8   0.0     0.0026   17.9   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0055   16.6   0.0      0.016   15.1   0.0    1.8  2  HTH_5           Bacterial regulatory protein, arsR family
     0.0081   16.3   0.0      0.014   15.5   0.0    1.4  1  HTH_28          Helix-turn-helix domain
     0.0087   15.8   0.0      0.019   14.8   0.0    1.4  1  HTH_23          Homeodomain-like domain
  ------ inclusion threshold ------
      0.024   15.0   0.1      0.063   13.6   0.0    1.7  1  Rrf2            Transcriptional regulator
      0.028   14.3   0.0       0.16   12.0   0.0    2.1  2  MarR            MarR family
       0.11   12.3   0.1       0.26   11.1   0.1    1.7  1  HTH_38          Helix-turn-helix domain
       0.12   11.8   0.0       0.25   10.8   0.0    1.5  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
       0.13   12.7   0.2        3.8    8.0   0.0    2.3  2  Med11           Mediator complex protein
       0.15   12.2   0.1          4    7.6   0.0    2.4  2  HTH_13          HTH DNA binding 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 !   47.5   0.6   1.2e-15   1.2e-12       1      59 [.     173     234 ..     173     242 .. 0.93

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.2e-15
                                       CEEEEEE--GGGTTSBHHHHT....HHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEH CS
                            TrkA_C   1 lvevtvpagsplvGktlkeln....lrargvlvvairRggeliipsgdtvLeeGDvllvvgsp 59 
                                       +v vtv++++p+v++tl+++n    l +  vl++ai Rg+e+i p gdt++++GD++ v++ +
  gi|344210057|ref|YP_004786233.1| 173 VVDVTVSPEAPIVDTTLRDANeqslLDE-EVLIIAIERGDEMITPKGDTEIRAGDLISVFARD 234
                                       6889***************999996666.*****************************99865 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 !   44.0   0.2   1.2e-14   1.2e-11       1      48 []       5      53 ..       5      53 .. 0.99

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 1.2e-14
                            HTH_24  1 ldetdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      lde+dr+I+ +Lq+++r is   +Ae+ ++Sp+t++ r+++Le++G+Ik
  gi|344210057|ref|YP_004786233.1|  5 LDEIDRRIIHALQQDARnISAPMVAEEMDVSPGTIRNRINQLEDAGIIK 53
                                      7***********************************************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 !   42.3   0.4   4.9e-14   4.9e-11       1      42 []       5      47 ..       5      47 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 4.9e-14
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaR.isyaeLAervGlSestvlrRvrrLe 42
                                      LDeiDr+I++aLq+daR is   +Ae+  +S+ t+++R+++Le
  gi|344210057|ref|YP_004786233.1|  5 LDEIDRRIIHALQQDARnISAPMVAEEMDVSPGTIRNRINQLE 47
                                      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 !   25.3   0.0   1.1e-08   1.1e-05       3      44 ..      10      51 ..       9      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.1e-08
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      + i++ L +   +is+   Aee++vS  t+r++I +Le++g+
  gi|344210057|ref|YP_004786233.1| 10 RRIIHALQQDARNISAPMVAEEMDVSPGTIRNRINQLEDAGI 51
                                      5799999787888****************************3 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   3.5e-08   3.5e-05      12      56 ..       9      54 ..       5      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.5e-08
                                      HHHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 12 RrrilraL.araegltaselaerldlskntlsyHLrvLeeagLvev 56
                                       rri  aL  +a+  +a+ +ae++d+s+ t+++++++Le+ag++++
  gi|344210057|ref|YP_004786233.1|  9 DRRIIHALqQDARNISAPMVAEEMDVSPGTIRNRINQLEDAGIIKG 54
                                      599*****99999******************************985 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.9e-07   0.00019       5      46 ..      12      54 ..       9      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.9e-07
                          HTH_DeoR  5 ilellkqq.gklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      i++ l+q+ + +s   ++e+ +vS+ TiR+ +n+Le +g+++ 
  gi|344210057|ref|YP_004786233.1| 12 IIHALQQDaRNISAPMVAEEMDVSPGTIRNRINQLEDAGIIKG 54
                                      7888877537899999************************865 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   6.3e-07   0.00062       7      51 ..       9      52 ..       5      69 .. 0.87
   2 ?   -1.1   0.0       1.8   1.8e+03      38      50 ..     119     131 ..     117     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.3e-07
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                      ++r+++aL    + ++++  +a+++++s++++ ++++ L++aG +
  gi|344210057|ref|YP_004786233.1|  9 DRRIIHALQQDAR-NISAPMVAEEMDVSPGTIRNRINQLEDAGII 52
                                      5899999999986.59***************************99 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHTTS CS
                            MarR_2  38 vsrilkrLvaaGL 50 
                                       ++ri   L++ GL
  gi|344210057|ref|YP_004786233.1| 119 LTRIAHQLSKLGL 131
                                       79********998 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 !   19.3   0.0   6.3e-07   0.00063       8      55 ..       7      54 ..       1      57 [. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.3e-07
                      HrcA_DNA-bdg  8 eilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLveg 55
                                      ei + +i+  +++ r + +  +Ae ++  +Gt+RN ++ L   g+++g
  gi|344210057|ref|YP_004786233.1|  7 EIDRRIIHALQQDARNISAPMVAEEMDVSPGTIRNRINQLEDAGIIKG 54
                                      6667788888999***************************99999988 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 !   17.9   0.0   2.6e-06    0.0026      12      52 ..      12      52 ..      11      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.6e-06
                                      HHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress 12 tIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                       I  l+ +   ++  ++ae+++vsp ++   ++ Le++G +
  gi|344210057|ref|YP_004786233.1| 12 IIHALQQDARNISAPMVAEEMDVSPGTIRNRINQLEDAGII 52
                                      58889999999***************************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 !   15.1   0.0   1.6e-05     0.016       5      46 ..      10      53 ..       6      53 .. 0.80
   2 ?   -3.1   0.0       7.7   7.7e+03      32      39 ..     122     129 ..     121     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                                      HHHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  5 lkILklLae..gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      ++I+++L++  ++ ++   aee+++s++t++   ++L++aG+++
  gi|344210057|ref|YP_004786233.1| 10 RRIIHALQQdaRNISAPMVAEEMDVSPGTIRNRINQLEDAGIIK 53
                                      57888888844444444589**********************95 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.7
                                       HHHHHHHH CS
                             HTH_5  32 vShHLkkL 39 
                                       + h+L+kL
  gi|344210057|ref|YP_004786233.1| 122 IAHQLSKL 129
                                       67999998 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.4e-05     0.014       6      41 ..      13      51 ..      10      57 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                            HTH_28  6 ikllaaGh...svreaArelgisrrtvyrWikryeegGi 41
                                      i +l++     s++ +A+e+ +s+ t++  i+++e  Gi
  gi|344210057|ref|YP_004786233.1| 13 IHALQQDArniSAPMVAEEMDVSPGTIRNRINQLEDAGI 51
                                      444444323246667********************9997 PP

>> HTH_23  Homeodomain-like 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     0.019       9      45 ..      11      50 ..      10      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                            HTH_23  9 rillllae...GlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      ri+++l++    +s + +A+e++vs+ T+++ ++  +  G
  gi|344210057|ref|YP_004786233.1| 11 RIIHALQQdarNISAPMVAEEMDVSPGTIRNRINQLEDAG 50
                                      79*****9999*******************9998875466 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.3e-05     0.063      18      56 ..      15      53 ..      11      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.3e-05
                                      HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 18 akeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      a++++ + +s+  +ae++++sp  ++  +++L+ ag++k
  gi|344210057|ref|YP_004786233.1| 15 ALQQDARNISAPMVAEEMDVSPGTIRNRINQLEDAGIIK 53
                                      67788888*****************************98 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   0.00016      0.16      24      48 ..      29      53 ..      16      58 .. 0.87
   2 ?   -1.3   0.0       2.2   2.1e+03      34      46 ..     119     131 ..     113     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                      HHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 24 akklgvskstvtrvldrLekkGlie 48
                                      a+ + vs++t+ + + +Le++G i+
  gi|344210057|ref|YP_004786233.1| 29 AEEMDVSPGTIRNRINQLEDAGIIK 53
                                      899*******************996 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHTTS CS
                              MarR  34 vtrvldrLekkGl 46 
                                       +tr++++L k Gl
  gi|344210057|ref|YP_004786233.1| 119 LTRIAHQLSKLGL 131
                                       8999999999886 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00026      0.26       3      39 ..       3      41 ..       1      45 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                            HTH_38  3 khLsleeReeIerll..aeGlslreIArrLgrspsTIsR 39
                                      ++L   +R+ I +l   a++ s   +A ++++sp+TI +
  gi|344210057|ref|YP_004786233.1|  3 RRLDEIDRRIIHALQqdARNISAPMVAEEMDVSPGTIRN 41
                                      6788889*******6335889999*************97 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 ?   10.8   0.0   0.00025      0.25      17      50 ..       9      45 ..       6      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                      HTH_Tnp_ISL3 17 eayilellles.rsvka..vArqlgvSwtTVwrildr 50
                                      ++ i+++l+++ r+++a  vA++++vS+ T+++++++
  gi|344210057|ref|YP_004786233.1|  9 DRRIIHALQQDaRNISApmVAEEMDVSPGTIRNRINQ 45
                                      5778888888888888888***************997 PP

>> Med11  Mediator complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.22   2.2e+02       6      22 ..       4      20 ..       3      27 .. 0.83
   2 ?    8.0   0.0    0.0038       3.8      66     127 ..      39     118 ..      36     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.22
                             Med11  6 qLneIDkdIvslLesas 22
                                      +L+eID++I+  L++ +
  gi|344210057|ref|YP_004786233.1|  4 RLDEIDRRIIHALQQDA 20
                                      79***********9855 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0038
                             Med11  66 LrrqIyaLeeagiitlessaaasagksaa..................karlepsgvgavgnldvgwlnsrsskverd 124
                                       +r+ I+ Le+agii+  ++    +  ++                   ++ l   gv +v +l  g+ n + + v+++
  gi|344210057|ref|YP_004786233.1|  39 IRNRINQLEDAGIIKGYHADIDYERCESRltnlfvcntsaserenlaRKALTVPGVVNVRELRTGRGNLQIKAVGEE 115
                                       7999**********766665555555544899999999999999999888999999999999999999999999999 PP

                             Med11 125 mea 127
                                       m +
  gi|344210057|ref|YP_004786233.1| 116 MSD 118
                                       865 PP

>> HTH_13  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.004         4      14      38 ..      23      47 ..      21      49 .. 0.90
   2 ?    1.7   0.0      0.28   2.8e+02      32      47 ..      90     106 ..      83     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.004
                            HTH_13 14 VsagmvakeLkvtpraalklvkelg 38
                                      +sa+mva+e++v+p   ++ +++l+
  gi|344210057|ref|YP_004786233.1| 23 ISAPMVAEEMDVSPGTIRNRINQLE 47
                                      79************99999888875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.28
                            HTH_13  32 klvkelglREl.TGRgr 47 
                                       ++   +++REl TGRg 
  gi|344210057|ref|YP_004786233.1|  90 TVPGVVNVRELrTGRGN 106
                                       55556899**889**96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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):              18  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1552.59
//
Query:       gi|344210058|ref|YP_004786234.1|  [L=290]
Description: hypothetical protein HAH_5116 [Haloarcula hispanica ATCC 33960]
Scores for 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-10   39.2   3.8    0.00012   22.6   1.4    3.2  2  Usp       Universal stress protein family
  ------ inclusion threshold ------
       0.13   11.7   0.2       0.17   11.3   0.2    1.2  1  MafB      Neisseria toxin MafB


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 !   14.7   0.0   3.7e-06     0.033       4     139 ..      22     144 ..      20     146 .. 0.67
   2 !   22.6   1.4   1.3e-08   0.00012       4     140 ..     156     276 ..     153     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-06
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                       rIl+++ + ++ +  +e Al+ a   g+el +l   d ++ +a+  ++ ++    l +++  +              
  gi|344210058|ref|YP_004786234.1|  22 RILYPI-FGTHDDFTFETALNIADGVGGELLVL---DLFTGDATRSSETTSVGRKLLQARLDE---------THTAD 85 
                                       777777.77777777888888888888884444...333333333222222222222222222.........23344 PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                       +  +v e   p  + + va++++++l V+  +    + + l G+ +++  ++a+c+V+ 
  gi|344210058|ref|YP_004786234.1|  86 AHLIVEETDTPLKTAINVAQQRHVQLAVLDEHTPELFGEGLRGDAADRMRKKASCDVVS 144
                                       4555555666677779*****************999999******************85 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 1.3e-08
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                        +lV++ + ++s   +  + +la   +a++ l hv+++++ +av+ a    e++++ l ea              + 
  gi|344210058|ref|YP_004786234.1| 156 SVLVPIAEGTHSALGVVVGGALAMGADAPVDLFHVSETKDETAVARASTLFETARSRLPEA--------------VT 218
                                       5788887666666666666668888899999999999999999999999999999999997..............88 PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       + + ++e  d+ae+i+ +     ++  V+G+  +s+l++++ GSv+ +v  +++  Vl V
  gi|344210058|ref|YP_004786234.1| 219 VDTWHLEAPDVAEAIINESAH--YNVTVMGKPTQSRLREFVTGSVTAAVTDESENAVLTV 276
                                       9999*********99987776..6667*************************99999987 PP

>> MafB  Neisseria toxin MafB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   1.9e-05      0.17     142     289 ..      98     247 ..      89     273 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.9e-05
                              MafB 142 kiklnltdqrsisqrlldefanagsnlldradeankkifeydpeldrsgnameavnGvadgavnpflaagealGv.. 216
                                       k+ +n+++qr ++  +lde++    +   r d a +   + + +    +    a  G+ ++ v +   +  alGv  
  gi|344210058|ref|YP_004786234.1|  98 KTAINVAQQRHVQLAVLDEHTPELFGEGLRGDAADRMRKKASCDVVSVT-YSRADSGISSVLVPIAEGTHSALGVvv 173
                                       5667777777777777777765433333333333333333333332222.223335666666655555566666533 PP

                              MafB 217 .GdivdgiseavdiaalhnlgllsaeaklaaitdladaaqlkkdaaeavrdWadenPnaaetv...eavvnvtkaak 289
                                        G++  g+  +vd   l  +++   e+ +a+++ l ++a  +   a +v+ W  e P++ae++    a  nvt   k
  gi|344210058|ref|YP_004786234.1| 174 gGALAMGADAPVD---LFHVSETKDETAVARASTLFETARSRLPEAVTVDTWHLEAPDVAEAIineSAHYNVTVMGK 247
                                       3555566666666...567888999************************************9833234445554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1818.61
//
Query:       gi|344210059|ref|YP_004786235.1|  [L=205]
Description: nitroreductase family protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   0.3    3.9e-08   33.5   0.1    2.1  2  Nitroreductase  Nitroreductase family
    6.7e-05   22.5   0.0     0.0002   21.0   0.0    1.7  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 !   33.5   0.1   4.4e-12   3.9e-08       3      49 ..      30      76 ..      28      91 .. 0.83
   2 !   29.7   0.0   6.6e-11   5.9e-07      81     169 ..      87     171 ..      75     172 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 4.4e-12
                                      H--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCC CS
                    Nitroreductase  3 kRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkel 49
                                      +R S R+   +++ +++l  + eaar+aPsa+n q wrfv +++++ 
  gi|344210059|ref|YP_004786235.1| 30 NRWSPRAMAGDSLAEDDLLPLFEAARWAPSAFNNQHWRFVYATREDD 76
                                      69999***********************************9954443 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 6.6e-11
                                       HHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S CS
                    Nitroreductase  81 lkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglp 157
                                       + ++++ ++a +li +   ++k +  ++ +++ +  +d+gaa qnl L+ ++++l++ p+ gfd ++  +++ lg+p
  gi|344210059|ref|YP_004786235.1|  87 EANRSWARNAGALIAV---FSKVTLEHNGESAGTRSFDTGAAWQNLALEGARRDLAVHPMAGFDWDR--IHEALGVP 158
                                       6789999*********...888888888888888999******************************..******** PP

                                       ...SEEEEEEEEE CS
                    Nitroreductase 158 .deeeivvliavG 169
                                        de +  ++iavG
  gi|344210059|ref|YP_004786235.1| 159 eDEFDAEAMIAVG 171
                                       7667777888888 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   2.2e-08    0.0002     163     185 ..      50      72 ..      38      90 .. 0.86
   2 ?   -1.7   0.0       0.2   1.8e+03     124     148 ..     164     198 ..     156     201 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.2e-08
                                       HHHHHHTS--GGG----EEE.E- CS
                    TM1586_NiRdase 163 ileaarlAPsAlNqqpwrfelkd 185
                                       + eaar APsA+N+q+wrf + +
  gi|344210059|ref|YP_004786235.1|  50 LFEAARWAPSAFNNQHWRFVYAT 72 
                                       679****************9765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.2
                                       -S-EEEEE-BS----...........-----HHHH CS
                    TM1586_NiRdase 124 lvivIalGyaktklv..........eakrkpleel 148
                                         ++Ia+G  ++  +          +  rkpl+e+
  gi|344210059|ref|YP_004786235.1| 164 AEAMIAVGERADPETlpedlkehekPSGRKPLDEI 198
                                       56899999988877444444443445566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1344.19
//
Query:       gi|344210060|ref|YP_004786236.1|  [L=441]
Description: hypothetical protein HAH_5119 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   15.2   6.8     0.0096   15.2   6.8    2.7  3  LtrA       Bacterial low temperature requirement A protein (L
  ------ inclusion threshold ------
       0.42   10.6   1.1       0.58   10.1   0.3    1.7  2  Nudix_N_2  Nudix N-terminal


Domain annotation for each model (and alignments):
>> 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 ?   -3.7   1.6       0.6   5.3e+03     332     340 ..     224     232 ..     196     249 .. 0.42
   2 !   15.2   6.8   1.1e-06    0.0096     263     338 ..     266     341 ..     261     350 .. 0.86
   3 ?   -1.0   5.2     0.091   8.2e+02     285     349 ..     351     413 ..     344     425 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.6
                              LtrA 332 alvlaalla 340
                                       + +la + +
  gi|344210060|ref|YP_004786236.1| 224 VKALAYITL 232
                                       111111111 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.1e-06
                              LtrA 263 vagiillavglelllahpeelldlaaalllfggvalfllgllllkrvllgsvslsrlvllllllallalalvlaal 338
                                       +ag  +la +l+ll a    +l ++aa l+ gg alf++g++l +r+++ + s++++v+ +++ a++al++ + a+
  gi|344210060|ref|YP_004786236.1| 266 FAGFGALATALSLLGATGVLRLGGIAAPLFGGGTALFVCGIALSQRRVRERASYRAVVGGAVVGAGIALGATIVAA 341
                                       778888888888888888899*****************************************99999998555443 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.091
                              LtrA 285 dlaaalllfggvalfllgllllkrvllgsvslsrlvllllllallalalvlaallalallalvll 349
                                       + + all++g++ + l + +++ +  ++   + + +++ ++l +l+++ vl+a + l++l + ++
  gi|344210060|ref|YP_004786236.1| 351 PPVSALLVLGPAFVLLPAGYAVGHGNRRL--AMKTAAIGFVLSMLPVLPVLPAPFGLGVLFVPIA 413
                                       66778888888888888888887655444..4444455555568888888888777777643332 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.3   6.5e-05      0.58       3      29 ..      13      40 ..      12      43 .. 0.88
   2 ?   -3.4   0.0       1.1   9.5e+03       6      14 ..     304     312 ..     303     320 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.5e-05
                                      -TTT--B-EEE--TT-S.S-EEEETTTT CS
                         Nudix_N_2  3 CsqCGtpvelripdgDn.reRlvCpaCg 29
                                      C  C++ + +++p+g    +R  C+aCg
  gi|344210060|ref|YP_004786236.1| 13 CLVCASLLVTAMPAGAApPPRPLCDACG 40
                                      999***********987258*******9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.1
                                       T--B-EEE- CS
                         Nudix_N_2   6 CGtpvelri 14 
                                       CG ++++r 
  gi|344210060|ref|YP_004786236.1| 304 CGIALSQRR 312
                                       888888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2662.74
//
Query:       gi|344210061|ref|YP_004786237.1|  [L=289]
Description: transcriptional regulator [Haloarcula hispanica ATCC 33960]
Scores for 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-09   36.0   0.1    9.4e-09   35.1   0.1    1.4  1  HTH_Crp_2  Crp-like helix-turn-helix domain
    3.1e-06   27.2   0.3    7.6e-06   25.9   0.3    1.7  1  DprA_WH    DprA winged helix domain
    3.4e-06   26.8   0.1    7.1e-06   25.8   0.1    1.5  1  MarR_2     MarR family
     0.0001   22.2   0.0    0.00016   21.5   0.0    1.3  1  MarR       MarR family
    0.00015   21.3   0.1    0.00024   20.6   0.1    1.4  1  HTH_24     Winged helix-turn-helix DNA-binding
    0.00031   20.5   0.0    0.00058   19.7   0.0    1.5  1  HTH_5      Bacterial regulatory protein, arsR family
    0.00047   20.0   0.0    0.00083   19.2   0.0    1.3  1  TrmB       Sugar-specific transcriptional regulator TrmB
    0.00096   19.2   0.3      0.002   18.2   0.3    1.6  1  HTH_20     Helix-turn-helix domain
     0.0021   17.7   0.0     0.0039   16.8   0.0    1.5  1  Crp        Bacterial regulatory proteins, crp family
      0.004   17.5   0.0     0.0081   16.5   0.0    1.5  1  Rrf2       Transcriptional regulator
     0.0048   16.7   0.3      0.022   14.6   0.0    2.2  2  HTH_IclR   IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.016   14.8   0.0      0.031   13.9   0.0    1.4  1  GntR       Bacterial regulatory proteins, gntR family
      0.018   15.0   0.0       0.03   14.3   0.0    1.4  1  HTH_11     HTH domain
      0.023   14.8   0.0      0.036   14.1   0.0    1.3  1  HTH_7      Helix-turn-helix domain of resolvase
        0.1   12.6   0.0       0.19   11.8   0.0    1.4  1  HTH_3      Helix-turn-helix
       0.16   12.2   0.0       0.27   11.4   0.0    1.5  1  GP17       Superinfection exclusion gene product 17


Domain annotation for each model (and alignments):
>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.1   8.4e-12   9.4e-09      20      55 ..      41      80 ..      26      93 .. 0.74

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 8.4e-12
                                      E....EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                         HTH_Crp_2 20 l....pltqeelAsmlGltretvsrilseLkreglisrgr 55
                                      l    p +++el+++ G+tr+t+sril++L+++ +i+r++
  gi|344210061|ref|YP_004786237.1| 41 LlsdgPCSRDELSDRTGVTRVTLSRILGDLEDRDWITRRN 80
                                      2334499******************************653 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.3   6.8e-09   7.6e-06      11      60 ..      32      81 ..      12      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 6.8e-09
                           DprA_WH 11 ddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlverlpG 60
                                      ++ + rvL++L+  P++ D+L+ rtg++  ++s++L  LE    ++r+ G
  gi|344210061|ref|YP_004786237.1| 32 SEHRLRVLELLSDGPCSRDELSDRTGVTRVTLSRILGDLEDRDWITRRNG 81
                                      78899***********************************8888888876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   6.3e-09   7.1e-06       8      56 ..      36      81 ..      17      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 6.3e-09
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      +rvL  L ++p   ++  el +r+g+++ ++sril +L+++ +++rr g
  gi|344210061|ref|YP_004786237.1| 36 LRVLELLSDGP---CSRDELSDRTGVTRVTLSRILGDLEDRDWITRRNG 81
                                      68888888888...9*******************************976 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.4e-07   0.00016       7      50 ..      37      79 ..      32      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.4e-07
                                      HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      ++L++l+  gp+s  eL ++ gv++ t++r+l  Le++++i+R+
  gi|344210061|ref|YP_004786237.1| 37 RVLELLS-DGPCSRDELSDRTGVTRVTLSRILGDLEDRDWITRR 79
                                      5555554.599********************************8 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   2.1e-07   0.00024       3      48 .]      33      77 ..      31      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.1e-07
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      e ++++LelL + + +s  eL++r+g+++ t++r l  Le+  +I+
  gi|344210061|ref|YP_004786237.1| 33 EHRLRVLELLSD-GPCSRDELSDRTGVTRVTLSRILGDLEDRDWIT 77
                                      566777777776.*******************************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 !   19.7   0.0   5.2e-07   0.00058       2      41 ..      33      72 ..      32      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.2e-07
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLre 41
                                      + Rl++L lL++g+++  el++ +g+++ t+S+ L  L++
  gi|344210061|ref|YP_004786237.1| 33 EHRLRVLELLSDGPCSRDELSDRTGVTRVTLSRILGDLED 72
                                      67******************************98888876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   7.4e-07   0.00083      16      59 ..      40      83 ..      38      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.4e-07
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrp 59
                                       Ll+ gp + de++ ++gv r +  ++L  Led+++++r+ g++
  gi|344210061|ref|YP_004786237.1| 40 ELLSDGPCSRDELSDRTGVTRVTLSRILGDLEDRDWITRRNGEK 83
                                      69**************************************8873 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3   1.8e-06     0.002       8      58 ..      30      80 ..      20      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.8e-06
                                      S-.HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20  8 ah.PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      a  + R+r+l +L ++++ +  el +r ++++ tls+ L  Le+ + ++++ 
  gi|344210061|ref|YP_004786237.1| 30 ARsEHRLRVLELL-SDGPCSRDELSDRTGVTRVTLSRILGDLEDRDWITRRN 80
                                      44499********.******************************99999875 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.5e-06    0.0039       4      27 ..      48      71 ..      46      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.5e-06
                                      -HHHHHHHHTS-HHHHHHHHHHHH CS
                               Crp  4 SRqdIAdylGlTrETVSRlLtrLr 27
                                      SR ++ d  G Tr+T SR L++L+
  gi|344210061|ref|YP_004786237.1| 48 SRDELSDRTGVTRVTLSRILGDLE 71
                                      99*********************8 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   7.2e-06    0.0081      16      61 ..      38      82 ..      19      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.2e-06
                                      HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                              Rrf2 16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                      +L++ +++ p+s +e+++r+++ ++ l++il  L+  ++++ + G 
  gi|344210061|ref|YP_004786237.1| 38 VLELLSDG-PCSRDELSDRTGVTRVTLSRILGDLEDRDWITRRNGE 82
                                      55666664.69********************************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 !   14.6   0.0   1.9e-05     0.022       6      50 ..      36      78 ..      33      80 .. 0.87
   2 ?   -1.0   0.0       1.4   1.5e+03      17      43 ..     142     168 ..     127     170 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-05
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      l++L++l+ +p   +  el++rtg+++ t +R+L  L+ + ++++
  gi|344210061|ref|YP_004786237.1| 36 LRVLELLSDGPC--SRDELSDRTGVTRVTLSRILGDLEDRDWITR 78
                                      677888876655..689************************9987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                                       SS-BHHHHHHHHTS-HHHHHHHHHHHH CS
                          HTH_IclR  17 qeltlselArrtglpkStvhRlLqtLv 43 
                                        +l  + + +++  + S+ + lL t++
  gi|344210061|ref|YP_004786237.1| 142 DPLAAARIVANAIQNASSFRSLLGTFI 168
                                       347777788888888888888888876 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.8e-05     0.031      28      60 ..      50      82 ..      34      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglverrqgr 60
                                       eL+++ gV+r t+ + L  Le +++++rr+g+
  gi|344210061|ref|YP_004786237.1| 50 DELSDRTGVTRVTLSRILGDLEDRDWITRRNGE 82
                                      69****************************997 PP

>> HTH_11  HTH 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      0.03       3      40 ..      36      71 ..      34      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLe 40
                                      l +lelL  ++gp s +eL+++++v+r t  r + +Le
  gi|344210061|ref|YP_004786237.1| 36 LRVLELL--SDGPCSRDELSDRTGVTRVTLSRILGDLE 71
                                      5678888..8999*****************99888887 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 ?   14.1   0.0   3.2e-05     0.036      12      43 ..      36      68 ..      29      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                                      GGGGSSTTTT.--STTTSSSS---SSSS--SS- CS
                             HTH_7 12 nrvvkLleeG.isiskIAkevnisRsTvYRyla 43
                                       rv++Ll++G  s+ ++ ++++++R T+ R+l 
  gi|344210061|ref|YP_004786237.1| 36 LRVLELLSDGpCSRDELSDRTGVTRVTLSRILG 68
                                      69****************************985 PP

>> HTH_3  Helix-turn-helix
   #    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      11      29 ..      48      66 ..      47      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                                      HHHHHHHHHTSSHHHHHHH CS
                             HTH_3 11 sqeeLAeklGvsrstisri 29
                                      s+ eL++++Gv+r t+sri
  gi|344210061|ref|YP_004786237.1| 48 SRDELSDRTGVTRVTLSRI 66
                                      789***************9 PP

>> GP17  Superinfection exclusion gene product 17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00024      0.27      37      82 ..     171     215 ..     119     227 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                              GP17  37 dlfqyennikpdycnasglqlydedltdddledmglddrwvdlyse 82 
                                        ++ ye+ +++   +a+g  ++d dlt+  l d +l  rw  ++  
  gi|344210061|ref|YP_004786237.1| 171 PMYTYEEAVRAG-NEADGTVVFDTDLTETMLSDADLRGRWQTIEAA 215
                                       467888888876.5799***********************877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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):              16  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1671.96
//
Query:       gi|344210062|ref|YP_004786238.1|  [L=249]
Description: ABC transporter ATP-binding protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   87.2   0.0    1.9e-24   86.7   0.0    1.2  1  ABC_tran     ABC transporter
    2.4e-12   47.3   0.0    7.6e-07   29.2   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    6.1e-05   22.1   0.1    9.5e-05   21.5   0.1    1.2  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
    0.00016   21.2   0.0       0.15   11.5   0.0    2.3  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00037   20.3   0.0       0.26   10.9   0.0    2.1  2  AAA_15       AAA ATPase domain
     0.0021   18.6   0.1     0.0034   17.9   0.1    1.3  1  AAA_23       AAA domain
     0.0091   15.7   0.0      0.026   14.3   0.0    1.7  3  AAA_30       AAA domain
  ------ inclusion threshold ------
      0.013   15.9   0.0      0.028   14.8   0.0    1.6  1  AAA_16       AAA ATPase domain
      0.021   15.2   0.5        1.1    9.7   0.1    2.7  3  AAA          ATPase family associated with various cellular a
      0.023   14.5   0.1      0.053   13.3   0.1    1.6  2  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.077   12.6   0.0       0.15   11.7   0.0    1.4  1  SRP54        SRP54-type protein, GTPase domain
      0.078   13.3   0.0       0.13   12.5   0.0    1.5  1  AAA_22       AAA domain
        0.1   12.4   0.1       0.18   11.6   0.1    1.3  1  MukB         MukB N-terminal
       0.19   11.6   0.0       0.58   10.0   0.0    1.7  2  RsgA_GTPase  RsgA GTPase
       0.22   11.1   0.0       0.33   10.5   0.0    1.2  1  AAA_27       AAA domain
       0.29    9.7   0.4         10    4.6   0.1    2.0  2  AAA_13       AAA domain
       0.99    9.5   4.9         27    5.1   0.2    3.7  3  LSPR         Coagulation Factor V LSPD Repeat


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 !   86.7   0.0   1.8e-27   1.9e-24       3     136 ..      21     162 ..      19     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 1.8e-27
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren 79 
                                       ++sl++  ge  +++G+nGaGK+t +++l+g+l+p+ G++ + g d  + + + +r++ g+lp++++  + +t re 
  gi|344210062|ref|YP_004786238.1|  21 DLSLSIDDGEFFGLLGPNGAGKTTTMEILTGQLSPDGGQVSVLGVDPAT-QPTAVRERAGILPEKESPPSFMTPREY 96 
                                       799****************************************999999.778999*********999999999999 PP

                                       .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                    + +e+ e ++++lg +e+ dt      s LS Gq+q+v++a a++ +p ++++DEp 
  gi|344210062|ref|YP_004786238.1|  97 fdfvgairdmpddAVTEQTESWADRLGFTEKLDTLS----SDLSRGQQQKVMIAGAFFHEPAVVFIDEPL 162
                                       9*********99999999************999998....*****************************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 !   16.4   0.0   5.9e-06    0.0062       1      23 [.      31      53 ..      31      95 .. 0.81
   2 !   29.2   0.0   7.2e-10   7.6e-07     232     299 ..     130     194 ..     109     198 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.9e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      + +l GpNg+GK++ +++l +  
  gi|344210062|ref|YP_004786238.1| 31 FFGLLGPNGAGKTTTMEILTGQL 53
                                      6789***************7654 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 7.2e-10
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                       + +++lS G+++   ++ a++  +   ++++iDEp ++L+P +++r+ ++l++ ++ g  +++tTH+ 
  gi|344210062|ref|YP_004786238.1| 130 TLSSDLSRGQQQKVMIAGAFFHEP---AVVFIDEPLANLDPIVQERVKRFLRSYRDDGNTIVVTTHDV 194
                                       557899*******99999999988...***************************99**********95 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1     9e-08   9.5e-05      31      70 ..      31      70 ..      19      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9e-08
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                        Gl G  GaGk t++e l+ +l   G +v+vl vDP+ +
  gi|344210062|ref|YP_004786238.1| 31 FFGLLGPNGAGKTTTMEILTGQLSPDGGQVSVLGVDPATQ 70
                                      57999********************************987 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0     0.002       2.1      24      42 ..      29      47 ..       1      56 [. 0.67
   2 !   11.5   0.0   0.00014      0.15     134     199 ..     132     193 ..      77     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.002
                                      SSEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlld 42
                                       +f  ++GpNG+GK+  ++
  gi|344210062|ref|YP_004786238.1| 29 GEFFGLLGPNGAGKTTTME 47
                                      458889*********9887 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00014
                                       TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislre 199
                                       ++ LS+G+++ v++a  f    ++  +++++De  a+LD    ++v ++l++ +++   iv++ ++
  gi|344210062|ref|YP_004786238.1| 132 SSDLSRGQQQKVMIAGAF----FHEPAVVFIDEPLANLDPIVQERVKRFLRSYRDDGNTIVVTTHD 193
                                       457999999988887665....566667889***********************998887776544 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0024       2.6      20      43 ..      25      49 ..      18      54 .. 0.80
   2 !   10.9   0.0   0.00025      0.26     315     365 ..     151     193 ..      72     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0024
                            AAA_15 20 dlsee.ltvliGkNnsGKSsileal 43
                                      ++++  +  l G+N++GK++ +e+l
  gi|344210062|ref|YP_004786238.1| 25 SIDDGeFFGLLGPNGAGKTTTMEIL 49
                                      45554577799************98 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00025
                            AAA_15 315 ekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       ++       +++++i+EP a+L p  q+ + + l++  +d++  +++tTH 
  gi|344210062|ref|YP_004786238.1| 151 HE-------PAVVFIDEPLANLDPIVQERVKRFLRSYRDDGN-TIVVTTHD 193
                                       34.......499*****************************9.9******7 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   3.2e-06    0.0034       9      40 ..      12      50 ..       4      59 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.2e-06
                            AAA_23  9 sfrdqe.i.dF.....skgltlItGpNGaGKTTildAik 40
                                      s++d++ i d+     +  ++ + GpNGaGKTT ++ ++
  gi|344210062|ref|YP_004786238.1| 12 SYGDVTaIpDLslsidDGEFFGLLGPNGAGKTTTMEILT 50
                                      5566555445555665667999*************9887 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   2.4e-05     0.026      20      53 ..      31      64 ..      24      87 .. 0.82
   2 ?   -2.4   0.0       3.1   3.3e+03      88      96 ..     152     160 ..     112     196 .. 0.57
   3 ?   -2.9   0.0       4.5   4.8e+03      41      67 ..     179     205 ..     171     209 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-05
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrviglA 53
                                      +  l Gp G+GKtt+++ l+  +  +gg+v +l 
  gi|344210062|ref|YP_004786238.1| 31 FFGLLGPNGAGKTTTMEILTGQLSPDGGQVSVLG 64
                                      55688******************99998888775 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.1
                            AAA_30  88 pgtllivDE 96 
                                       +  ++ +DE
  gi|344210062|ref|YP_004786238.1| 152 EPAVVFIDE 160
                                       334555555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.5
                            AAA_30  41 aweaaggrviglAptgkaAkvLaeelg 67 
                                        ++++g ++++ ++   +A++L   +g
  gi|344210062|ref|YP_004786238.1| 179 SYRDDGNTIVVTTHDVDVAAELCSRVG 205
                                       566677888888888888888777666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.6e-05     0.028      25     149 ..      30     199 ..      21     241 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggif.lrgkcdql.esa..............ipysalaqalareellrql 85 
                                       e   l G+ G GK++ ++ l  +l+ dgg + + g      ++a               ++ +  +++++ + +r++
  gi|344210062|ref|YP_004786238.1|  30 EFFGLLGPNGAGKTTTMEILTGQLSPDGGQVsVLGVDPATqPTAvreragilpekespPSFMTPREYFDFVGAIRDM 106
                                       566699*********************87775333222222111344446666666653334466889999999999 PP

                            AAA_16  86 ldeaesaeleawrekleeala.................................avpelagaeasrllellkrllal 129
                                        d+a + + e w+++l  + +                                 + ++l++     + e +kr+l+ 
  gi|344210062|ref|YP_004786238.1| 107 PDDAVTEQTESWADRLGFTEKldtlssdlsrgqqqkvmiagaffhepavvfidePLANLDP----IVQERVKRFLRS 179
                                       9998888888888877665556676667776666666666666666666655555555555....488888888888 PP

                            AAA_16 130 lsrderplvlvlDdlqwade 149
                                       ++ d+ ++v++  d++ a e
  gi|344210062|ref|YP_004786238.1| 180 YRDDGNTIVVTTHDVDVAAE 199
                                       88888888888888886654 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 ?    9.7   0.1    0.0011       1.1       3      23 ..      34      54 ..      32      87 .. 0.85
   2 ?    3.2   0.0       0.1   1.1e+02      50      66 ..     145     160 ..     105     206 .. 0.71
   3 ?   -2.1   0.0       4.5   4.8e+03      62      73 ..     230     241 ..     223     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                                      EESSTTSSHHHHHHHHHHHHT CS
                               AAA  3 lyGppGtGKTllakavakelg 23
                                      l Gp G GKT++++ +  +l+
  gi|344210062|ref|YP_004786238.1| 34 LLGPNGAGKTTTMEILTGQLS 54
                                      78************9999885 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.1
                                       HHHHHHTSTSEEEEEET CS
                               AAA  50 fkeakekakpsilfiDE 66 
                                       ++ a  + +p ++fiDE
  gi|344210062|ref|YP_004786238.1| 145 IAGAFFH-EPAVVFIDE 160
                                       3334445.499*****9 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.5
                                       EEEETGGGHHHH CS
                               AAA  62 lfiDEidalaks 73 
                                       +f+D++da + +
  gi|344210062|ref|YP_004786238.1| 230 VFLDNVDATVDR 241
                                       79*****98765 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 ?   13.3   0.1     5e-05     0.053       2      37 ..      35      70 ..      34      76 .. 0.94
   2 ?   -2.4   0.0       3.1   3.2e+03      50      73 ..     188     211 ..     164     229 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-05
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNLDPAae 37
                                      +Gp G+GKtt ++ l+  l+  g +v v+  DPA +
  gi|344210062|ref|YP_004786238.1| 35 LGPNGAGKTTTMEILTGQLSPDGGQVSVLGVDPATQ 70
                                      7*********************************87 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.1
                        ATP_bind_1  50 litledvmedlglgpngalvvale 73 
                                       ++t+ dv++ ++l +  ++++  +
  gi|344210062|ref|YP_004786238.1| 188 VVTTHDVDVAAELCSRVGIMYGGD 211
                                       355556666666666666666555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.15       6      38 ..      34      66 ..      30      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      l+G++GaGKTtt+  L  +l+ +g +v +  +D
  gi|344210062|ref|YP_004786238.1| 34 LLGPNGAGKTTTMEILTGQLSPDGGQVSVLGVD 66
                                      79************9999999988888777766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013      0.13      10      67 ..      34      87 ..      27     195 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                            AAA_22 10 vtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralgle 67
                                      + G+ G+GKTt+++ l+ ql     ++  +++v+ v+++ + +    +  +l + +++
  gi|344210062|ref|YP_004786238.1| 34 LLGPNGAGKTTTMEILTGQLS----PDGGQVSVLGVDPATQPTAVRERAGILPEKESP 87
                                      67*****************95....333455555555554444444444444444443 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00017      0.18      30      57 ..      33      60 ..      25      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                                      HHHS--SHHHHHHHHHHHHHHS--TTT- CS
                              MukB 30 tlsGgnGaGksttmaafvtaliPdlsll 57
                                       l G nGaGk+ttm  +   l Pd   +
  gi|344210062|ref|YP_004786238.1| 33 GLLGPNGAGKTTTMEILTGQLSPDGGQV 60
                                      5789*****************9997665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00055      0.58      75     131 ..       4      61 ..       1      66 [. 0.82
   2 ?   -1.8   0.0       2.4   2.5e+03      32      59 ..     170     197 ..     156     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00055
                                       TTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  75 lgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                       +++e l  s  + +++ +l+  ++d ++  l+G+ G+GK+t ++ l+++l+   g+vs
  gi|344210062|ref|YP_004786238.1|   4 IEIESLRKSYGDVTAIPDLSLSIDDgEFFGLLGPNGAGKTTTMEILTGQLSPDGGQVS 61 
                                       566666667777788889999999889999*****************99887777776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHHHTT-EEEEEEE-GGG- CS
                       RsgA_GTPase  32 lnlldrfLvlaeekgiepvivlnKiDll 59 
                                       +++++rfL  + + g ++v+    +D++
  gi|344210062|ref|YP_004786238.1| 170 QERVKRFLRSYRDDGNTIVVTTHDVDVA 197
                                       5677888887777777777666666655 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00031      0.33      10      46 ..      12      49 ..       5      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                            AAA_27 10 ryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAi 46
                                       yG +t    l++s ++ ++  ++GpN AGK+t+++ +
  gi|344210062|ref|YP_004786238.1| 12 SYGDVTAIpDLSLSIDDGEFFGLLGPNGAGKTTTMEIL 49
                                      57777764367777778999999***********9865 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    0.0097        10      23      38 ..      36      51 ..      33      63 .. 0.86
   2 ?    3.2   0.0     0.025        27     525     574 ..     151     197 ..     142     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0097
                            AAA_13 23 GwNGaGKTtLSrllrs 38
                                      G NGaGKTt  ++l  
  gi|344210062|ref|YP_004786238.1| 36 GPNGAGKTTTMEILTG 51
                                      99*******9998875 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.025
                            AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleff 574
                                        +  +v+iD P   LD  ++  v  +++s+    ++ + + + TH ++  
  gi|344210062|ref|YP_004786238.1| 151 HEPAVVFIDEPLANLDPIVQERVKRFLRSYR---DDGNTIVVTTHDVDVA 197
                                       5788**************************7...99999******99865 PP

>> LSPR  Coagulation Factor V LSPD Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.1   1.1e+03       1       7 [.      23      29 ..      23      30 .. 0.86
   2 ?    3.5   0.0     0.088        93       2       9 .]      53      60 ..      53      60 .. 0.89
   3 ?    5.1   0.2     0.026        27       1       7 [.     130     136 ..     130     137 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.1
                              LSPR  1 tLSPDLs 7 
                                      +LS D +
  gi|344210062|ref|YP_004786238.1| 23 SLSIDDG 29
                                      8****87 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.088
                              LSPR  2 LSPDLsQT 9 
                                      LSPD +Q+
  gi|344210062|ref|YP_004786238.1| 53 LSPDGGQV 60
                                      9***9996 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.026
                              LSPR   1 tLSPDLs 7  
                                       tLS+DLs
  gi|344210062|ref|YP_004786238.1| 130 TLSSDLS 136
                                       9*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); 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 0.35s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1428.10
//
Query:       gi|344210063|ref|YP_004786239.1|  [L=469]
Description: hypothetical protein HAH_5122 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); 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):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2782.61
//
Query:       gi|344210064|ref|YP_004786240.1|  [L=77]
Description: hypothetical protein HAH_5123 [Haloarcula hispanica ATCC 33960]
Scores for 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-24   83.7   0.2    6.6e-24   83.6   0.2    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 !   83.6   0.2   3.7e-28   6.6e-24       2      68 ..       6      74 ..       5      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 3.7e-28
                           DUF2249  2 lDvRelppperhaaIfeafeaLapGetlelvndhdPkpLlyqLearr..pgffsweylergpgewrvli 68
                                      lD+Re+ppp+rh++If+afe+L++Ge+l++vndh+P+pL++q++a+r  +++  +++ + gp+e+ +++
  gi|344210064|ref|YP_004786240.1|  6 LDLREIPPPKRHPKIFDAFEELDSGEALTIVNDHKPTPLYHQMAAERqsFDAEGYTVDRIGPNEFIATL 74
                                      9**********************************************9967779*********998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 516.26
//
Query:       gi|344210065|ref|YP_004786241.1|  [L=277]
Description: hypothetical protein HAH_5124 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); 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:                         0  (0); expected 0.2 (1e-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 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1795.52
//
Query:       gi|344210066|ref|YP_004786242.1|  [L=183]
Description: hypothetical protein HAH_5125 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   0.0        1.7    8.5   0.0    2.3  2  DUF2378   Protein of unknown function (DUF2378)


Domain annotation for each model (and alignments):
>> DUF2378  Protein of unknown function (DUF2378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   9.3e-05       1.7      22      63 ..      35      75 ..      13      82 .. 0.74
   2 ?    4.7   0.0    0.0014        25     115     165 ..     116     165 ..     100     183 .] 0.70

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 9.3e-05
                           DUF2378 22 eelaerlraagldldrplfsaYPlevflrllrvaarelapql 63
                                      e++  +l a g+  d    + YP + +l+++++ a++l+p++
  gi|344210066|ref|YP_004786242.1| 35 ERALTALDAEGI-TDPAADEWYPQQAWLNAFETIADDLQPHV 75
                                      555556666665.44455789*******************98 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0014
                           DUF2378 115 ygerrleelgpksvrlavkrdlmppefheGvleaaleavgakgprveveer 165
                                        g+ r+e++g++++++++++ +    f +G+++++ +++   g+ v +ee+
  gi|344210066|ref|YP_004786242.1| 116 IGHYRFESVGERTGEVTCENPYP-CPFDRGLIRGVAQQYAPVGAFVFIEET 165
                                       5788999***********99876.889999999998886555555544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 1500.98
//
Query:       gi|344210067|ref|YP_004786243.1|  [L=167]
Description: transcription regulator [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-06   27.5   0.7    5.4e-06   26.2   0.0    2.0  2  MarR_2        MarR family
    5.4e-06   26.1   0.0    1.2e-05   25.0   0.0    1.6  1  HTH_IclR      IclR helix-turn-helix domain
    6.7e-05   22.6   2.9    0.00033   20.3   0.0    2.7  3  RP-C          Replication protein C N-terminal domain
    0.00013   21.8   0.0    0.00029   20.7   0.0    1.6  1  MarR          MarR family
     0.0003   20.6   0.0     0.0006   19.6   0.0    1.5  1  TrmB          Sugar-specific transcriptional regulator TrmB
    0.00033   21.1   0.1     0.0018   18.7   0.0    2.1  2  HTH_27        Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.011   15.4   1.1      0.036   13.7   0.0    2.4  3  GntR          Bacterial regulatory proteins, gntR family
       0.02   14.8   0.0      0.045   13.6   0.0    1.6  1  HTH_5         Bacterial regulatory protein, arsR family
      0.024   15.0   0.0       0.05   14.0   0.0    1.5  1  Rrf2          Transcriptional regulator
       0.12   12.8   4.0       0.19   12.2   4.0    1.3  1  DUF1690       Protein of Unknown function (DUF1690)
       0.95   10.1   6.7       0.78   10.3   4.3    2.1  2  Syntaxin-6_N  Syntaxin 6, N-terminal


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 !   26.2   0.0   3.3e-09   5.4e-06      17      62 .]      41      84 ..      24      84 .. 0.80
   2 ?   -1.4   0.1       1.4   2.3e+03      36      49 ..     110     123 ..     103     136 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.3e-09
                                      TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSSS CS
                            MarR_2 17 rpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkRa 62
                                      +++  l++ el++++g+ ks+vs++ + L++ GL+ rr++ + +R+
  gi|344210067|ref|YP_004786243.1| 41 SDP--LSIPELVEETGYAKSTVSNVTRTLSRIGLIHRRSSAGGGRR 84
                                      344..9********************************99999886 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHTT CS
                            MarR_2  36 savsrilkrLvaaG 49 
                                       +++ r+++r++++ 
  gi|344210067|ref|YP_004786243.1| 110 QTTLRTIRRAEEQV 123
                                       55667777777764 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 !   25.0   0.0   7.4e-09   1.2e-05      17      50 ..      42      75 ..      36      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 7.4e-09
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                       +l++ el ++tg +kStv++ ++tL + G++ +
  gi|344210067|ref|YP_004786243.1| 42 DPLSIPELVEETGYAKSTVSNVTRTLSRIGLIHR 75
                                      6899***************************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 ?   -1.3   0.0      0.88   1.4e+03      23      48 ..       7      32 ..       2      42 .. 0.76
   2 !   20.3   0.0   2.1e-07   0.00033      76     118 ..      48      90 ..      44      94 .. 0.90
   3 ?    0.4   1.5      0.27   4.4e+02     139     158 ..     116     135 ..     103     161 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.88
                              RP-C 23 gvdkwqllralkeakaalgvsdrala 48
                                      +v + ++++++++ +++ g+s+ a +
  gi|344210067|ref|YP_004786243.1|  7 AVARERVIESMEQSAEVYGLSRSAGR 32
                                      38888999999999999999887655 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 2.1e-07
                              RP-C  76 qLsralglsestlrrhlaaLveaGliirrDspngkRyarrdre 118
                                       +L +++g ++st++++ + L   Gli+rr s+ g R +r + e
  gi|344210067|ref|YP_004786243.1|  48 ELVEETGYAKSTVSNVTRTLSRIGLIHRRSSAGGGRRVRFEAE 90 
                                       6899******************************999986655 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.27
                              RP-C 139 lealaeevraerralrrlre 158
                                       ++++ e+v ae r+++r+r+
  gi|344210067|ref|YP_004786243.1| 116 IRRAEEQVSAETREQERVRN 135
                                       34444444444444444333 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   1.8e-07   0.00029      15      58 ..      41      84 ..      39      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.8e-07
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                      ++pls+ eL +  g  kstv++v+++L + Gli+R+ s +  R 
  gi|344210067|ref|YP_004786243.1| 41 SDPLSIPELVEETGYAKSTVSNVTRTLSRIGLIHRRSSAGGGRR 84
                                      5789999*****************************99876665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.7e-07    0.0006       3      57 ..      23      78 ..      21      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.7e-07
                                      HCHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB  3 klGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      ++GLs    ++Y +L  +++p+++ e+ ee+g  +s+v +v r L++ Gl++r+ +
  gi|344210067|ref|YP_004786243.1| 23 VYGLSRSAGRIYGVLYfASDPLSIPELVEETGYAKSTVSNVTRTLSRIGLIHRRSS 78
                                      799999999******99***********************************9976 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 !   18.7   0.0   1.1e-06    0.0018      17      63 ..      42      88 ..      36      89 .. 0.89
   2 ?   -0.4   0.1       1.1   1.7e+03       5      18 ..     108     122 ..     106     140 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                            HTH_27 17 rrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvr 63
                                      ++ ++ +l++ + + +s++s++ + L + GL++r  ++  +r++r++
  gi|344210067|ref|YP_004786243.1| 42 DPLSIPELVEETGYAKSTVSNVTRTLSRIGLIHRRSSAGGGRRVRFE 88
                                      6778899*******************************888888775 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                            HTH_27   5 qalv.Lhlirhrrrr 18 
                                       ++++ L++ir+ +++
  gi|344210067|ref|YP_004786243.1| 108 EVQTtLRTIRRAEEQ 122
                                       566669999933333 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.2e-05     0.036      21      61 ..      41      80 ..      32      82 .. 0.91
   2 ?   -3.0   0.1       3.7     6e+03      36      44 ..     111     119 ..     105     126 .. 0.64
   3 ?   -1.2   0.1         1   1.7e+03      37      46 ..     154     163 ..     141     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                                      TSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCE CS
                              GntR 21 GdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrG 61
                                       d+L s  eL++e g  ++tv  + r+L++ gl++rr+  G
  gi|344210067|ref|YP_004786243.1| 41 SDPL-SIPELVEETGYAKSTVSNVTRTLSRIGLIHRRSSAG 80
                                      5889.999****************************98665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.7
                                       S-HHHHHHH CS
                              GntR  36 VsrttvReA 44 
                                       ++  t+R+A
  gi|344210067|ref|YP_004786243.1| 111 TTLRTIRRA 119
                                       455677777 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1
                                       -HHHHHHHHH CS
                              GntR  37 srttvReALr 46 
                                       s+  +ReAL 
  gi|344210067|ref|YP_004786243.1| 154 SAAELREALE 163
                                       5666788875 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     0.045       9      34 ..      37      62 ..      31      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                                      HHHTTSSEEHHHHHHHHTS-HHHHHH CS
                             HTH_5  9 klLaegelcvcelaeelglsqstvSh 34
                                       + a+ +l++ el+ee+g  +stvS 
  gi|344210067|ref|YP_004786243.1| 37 LYFASDPLSIPELVEETGYAKSTVSN 62
                                      678999*******************7 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.1e-05      0.05      24      67 ..      42      85 ..      30      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.1e-05
                                      C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEE CS
                              Rrf2 24 epvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrL 67
                                       p+s+ e+ e+++  +s ++ ++++L++ gl++ +  +gGG r 
  gi|344210067|ref|YP_004786243.1| 42 DPLSIPELVEETGYAKSTVSNVTRTLSRIGLIHRRSSAGGGRRV 85
                                      579*********************************99999765 PP

>> DUF1690  Protein of Unknown function (DUF1690)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   4.0   0.00011      0.19      27      94 ..      97     164 ..      86     167 .] 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                           DUF1690  27 raqalekliqerVaeeLkkLraeeeetlkkfeeklekellkdeadakdelsskalnekieeLrkklee 94 
                                        +    ++iq+ V+  L+ +r++ee++ ++  e+    +l ++ ++ +e+ + a +   +eLr+ le 
  gi|344210067|ref|YP_004786243.1|  97 LQDVFQQYIQREVQTTLRTIRRAEEQVSAETREQERVRNLRETYEDLEEIVQLASEYSAAELREALES 164
                                       567789*******************************9999996666666666666666777776665 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 ?   -1.6   0.0       2.5   4.1e+03       6      22 ..       9      25 ..       6      32 .. 0.71
   2 ?   10.3   4.3   0.00048      0.78      18      69 ..      98     152 ..      87     167 .] 0.78

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.5
                      Syntaxin-6_N  6 vkeeVqkslnkaeslyr 22
                                      ++e V +s+++ +++y+
  gi|344210067|ref|YP_004786243.1|  9 ARERVIESMEQSAEVYG 25
                                      67777777777777665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00048
                      Syntaxin-6_N  18 eslyrrw..erlledtss.stseeldetrteLrkalrsiewdledLeetvrivek 69 
                                       + +++++  ++++++ ++ ++ ee  +++t  ++ +r+++++ edLee v+ +++
  gi|344210067|ref|YP_004786243.1|  98 QDVFQQYiqREVQTTLRTiRRAEEQVSAETREQERVRNLRETYEDLEEIVQLASE 152
                                       56677776446677777777899999999999******************87654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1879  (0.104802); expected 358.6 (0.02)
Passed bias filter:                      964  (0.0537676); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); 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 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1052.06
//
Query:       gi|344210068|ref|YP_004786244.1|  [L=117]
Description: DNA binding domain-containing protein [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-12   45.4   0.3    8.1e-12   45.0   0.3    1.2  1  HTH_20          Helix-turn-helix domain
    7.3e-07   29.0   0.1    1.4e-06   28.0   0.1    1.4  1  MarR_2          MarR family
    1.4e-06   28.0   0.0    3.2e-06   26.9   0.0    1.6  2  HTH_5           Bacterial regulatory protein, arsR family
      6e-06   25.7   0.0    1.1e-05   24.9   0.0    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    8.5e-06   26.2   0.0    5.2e-05   23.7   0.0    2.0  2  HTH_27          Winged helix DNA-binding domain
     0.0028   17.9   0.0     0.0034   17.7   0.0    1.1  1  DUF2513         Hypothetical protein (DUF2513)
     0.0048   16.7   0.0     0.0078   16.1   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0095   15.8   0.0      0.017   15.0   0.0    1.4  1  MarR            MarR family
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.15   12.3   0.0    1.2  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
       0.11   12.5   0.0       0.15   12.1   0.0    1.2  1  HTH_45          Winged helix-turn-helix
       0.13   11.8   0.0       0.21   11.1   0.0    1.4  1  Sigma70_r4      Sigma-70, region 4


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.3     5e-15   8.1e-12       2      56 ..      30      83 ..      29      86 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 5e-15
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      +++ +L+++   +il a  r+e++tas++a+++d s +++syHL+ L ea+L+e 
  gi|344210068|ref|YP_004786244.1| 30 DVLQILSSEAAQEILGAV-RNEPRTASDIADAVDRSLQSVSYHLDRLCEADLIEP 83
                                      68999*************.**********************************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   8.8e-10   1.4e-06      10      52 ..      43      82 ..      37      86 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 8.8e-10
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      +L+a++++p+   t++++a++ + s ++vs++l+rL +a L+e
  gi|344210068|ref|YP_004786244.1| 43 ILGAVRNEPR---TASDIADAVDRSLQSVSYHLDRLCEADLIE 82
                                      899**99996...*****************************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 !   26.9   0.0     2e-09   3.2e-06       6      46 ..      42      82 ..      37      82 .. 0.95
   2 ?   -3.7   0.0       7.1   1.2e+04      15      22 ..      94     101 ..      93     103 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2e-09
                                      HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  6 kILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +IL ++++++++++++a++++ s   vS+HL +L ea+L+e
  gi|344210068|ref|YP_004786244.1| 42 EILGAVRNEPRTASDIADAVDRSLQSVSYHLDRLCEADLIE 82
                                      8**************************************96 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.1
                                       SEEHHHHH CS
                             HTH_5  15 elcvcela 22 
                                       e++v  la
  gi|344210068|ref|YP_004786244.1|  94 EMTVYALA 101
                                       67887776 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 !   24.9   0.0   6.7e-09   1.1e-05       8      48 .]      43      82 ..      37      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 6.7e-09
                            HTH_24  8 ILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      IL +++ +pr + +++A++++ S++ v+++l+rL+e+ lI+
  gi|344210068|ref|YP_004786244.1| 43 ILGAVRNEPR-TASDIADAVDRSLQSVSYHLDRLCEADLIE 82
                                      5555555555.789*************************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 !   23.7   0.0   3.2e-08   5.2e-05       9      49 ..      44      82 ..      37      97 .. 0.88
   2 ?    0.7   0.0      0.48   7.8e+02      40      57 ..      98     115 ..      86     117 .] 0.84

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.2e-08
                            HTH_27  9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLve 49
                                      L  +r  +++ +++d++++++++ +++sy l++L+e++L+e
  gi|344210068|ref|YP_004786244.1| 44 LGAVR--NEPRTASDIADAVDRSLQSVSYHLDRLCEADLIE 82
                                      55566..899999***************************4 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.48
                            HTH_27  40 kkLtekGLvertgdeadr 57 
                                        +L    Lv++ gd +dr
  gi|344210068|ref|YP_004786244.1|  98 YALATERLVVQFGDSTDR 115
                                       57888999*9****9998 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.1e-06    0.0034      32      76 ..      55     102 ..      31     108 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-06
                           DUF2513  32 s...aidgyskeeiiyhlkllaeagLieaekkkakssiislvvkrLtw 76 
                                       s   ++ ++s ++++yhl  l+ea+Lie ++++++++ ++++v+ L +
  gi|344210068|ref|YP_004786244.1|  55 SdiaDAVDRSLQSVSYHLDRLCEADLIEPAETWYSEKGTEMTVYALAT 102
                                       2233455677889***********************977777776654 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.8e-06    0.0078      18      55 ..      47      84 ..      41     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.8e-06
                                      HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      ++++p ta++ia +++++ ++v   L +L +++l+e  
  gi|344210068|ref|YP_004786244.1| 47 VRNEPRTASDIADAVDRSLQSVSYHLDRLCEADLIEPA 84
                                      689********************************976 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   1.1e-05     0.017      16      48 ..      50      82 ..      47      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlie 48
                                      +p + s++a+++  s  +v+  ldrL +++lie
  gi|344210068|ref|YP_004786244.1| 50 EPRTASDIADAVDRSLQSVSYHLDRLCEADLIE 82
                                      677899*************************97 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   8.9e-05      0.15      12      58 ..      45      91 ..      40     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.9e-05
                    B-block_TFIIIC 12 assRysGitqsdLakeskqdprslfyrlksLekkgLIvkqsiidsat 58
                                      ++ R +  t sd+a +++ +  s+ y+l+ L++  LI+  ++  s++
  gi|344210068|ref|YP_004786244.1| 45 GAVRNEPRTASDIADAVDRSLQSVSYHLDRLCEADLIEPAETWYSEK 91
                                      5666666789***************************9777655555 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   9.2e-05      0.15       8      64 ..      40      94 ..      33     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.2e-05
                            HTH_45  8 iadILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGle 64
                                        +IL a++++  + + i  +++ s + ++  Ld L e +li+  ++ Y+  ekG e
  gi|344210068|ref|YP_004786244.1| 40 AQEILGAVRNEPRTASDIADAVDRSLQSVSYHLDRLCEADLIEPAETWYS--EKGTE 94
                                      579***************************************99999986..66665 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   0.00013      0.21       7      43 ..      38      74 ..      32      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                                      HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4  7 ererevlelrfgeglTleEIgerlgiSrerVrqiekr 43
                                      e  +e+l  ++ e++T ++I++  + S+  V+ ++ r
  gi|344210068|ref|YP_004786244.1| 38 EAAQEILGAVRNEPRTASDIADAVDRSLQSVSYHLDR 74
                                      66799************************99977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 791.77
//
Query:       gi|344210069|ref|YP_004786245.1|  [L=294]
Description: fructosamine kinase [Haloarcula hispanica ATCC 33960]
Scores for complete 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  141.0   0.0    5.5e-41  140.7   0.0    1.0  1  Fructosamin_kin  Fructosamine kinase
    1.3e-14   54.7   5.1    1.7e-14   54.3   5.1    1.1  1  APH              Phosphotransferase enzyme family
     0.0023   17.4   0.0     0.0049   16.3   0.0    1.5  1  APH_6_hur        Aminoglycoside/hydroxyurea antibiotic resist


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 !  140.7   0.0   9.2e-45   5.5e-41       9     283 ..      21     290 ..      12     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 140.7 bits;  conditional E-value: 9.2e-45
                   Fructosamin_kin   9 lsealgkafeiteaekveggeineaylls.eeeqrfFvklnekealemFeaEaesLealaetqtirvPkvlavGelk 84 
                                       +s++l +  + ++a+ + gge+ + y+++ ++  ++ vk++++        Ea+ L+ l + +++ vP+vl+v +  
  gi|344210069|ref|YP_004786245.1|  21 VSSVLDA--DAQSATALDGGEVGSVYRVTfRDRPDVAVKVDDSP----LGIEAAMLQYLDRDTPLPVPDVLHVEP-- 89 
                                       4444444..4889999***********9967777999***9875....578********************9865.. PP

                   Fructosamin_kin  85 dasfLvleyLelk.lekkesaaelgqqLaklHraseqkefGfdvdntigktpqpNewqssWaeFfaeqRlgvqlela 160
                                         + Lvl ++  + + ++++  +l++++a+lH   +++ fGf++d++ g  +q N w++sW++Ff+e+Rl+   + a
  gi|344210069|ref|YP_004786245.1|  90 --ELLVLSFVRGDgRFGERAERDLARHVASLHD-VSADAFGFPFDTLSGPFSQSNPWTESWIDFFRERRLLPFARTA 163
                                       ..68*******998888999*************.78999************************************** PP

                   Fructosamin_kin 161 kekgle....fakieelvervaellskhqpkpsllHGdLWsgNaaltkdgepvifdPaayygdrEvdlamtelfggf 233
                                       ++ g      f+++++l e+++++l  +  +psllHGd+  gN+ + +     ++dPa y+g+ Evdla ++  + +
  gi|344210069|ref|YP_004786245.1| 164 RDAGALpateFDRVQRLAETLDTRLV-EPATPSLLHGDIHPGNVVVADGTVRAVLDPAIYFGHAEVDLAYVDRLDSI 239
                                       ***99633345555666665555554.35689*************9999999************************* PP

                   Fructosamin_kin 234 psefyegYqsivpldegy.eeRkelYqLYhlLnhlnlFgggylsqaqkliq 283
                                       +++fy+ Y++   ++e y +eR+++Y  +h L  ++ Fg++ l    ++++
  gi|344210069|ref|YP_004786245.1| 240 GAAFYDEYRRHRNISERYfDERRDVYIAFHALENVRFFGDDGLPRLDSALD 290
                                       *************99765489******************987776666665 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   5.1   2.8e-18   1.7e-14       3     229 ..      33     252 ..      31     264 .. 0.75

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 2.8e-18
                                       EEE--.SSCEEEEEEETT-.-EEEEEE-TTS-HHHHHHHHHHHHHHHHTT-.B--B-CTTBS-EEETTEEEEEEE-- CS
                               APH   3 relsggasnrtylvttpag.ryvlrrnpparaaeeirrevallrlLakagv.pvPevlagdtddeeigllfalieyv 77 
                                       ++l gg    +y+vt  ++ ++++++   +     +  e+a+l++L +  + pvP vl+    +     + +++++v
  gi|344210069|ref|YP_004786245.1|  33 TALDGGEVGSVYRVTFRDRpDVAVKVDDSP-----LGIEAAMLQYLDRDTPlPVPDVLH---VEP----ELLVLSFV 97 
                                       678889999999999999659999999999.....99**********66556*******...222....45577777 PP

                                       --EE-SSHHHHHHHHHHHHHHHHHHCCHHCH.-STTTB-....................SHHCHTCCHHHHHHCHHH CS
                               APH  78 pgrsllrklsaaqlpellealgeflaalhqvdpaalpla....................dflaqdlellrqlesata 134
                                        g  +         +++ ++l++  a lh+v+++a +++                    +f++++l +++  ++ + 
  gi|344210069|ref|YP_004786245.1|  98 RGDGRFG-------ERAERDLARHVASLHDVSADAFGFPfdtlsgpfsqsnpwteswidFFRERRLLPFARTARDAG 167
                                       7777777.......6699*************9999999988888888888887777666555555555555555544 PP

                                       CCCGCCTCCHHHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCHHH CS
                               APH 135 rllaselldlleeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavllrs 211
                                       +l+a e++  +    ++++++l+ +l  +  ++llHgD+hpgN++v   dg v++v+D      g++ +Dla++ r 
  gi|344210069|ref|YP_004786245.1| 168 ALPATEFDR-V----QRLAETLDTRLVEPATPSLLHGDIHPGNVVVA--DGTVRAVLDPAI-YFGHAEVDLAYVDRL 236
                                       444444444.3....3366666666666779****************..99999****975.67999*****99955 PP

                                       CSCHCCCHCHHHHHHHHC CS
                               APH 212 wtseldpeflaallraye 229
                                         +  +++f++++ r   
  gi|344210069|ref|YP_004786245.1| 237 --DSIGAAFYDEYRRHRN 252
                                       ..6788888888888766 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 !   16.3   0.0   8.1e-07    0.0049     127     197 ..     159     232 ..     137     254 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.1e-07
                         APH_6_hur 127 freaasdaga....gasrlyveaaaiaaeLleepselrpLHgdlhhenvLagerrgWlaidPkglvGergfdlan 197
                                       f++ a+daga    +  r ++  a   +  l ep    +LHgd+h  nv+ ++     ++dP   +G    dla 
  gi|344210069|ref|YP_004786245.1| 159 FARTARDAGAlpatEFDR-VQRLAETLDTRLVEPATPSLLHGDIHPGNVVVADGTVRAVLDPAIYFGHAEVDLAY 232
                                       444455555555432223.345555555556677777****************99999*****999999988874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1742.71
//
Query:       gi|344210070|ref|YP_004786246.1|  [L=459]
Description: metabolite transport protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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-123  412.2  20.9     3e-123  412.0  20.9    1.0  1  Sugar_tr      Sugar (and other) transporter
    1.4e-42  145.9  77.4    4.5e-33  114.6  42.6    2.0  2  MFS_1         Major Facilitator Superfamily
    1.9e-08   33.2   2.8    1.9e-08   33.2   2.8    2.1  2  TRI12         Fungal trichothecene efflux pump (TRI12)
    0.00077   18.4   0.2    0.00077   18.4   0.2    2.8  3  MFS_1_like    MFS_1 like family
  ------ inclusion threshold ------
      0.021   14.8   0.3      0.021   14.8   0.3    3.6  3  Bac_export_3  Bacterial export proteins, family 3
      0.083   11.3  18.1      0.015   13.7   7.8    2.3  2  MFS_3         Transmembrane secretion effector


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 !  412.0  20.9    1e-126    3e-123       2     450 ..      22     449 ..      21     451 .. 0.95

  Alignments for each domain:
  == domain 1  score: 412.0 bits;  conditional E-value: 1e-126
                                       HHHHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHH CS
                          Sugar_tr   2 alvaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkks 78 
                                         +aal gllfg+dtg+i+++  +++    f +s  ++         g+ivs +++Ga++G+ ++g l+dr+GR+  
  gi|344210070|ref|YP_004786246.1|  22 SALAALNGLLFGFDTGIISGAFLFIQ--DSFVMSPLVE---------GIIVSGAMAGAAAGAAVGGQLADRLGRRRL 87 
                                       5789**********************..7777777775.........8***************************** PP

                                       HHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  79 lliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaa 155
                                       +liaa++f++g++ +a+a+   +v vl++gR++ G+++G+as++ P+yisEiAp+++Rg l+sl+ql++t+Gil+++
  gi|344210070|ref|YP_004786246.1|  88 ILIAAIVFFVGSFTMAVAP---NVPVLVAGRLIDGVAIGFASIVGPLYISEIAPPRIRGGLTSLNQLMVTTGILLSY 161
                                       *******************...******************************************************* PP

                                       HHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHH CS
                          Sugar_tr 156 ifglglnktsnadgwrillglqlvpallllilllflPESPrylvekgkeeeakevlaklrgeedadrelaeekdsle 232
                                       ++++++++ ++   wr++lg  +vpa++l+i++l +PESPr+l+e+g+++ea++vl++      ++ +++ee   +e
  gi|344210070|ref|YP_004786246.1| 162 FVNYAFADAGA---WRWMLGAGMVPAVVLAIGILKMPESPRWLFEHGRKDEARAVLKR-----TRSGSVEEELGDIE 230
                                       ***********...********************************************.....77888888888888 PP

                                       HHHH......HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH..HHHHHHHHHHHHHHHHH CS
                          Sugar_tr 233 aeqeee.kaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsks..llvtiivgvvnfvatfv 306
                                       +++e++ ++ ++ ll  +  r +l++g++l++fqq tGina++yy+pti+e++gl +   +l+t+++g++n+v+t+v
  gi|344210070|ref|YP_004786246.1| 231 ETVETQsETGVRDLLAPWL-RPALVVGLGLAVFQQITGINAVIYYAPTILESTGLGNVasILATVGIGTINVVMTIV 306
                                       8877777788999999966.99************************************99***************** PP

                                       HHHHHHHS-SHHHHHHHHHHHHHHHHHHH...HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTT CS
                          Sugar_tr 307 aiflvdrfGRRtllllGaagmaicfvilg.ivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqs 382
                                       ai+lvdr+GRR+lll+G+ gm + +++lg    l++  +  + +++a++ ++lf+ +fa+g+gpv+w+l+sE++p+s
  gi|344210070|ref|YP_004786246.1| 307 AILLVDRVGRRRLLLVGVGGMVATLAVLGtVFYLPGLGG--GLGVIATISLMLFVSFFAIGLGPVFWLLISEIYPLS 381
                                       *****************************5555556666..9*********************************** PP

                                       THHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCCGG CS
                          Sugar_tr 383 vRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleeiee 450
                                       vR++a+ +++++nw an+l+sl+fp++t+ +g   +f++f+ + +++++fv+  vpetkgrtle ie 
  gi|344210070|ref|YP_004786246.1| 382 VRGSAMGVVTVANWGANLLVSLTFPVLTDGVGTSATFWLFGLCSLVGLVFVYRYVPETKGRTLEAIED 449
                                       *****************************************************************986 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.6  42.6   1.5e-36   4.5e-33       2     343 ..      26     392 ..      25     393 .. 0.82
   2 !   45.3  26.8   1.8e-15   5.5e-12       2     183 ..     258     445 ..     257     456 .. 0.82

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 1.5e-36
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       +l ++l +++ +i++ a+  ++++++ +sp + g+++++ ++gaa+++ ++G l+dr+Grrr++l+++++f++g++ 
  gi|344210070|ref|YP_004786246.1|  26 ALNGLLFGFDTGIISGAFL-FIQDSFVMSPLVEGIIVSGAMAGAAAGAAVGGQLADRLGRRRLILIAAIVFFVGSFT 101
                                       577899************9.******************************************999999999999455 PP

                             MFS_1  79 llfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfy 155
                                       +++a+++++l+++r++ G++ g++  +g  +i++++p++ rg  ++l ++++  G++l + +  ++a+++ Wr++  
  gi|344210070|ref|YP_004786246.1| 102 MAVAPNVPVLVAGRLIDGVAIGFASIVGPLYISEIAPPRIRGGLTSLNQLMVTTGILLSYFVNYAFADAGAWRWMLG 178
                                       55469**********************************************************************99 PP

                             MFS_1 156 ilaivsllafvlfllllpeepperkrkspkeee.........................kgtgpaplvpawkallkdp 207
                                       +  + ++++++     l  ++++r+ +++ ++                          + + +++     + ll++ 
  gi|344210070|ref|YP_004786246.1| 179 AGMVPAVVLAI---GILKMPESPRWLFEHGRKDearavlkrtrsgsveeelgdieetvETQSETG----VRDLLAPW 248
                                       99999999999...999999999999999999889999988888888888777765554444444....44444444 PP

                             MFS_1 208 vlw....illialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrllla 280
                                               l +a++   +g++++ ++ p++  e  gl++ + + l+   ++ +++++ ++a  l+dr+grrr ll++
  gi|344210070|ref|YP_004786246.1| 249 LRPalvvGLGLAVFQQITGINAVIYYAPTI-LESTGLGN-VASILATVGIGTINVVMTIVAILLVDRVGRRRLLLVG 323
                                       2211113344444444667777*******7.*******5.4444445555666678888999999************ PP

                             MFS_1 281 llllllaalglallavt......ssavllll....vlvliGfglgfvfpsllalasdlappeeagtasglfnt 343
                                       +++++++++ l  +                +    ++++++f++    p ++ l+s+ +p + +g+a+g++++
  gi|344210070|ref|YP_004786246.1| 324 VGGMVATLAVLGTVFYLpglgggLGV----IatisLMLFVSFFAIGLGPVFWLLISEIYPLSVRGSAMGVVTV 392
                                       **999988888888888666553222....134457777888777779**********************986 PP

  == domain 2  score: 45.3 bits;  conditional E-value: 1.8e-15
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.ll 77 
                                        la+f  ++++++++  +p ++ e+ g+   +  l++++ +   +v+++++  l+dr+Grrr+ll+g+ +++++ ++
  gi|344210070|ref|YP_004786246.1| 258 GLAVFQQITGINAVIYYAP-TILESTGLGNVASILATVGIGTINVVMTIVAILLVDRVGRRRLLLVGVGGMVATlAV 333
                                       5789999999999999999.999999966665555666677788******************************555 PP

                             MFS_1  78 lll.f......a.....sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllg 141
                                       l++ f      +     +++  +l+v+ +  Glg     p+   li++++p + rg+a+g++++++  + +l  l  
  gi|344210070|ref|YP_004786246.1| 334 LGTvFylpglgGglgviATISlMLFVSFFAIGLG-----PVFWLLISEIYPLSVRGSAMGVVTVANWGANLLVSLTF 405
                                       5558667765514556788888888888888888.....8888899******************************* PP

                             MFS_1 142 gllasslgWravfyilaivsllafvlfllllpeepperkrks 183
                                       ++l++ +g +a+f+++++ sl+++v+++ ++pe  ++ ++ +
  gi|344210070|ref|YP_004786246.1| 406 PVLTDGVGTSATFWLFGLCSLVGLVFVYRYVPE--TKGRTLE 445
                                       ***********************8885555555..5444444 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   2.8   6.3e-12   1.9e-08      89     236 ..      66     214 ..      55     219 .. 0.79
   2 ?    2.0   1.3     0.018        53      57     120 ..     265     328 ..     251     360 .. 0.74

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 6.3e-12
                             TRI12  89 tgqavsilvmgrltdrfgrrpfvilthilglvgaivgctatkfntllaamtllgvaagpag.asplfvgelmsnktk 164
                                        g a    v g+l+dr+grr +++++ i+ +vg+   + a ++  l+a   + gva g a    pl++ e+   + +
  gi|344210070|ref|YP_004786246.1|  66 AGAAAGAAVGGQLADRLGRRRLILIAAIVFFVGSFTMAVAPNVPVLVAGRLIDGVAIGFASiVGPLYISEIAPPRIR 142
                                       5778888999************************************************997358*******988765 PP

                             TRI12 165 flgllivsipvvvtsglspyl.gqrlaiqgswrwifyiyiitsaiavllivvwyyppsfaqlhgkkvrkreel 236
                                         gl  +   +v+t  l  y+    +a  g+wrw++   ++ + +  + i+     p +   hg+k + r  l
  gi|344210070|ref|YP_004786246.1| 143 -GGLTSLNQLMVTTGILLSYFvNYAFADAGAWRWMLGAGMVPAVVLAIGILKMPESPRWLFEHGRKDEARAVL 214
                                       .355555544444444445551678999*******99988877666655665566666667799998887665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.018
                             TRI12  57 yfvlqasasalpnilqdvgqsensslfstlwttg.qavsilvmgrltdrfgrrpfvilthilglv 120
                                          ++a     p il+  g  +  s+++t+     + v  +v   l dr+grr ++++  + g+v
  gi|344210070|ref|YP_004786246.1| 265 ITGINAVIYYAPTILESTGLGNVASILATVGIGTiNVVMTIVAILLVDRVGRRRLLLV-GVGGMV 328
                                       55566667778999*****9999999999865441445556666799******98654.344444 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   2.6e-07   0.00077     239     355 ..      26     150 ..      16     156 .. 0.83
   2 ?   -0.2   0.1      0.11   3.4e+02     239     277 ..     153     192 ..     148     203 .. 0.89
   3 ?   -2.0   5.8      0.42   1.3e+03     264     311 ..     292     345 ..     231     401 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.6e-07
                        MFS_1_like 239 mswgiienF.......lflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrflly 307
                                       +++g++  F       +fl++ ++   s  + G++v   +++      ++ +l ++lG ++l++ia +++++  + +
  gi|344210070|ref|YP_004786246.1|  26 ALNGLLFGFdtgiisgAFLFIqDSFVMSPLVEGIIVSGAMAGAAAGAAVGGQLADRLGRRRLILIAAIVFFVGSFTM 102
                                       45555555555555557777767778888888888888888888888999*************************** PP

                        MFS_1_like 308 aiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqglls 355
                                       a+  n+ +++   ++ g+++g    ++  y+s+iap+++++ + +l +
  gi|344210070|ref|YP_004786246.1| 103 AVAPNVPVLVAGRLIDGVAIGFASIVGPLYISEIAPPRIRGGLTSLNQ 150
                                       ***************************************998877765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.11
                        MFS_1_like 239 mswgiienFlflYL.kelgasntllGslvalgvvaeiplf 277
                                       ++ gi+ +++  Y   + ga + +lG+ ++  vv+ i ++
  gi|344210070|ref|YP_004786246.1| 153 VTTGILLSYFVNYAfADAGAWRWMLGAGMVPAVVLAIGIL 192
                                       7889999******999************999999999887 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.42
                        MFS_1_like 264 slvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaii.......e 311
                                       ++v +g++ ++++ ++a  l++++G ++ll++++  +++++ +++++        
  gi|344210070|ref|YP_004786246.1| 292 ATVGIGTI-NVVMTIVAILLVDRVGRRRLLLVGVGGMVATLAVLGTVfylpglgG 345
                                       33334443.4566677888999999999999999999999988887754443332 PP

>> Bac_export_3  Bacterial export proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.3         1   3.1e+03      51      66 ..      87     102 ..      86     124 .. 0.68
   2 ?   14.8   0.3     7e-06     0.021      16      41 ..     244     269 ..     239     279 .. 0.93
   3 ?   -3.6   0.6       3.8   1.1e+04      12      28 ..     349     365 ..     346     367 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1
                      Bac_export_3  51 llavllvllllgpwml 66 
                                       l+ ++++++++g++ +
  gi|344210070|ref|YP_004786246.1|  87 LILIAAIVFFVGSFTM 102
                                       5666666666666655 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 7e-06
                      Bac_export_3  16 lsaplllvalvvGlvvsifQaaTqIq 41 
                                       l ap l +alvvGl  ++fQ +T I+
  gi|344210070|ref|YP_004786246.1| 244 LLAPWLRPALVVGLGLAVFQQITGIN 269
                                       679*********************98 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.8
                      Bac_export_3  12 lvlllsaplllvalvvG 28 
                                       +++++s+ l +  +++G
  gi|344210070|ref|YP_004786246.1| 349 VIATISLMLFVSFFAIG 365
                                       45555555555555555 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   7.8   4.9e-06     0.015     224     362 ..      26     163 ..       6     222 .. 0.76
   2 ?    3.2   2.6    0.0076        23      59     100 ..     301     343 ..     280     446 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.9e-06
                             MFS_3 224 lvRaalFglsasavlaLLPlvardqldgdalvyGillgalGvGAilgalllsrLRerlsserlvllaavalAlvlls 300
                                        + + lFg+ +  +++   l ++d     +lv Gi++++  +GA +ga++  +L +rl+  rl+l+aa+++ +  ++
  gi|344210070|ref|YP_004786246.1|  26 ALNGLLFGFDTG-IISGAFLFIQDSFVMSPLVEGIIVSGAMAGAAAGAAVGGQLADRLGRRRLILIAAIVFFVGSFT 101
                                       456778887654.5555668889999999************************************************ PP

                             MFS_3 301 lalasslwvavlvlllgGaaWitalstlnvavqlavPrWvvgRalavYltvlaGglaaGsll 362
                                       +a+a+++ v+v   l+ G a   a       +  + P  ++g   ++ + +++ g+ +  ++
  gi|344210070|ref|YP_004786246.1| 102 MAVAPNVPVLVAGRLIDGVAIGFASIVGPLYISEIAPPRIRGGLTSLNQLMVTTGILLSYFV 163
                                       **********9999999987444433333445555666677766677666666666655555 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0076
                             MFS_3  59 fllsilaGalaDnfdrRkvllavqlll.alvsvlltvlaalgl 100
                                       ++++i+a  l D + rR++ll++   + a+ +vl tv+ + gl
  gi|344210070|ref|YP_004786246.1| 301 VVMTIVAILLVDRVGRRRLLLVGVGGMvATLAVLGTVFYLPGL 343
                                       57899****************9886551555666666554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); 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:                         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: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 2805.94
//
Query:       gi|344210071|ref|YP_004786247.1|  [L=156]
Description: universal stress protein UspA-like protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   61.6   0.8    1.4e-16   61.3   0.8    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 !   61.3   0.8   7.9e-21   1.4e-16       4     141 .]      12     154 ..       9     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 7.9e-21
                                       EEEEEE-SSHHHH.HHHHHHHH.HHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH...HHHHH CS
                               Usp   4 rIlVavDgseesk.kAlewAle.lakargaelillhvidprasgavsdadeeaeeeeleleeaeleada...akaaa 75 
                                       ++l+av   ++++   l  A+      ++a++i++hv dp+++ ++ +   e+++e  +  e +++        +++
  gi|344210071|ref|YP_004786247.1|  12 TVLLAVGSRDDARvDTLVDAVTeVTVPTDATVIIAHVFDPDSYREAVEQLLETPDENIDPDELAAQMSVtqeIIDEL 88 
                                       6888885555555545555555355559**************99998888877776555444444333355689999 PP

                                       HCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  76 eaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       ea+ v+++   + g  +e+i+ +a++ +ad ++vG r+rs   ++++GS+++ v+ +apcpV+ Vr
  gi|344210071|ref|YP_004786247.1|  89 EAESVTTVPRATTGTSGEGIVSIAKDVSADRVIVGGRQRSPAGKAIFGSTAQEVMLNAPCPVTFVR 154
                                       99999999999****************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); 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: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 982.05
//
Query:       gi|344210072|ref|YP_004786248.1|  [L=399]
Description: ferrichrome-binding protein [Haloarcula hispanica ATCC 33960]
Scores for 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   68.7   0.0    8.3e-19   68.1   0.0    1.4  1  Peripla_BP_2  Periplasmic binding protein
     0.0019   18.0   0.5     0.0033   17.2   0.5    1.4  1  TAT_signal    TAT (twin-arginine translocation) pathway signa
  ------ inclusion threshold ------
       0.14   12.2   0.1        6.8    6.7   0.0    2.5  2  Sdh5          Flavinator of succinate dehydrogenase


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 !   68.1   0.0   1.4e-22   8.3e-19       4     237 ..      89     355 ..      86     356 .. 0.85

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 1.4e-22
                                       -SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-H.......HHHHHH--SEEEE-GGG...G CS
                      Peripla_BP_2   4 lspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidv.......EklaalkPDlvilskglgltd 73 
                                        + ++ ++l+alG+ d v +++   ++ +  ++++ + v+++ +    +       E+  +++ Dl + ++   lt+
  gi|344210072|ref|YP_004786248.1|  89 FTADYIDMLVALGHGDAVQSIWYRGRYKTLHYEEL-DGVSIDLNALTQLwsdgvskEAFYEMDADLHLIDPHA-LTH 163
                                       57899***************************999.55555555555555555555**********9999999.666 PP

                                       GGHHHHHHHS-EEE----TTS................HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-T CS
                      Peripla_BP_2  74 edeellksgiptvivessntg................eslkeqiralgellgledeaeklvaeidsklaaaksaids 134
                                         +  ++s+   v  +  +++                +sl+e ++ ++e++++++++e++ + + +  + ++++++ 
  gi|344210072|ref|YP_004786248.1| 164 WLKAWEQSDLTEVRENVAPFIgnlvfrrtddwhnyryYSLYEAFEKVAEMVQEQARFEAIRSIHAELAETVQARLPA 240
                                       666666666666666666666666666666777******************************************99 PP

                                       T...-EEEEEEEETTE....EEEE-TTSTTTHHHHTS--EESTTT--...STT-EEE-HHHHHHH--SEEEEEEH.. CS
                      Peripla_BP_2 135 e..kpkpvlvfggade..ggyvvagsnsyigdlldalgieniaaesk...kseyeeisaEqilasdpdvifvsgr.. 202
                                           p ++l+f+g ++   +++ ++ n+  ++ + +lgi++++++ +    s++e+++ E++l+ dpd ++ + +  
  gi|344210072|ref|YP_004786248.1| 241 PeeRPNAALMFAGEEPeaFTPYRISGNGANKEHFQTLGIADAFSDTGiegYSGSESLDYEALLEIDPDSLLLRYHre 317
                                       986777777777777677667778888888999999*************99************************** PP

                                       ...HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-HH CS
                      Peripla_BP_2 203 ...aeadnktgleflkenpllaelpAvkngrVyaldss 237
                                           e++ + +l+++ke+++ ++l Av+n rV++ ++ 
  gi|344210072|ref|YP_004786248.1| 318 gktREEFENSVLAHMKEHEVGSRLRAVQNDRVFRGGPI 355
                                       *********************************99875 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 !   17.2   0.5   5.6e-07    0.0033       3      25 ..      13      35 ..      11      36 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.6e-07
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggcaa 25
                                      +RR   Kg++ +a +++l+gc++
  gi|344210072|ref|YP_004786248.1| 13 TRREVVKGGGTLALGGLLAGCLG 35
                                      8********************97 PP

>> Sdh5  Flavinator of succinate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0011       6.8      22      71 ..     282     330 ..     279     332 .. 0.87
   2 ?    2.6   0.0     0.022   1.3e+02      18      38 ..     364     385 ..     357     393 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0011
                                       THHHHHTTT--HHHHHHHHHHHTS-.-HHHHHHHHT-.---S-HHHHHHHH CS
                              Sdh5  22 rFaekhlatlseeeldaferLLdle.DpdLldwltgrkeepedaelaalle 71 
                                        F ++ ++  s +e  ++e+LL+++ D+ Ll++  +  ++ e++e+ ++l+
  gi|344210072|ref|YP_004786248.1| 282 AFSDTGIEGYSGSESLDYEALLEIDpDSLLLRYHREG-KTREEFEN-SVLA 330
                                       689999999***************9899999999988.99999998.6665 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.022
                                       HTTTTHHHHHTT.T--HHHHHH CS
                              Sdh5  18 llLgrFaekhla.tlseeelda 38 
                                       ++++r+a+++++ t++e++l +
  gi|344210072|ref|YP_004786248.1| 364 FMIERYAKRYFPeTFTEAQLFD 385
                                       799********87899998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 2801.30
//
Query:       gi|344210073|ref|YP_004786249.1|  [L=396]
Description: ABC-type transport system periplasmic substrate-binding protein [Haloarcula hispanica ATCC 33960]
Scores for 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   84.8   0.0    1.1e-23   84.1   0.0    1.3  1  Peripla_BP_2  Periplasmic binding protein
     0.0019   18.0   0.0     0.0031   17.3   0.0    1.4  1  TAT_signal    TAT (twin-arginine translocation) pathway signa
  ------ inclusion threshold ------
      0.073   12.8   0.0       0.13   12.1   0.0    1.4  1  YqgF          Holliday-junction resolvase-like of SPT6


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 !   84.1   0.0   1.8e-27   1.1e-23       5     234 ..      84     346 ..      83     348 .. 0.88

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 1.8e-27
                                       SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT......TS-BSBESSSB-H.HHHHHH--SEEEE-GGG....... CS
                      Peripla_BP_2   5 spsvteillalGatdkvvgvdtttsdpldadklee....aivevgadgeidv.EklaalkPDlvilskgl....... 69 
                                       + +++++ +alG++d ++g+++++++ +  ++++     +  +++a+ e+ + E+  +l+ D+ + ++g+       
  gi|344210073|ref|YP_004786249.1|  84 GGTYADMGVALGQADGLTGIGGADRYYTYVYDELPgvsvDQETIDANPEVRTkEEFYELDSDVHLYDPGMlinwfdw 160
                                       6789***************************9887676644555555555558888888888888888877888887 PP

                                       .....GGGHHHHHHHS-EEE----TTS.....HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT...- CS
                      Peripla_BP_2  70 ..gltdedeellksgiptvivessntg.....eslkeqiralgellgledeaeklvaeidsklaaaksaidse..kp 137
                                         +++de+ e  ++ i  +i++ s +      + l+  ++ ++e++++++++e++ + +d+ +a+++s ++ +   p
  gi|344210073|ref|YP_004786249.1| 161 sqSDVDEIAENVAPFIGNLIFRRSDEWhdyryYTLYQAFEKVAEVFQEQARYEAFKQLHDDYIADLQSQLPPAeeRP 237
                                       9999999999999999999999998889*********************************************9788 PP

                                       EEEEEEEETTE......EEEE-TTSTTTHHHHTS--EESTTT--.....STT-EEE-HHHHHHH--SEEEEEEH... CS
                      Peripla_BP_2 138 kpvlvfggade....ggyvvagsnsyigdlldalgieniaaesk.....kseyeeisaEqilasdpdvifvsgr... 202
                                         +l+f g de    ++y ++ +++ +++  ++lg+ +++a        + +++e + E++l+ dpdvi+v+g+   
  gi|344210073|ref|YP_004786249.1| 238 NVLLTFEGTDEpesfSPYRLNDNGTSKKQ-WRDLGVTDALAGTDienlsTTNRGEYDYETLLSVDPDVILVRGHerk 313
                                       88888888888999666666655555555.566******999999******************************** PP

                                       .HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE CS
                      Peripla_BP_2 203 .aeadnktgleflkenpllaelpAvkngrVyal 234
                                        a++++ t+l+f++ + + ++l+Av+ngrVy+ 
  gi|344210073|ref|YP_004786249.1| 314 sATEFRETVLQFMQDHSVGSQLTAVQNGRVYRG 346
                                       *******************************86 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   0.0   5.1e-07    0.0031       2      25 ..      12      35 ..      11      36 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.1e-07
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                       +RRd +Kg++  a + +l+gc++
  gi|344210073|ref|YP_004786249.1| 12 PTRRDYIKGAGLIAGGSLLAGCSS 35
                                      69********************97 PP

>> YqgF  Holliday-junction resolvase-like of SPT6
   #    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      57     100 ..     295     339 ..     258     343 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.1e-05
                                       HHHHHH--SEEEE--SSTH.HHHHHHHHHHHHHHTTB-TTS-B-- CS
                              YqgF  57 kfllskkPdvigvsGenrd.aqkliedvkevlhekeqdsrlstvg 100
                                       + lls+ Pdvi v G++r+ a  ++e v + ++++ ++s+l++v+
  gi|344210073|ref|YP_004786249.1| 295 ETLLSVDPDVILVRGHERKsATEFRETVLQFMQDHSVGSQLTAVQ 339
                                       46899**********88753889*****************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); 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: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2492.20
//
Query:       gi|344210074|ref|YP_004786250.1|  [L=346]
Description: putative iron transport protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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-11   44.2   0.0    2.3e-11   43.7   0.0    1.1  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 !   43.7   0.0   1.3e-15   2.3e-11       9     234 ..      21     284 ..      18     287 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.3e-15
                                       HHHHHHTT-GGGEEEB-GGG--GGGGGGT.........TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHHH CS
                      Peripla_BP_2   9 teillalGatdkvvgvdtttsdpldadklee.......aivevgadgeidvEklaalkPDlvilskglgltdedeel 78 
                                       +++l+alG  d + +  +  ++ + ++k +        +  ++ +++ ++ Ekl +l+ D+ i+++    ++ +e  
  gi|344210074|ref|YP_004786250.1|  21 VDMLVALGRGDAINAMHAPEYHQSLYQKFLHrlegvsiDWDDLYSSWPPSKEKLYELDSDVHIADPAK--VATAEGW 95 
                                       689999999998888888888888888777788555444466666777777*****************..******* PP

                                       HHHHS-EEE----TTS.....................HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-T CS
                      Peripla_BP_2  79 lksgiptvivessntg.....................eslkeqiralgellgledeaeklvaeidsklaaaksaids 134
                                       ++s  + +  + ++++                     + l e +  +++++ + d++e+l +  +s l+ +++ ++ 
  gi|344210074|ref|YP_004786250.1|  96 DDSSLEEIGSNVGPWFgntlsgthqkppsgwadayeyYTLWEIFGKIAQVFRESDRYEALTSVRESMLQTIRAGLPP 172
                                       **********************************99999999999******************************** PP

                                       T....-EEEEEEEETTE..EEEE-TTSTTTHHHHT.S--EESTTT--......STT-EEE-HHHHHHH--SEEEEEE CS
                      Peripla_BP_2 135 e...kpkpvlvfggadeggyvvagsnsyigdllda.lgieniaaesk......kseyeeisaEqilasdpdvifvsg 201
                                       e      ++++f+++de+++ +  + ++  + +   lg+ +++a+         + +++++ E +l +dpdv++v g
  gi|344210074|ref|YP_004786250.1| 173 EqerPSAAMVLFSTSDEKIWGYKMNHPGYYAAHTRpLGATDALADAVgdeygdDGRNITLDSELLLDADPDVLLVLG 249
                                       *8544444555666666666666666655555666899999988876899*99999********************* PP

                                       H..HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE CS
                      Peripla_BP_2 202 r..aeadnktgleflkenpllaelpAvkngrVyal 234
                                             + + + ++l+ +++l +++Av++gr+ya 
  gi|344210074|ref|YP_004786250.1| 250 PmtGYHNLDDIRSQLADDEVLRKITAVQEGRIYAQ 284
                                       977677889999*********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 2042.58
//
Query:       gi|344210075|ref|YP_004786251.1|  [L=157]
Description: transcription regulator [Haloarcula hispanica ATCC 33960]
Scores for complete 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   46.0   0.2    4.4e-12   45.4   0.2    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
    3.4e-11   42.8   0.9    6.3e-11   41.9   0.9    1.5  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    1.2e-05   25.2   0.0      2e-05   24.4   0.0    1.4  1  HTH_11          HTH domain
    4.1e-05   23.6   0.0     0.0001   22.3   0.0    1.6  1  HTH_20          Helix-turn-helix domain
    0.00016   21.3   0.1      0.005   16.6   0.1    2.2  2  HTH_DeoR        DeoR-like helix-turn-helix domain
    0.00022   21.0   0.0    0.00042   20.1   0.0    1.4  1  MarR_2          MarR family
    0.00026   20.8   0.0    0.00052   19.8   0.0    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
    0.00035   20.3   0.0    0.00063   19.5   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
     0.0005   20.4   0.0     0.0011   19.2   0.0    1.6  1  Rrf2            Transcriptional regulator
     0.0014   18.8   0.0     0.0027   17.9   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0032   17.1   0.0     0.0058   16.3   0.0    1.4  1  Sigma70_r4_2    Sigma-70, region 4
     0.0075   16.7   0.1      0.018   15.5   0.0    1.7  2  HTH_27          Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.017   15.1   0.5      0.064   13.3   0.5    1.9  1  HTH_19          Helix-turn-helix domain
      0.018   15.0   0.1      0.031   14.3   0.1    1.4  1  Put_DNA-bind_N  Putative DNA-binding protein N-terminus
      0.022   14.8   0.0      0.036   14.1   0.0    1.3  1  HTH_Mga         M protein trans-acting positive regulator (MG
      0.051   13.0   0.2       0.11   11.9   0.1    1.7  2  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.078   12.9   0.0       0.23   11.4   0.0    1.7  2  MarR            MarR family
       0.11   12.5   0.1       0.23   11.4   0.0    1.5  2  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.15   12.1   0.0       0.24   11.4   0.0    1.4  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 !   45.4   0.2   4.7e-15   4.4e-12       2      48 .]       7      54 ..       6      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 4.7e-15
                            HTH_24  2 detdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      d+ dr+IL +Lq+++r +s  ++Aer++ S stv++r++ Le++++Ik
  gi|344210075|ref|YP_004786251.1|  7 DDVDRAILYALQEDARnMSSGDIAERTDTSDSTVRKRINHLESSEVIK 54
                                      999********************************************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 !   41.9   0.9   6.7e-14   6.3e-11       1      42 []       6      48 ..       6      48 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 6.7e-14
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaR.isyaeLAervGlSestvlrRvrrLe 42
                                      +D++Dr+IL aLqedaR +s  ++Aer+  S stv++R++ Le
  gi|344210075|ref|YP_004786251.1|  6 IDDVDRAILYALQEDARnMSSGDIAERTDTSDSTVRKRINHLE 48
                                      6**************8879*********************998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.2e-08     2e-05       3      42 ..      11      50 ..      10      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.2e-08
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                                      ++il  L e   ++s+ ++Ae+++ S +tvr++I  Le++
  gi|344210075|ref|YP_004786251.1| 11 RAILYALQEDARNMSSGDIAERTDTSDSTVRKRINHLESS 50
                                      579999*888888************************986 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   1.1e-07    0.0001      10      55 ..       8      54 ..       6      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.1e-07
                                      HHHHHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 10 PvRrrilraL.araegltaselaerldlskntlsyHLrvLeeagLve 55
                                       v r+il aL  +a+ ++ +++aer d+s++t++++++ Le+ + ++
  gi|344210075|ref|YP_004786251.1|  8 DVDRAILYALqEDARNMSSGDIAERTDTSDSTVRKRINHLESSEVIK 54
                                      5779999999999999*************************998886 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   5.3e-06     0.005      12      44 ..      21      53 ..      11      57 .. 0.84
   2 ?    2.5   0.0      0.13   1.2e+02       2      21 ..      83     102 ..      82     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.3e-06
                          HTH_DeoR 12 qgklsveelvellgvSeaTiRRDLneLeeqgll 44
                                       + +s  +++e+ ++S+ T+R+ +n Le + ++
  gi|344210075|ref|YP_004786251.1| 21 ARNMSSGDIAERTDTSDSTVRKRINHLESSEVI 53
                                      56788899********************99886 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                          HTH_DeoR   2 ieqilellkqqgklsveelv 21 
                                        + i + l  +g +sv+elv
  gi|344210075|ref|YP_004786251.1|  83 GDLIPKILDIDGVVSVQELV 102
                                       5668899999********98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   4.5e-07   0.00042       8      51 ..      11      53 ..       6      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.5e-07
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                      + +L+aL    + +++ g++a+r++ s s+v ++++ L++   +
  gi|344210075|ref|YP_004786251.1| 11 RAILYALQEDAR-NMSSGDIAERTDTSDSTVRKRINHLESSEVI 53
                                      679999988885.69************************98776 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   5.5e-07   0.00052       6      43 ..      12      51 ..       8      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.5e-07
                                      HHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                             HTH_5  6 kILklLae..gelcvcelaeelglsqstvShHLkkLreaG 43
                                       IL++L+e  ++++++++ae ++ s stv+   + L+ + 
  gi|344210075|ref|YP_004786251.1| 12 AILYALQEdaRNMSSGDIAERTDTSDSTVRKRINHLESSE 51
                                      6****************************98777776655 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   6.7e-07   0.00063       7      43 ..      12      48 ..      10      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.7e-07
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHH CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLv 43
                                      aiL al e ++ ++  ++A+rt+ + Stv+  ++ L+
  gi|344210075|ref|YP_004786251.1| 12 AILYALQEDARNMSSGDIAERTDTSDSTVRKRINHLE 48
                                      699***************************9999987 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-06    0.0011      18      56 ..      16      54 ..       4      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                                      HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 18 akeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      a++e+ + +ss +iaer+++s+s ++k +++L+ ++++k
  gi|344210075|ref|YP_004786251.1| 16 ALQEDARNMSSGDIAERTDTSDSTVRKRINHLESSEVIK 54
                                      66777777***************************9997 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 !   17.9   0.0   2.8e-06    0.0027      13      50 ..      14      51 ..       2      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-06
                                      HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTT CS
                    Fe_dep_repress 13 IYtlseekkvvktkdlaerLnvspssVsemlkkLekdG 50
                                      +Y l+e+    +  d+aer + s s+V + ++ Le+ +
  gi|344210075|ref|YP_004786251.1| 14 LYALQEDARNMSSGDIAERTDTSDSTVRKRINHLESSE 51
                                      4999******************************9876 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 !   16.3   0.0   6.2e-06    0.0058      26      47 ..      23      44 ..      10      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.2e-06
                                      ---HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 26 glsykEIAellgisegtVksrl 47
                                      ++s  +IAe++++s++tV++r+
  gi|344210075|ref|YP_004786251.1| 23 NMSSGDIAERTDTSDSTVRKRI 44
                                      69999***************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 !   15.5   0.0   1.9e-05     0.018       5      48 ..      10      53 ..       7      67 .. 0.90
   2 ?   -2.6   0.0       8.5   8.1e+03      31      48 ..     116     133 ..     103     141 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-05
                            HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv 48
                                      ++++L  +++  r ++  d+++r++++ds++ + +++L+  +++
  gi|344210075|ref|YP_004786251.1| 10 DRAILYALQEDARNMSSGDIAERTDTSDSTVRKRINHLESSEVI 53
                                      7899*****88999999**********************99888 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.5
                            HTH_27  31 edshisyslkkLtekGLv 48 
                                       +ds i  +  +L  +GL 
  gi|344210075|ref|YP_004786251.1| 116 SDSDITPVAQALLDMGLT 133
                                       444444455566666665 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.5   6.8e-05     0.064      11      41 ..      22      54 ..      20     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.8e-05
                            HTH_19 11 lgltqeelaerlgis....rskisaiEngkkdvps 41
                                      ++++  ++aer+++s    r++i+++E  +++v++
  gi|344210075|ref|YP_004786251.1| 22 RNMSSGDIAERTDTSdstvRKRINHLE--SSEVIK 54
                                      8**************************..666665 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 ?   14.3   0.1   3.3e-05     0.031      18      46 ..      15      42 ..      11      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.3e-05
                                      HHHHHTT--EE-HHHHHHHCTS-HHHHHH CS
                    Put_DNA-bind_N 18 eelkeegveriSSteLaealgvtaaqvRK 46
                                       +l+e +  + SS ++ae+++ ++++vRK
  gi|344210075|ref|YP_004786251.1| 15 YALQE-DARNMSSGDIAERTDTSDSTVRK 42
                                      45555.5899******************9 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 ?   14.1   0.0   3.8e-05     0.036      11      45 ..      14      48 ..       9      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.8e-05
                           HTH_Mga 11 lelLteneksltldelakeLglseltlqsdiseLn 45
                                      l +L e ++ ++  ++a+++++s +t++++i++L 
  gi|344210075|ref|YP_004786251.1| 14 LYALQEDARNMSSGDIAERTDTSDSTVRKRINHLE 48
                                      66677779999999*******************96 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 ?   11.9   0.1   0.00012      0.11      19      51 ..      12      47 ..       7      48 .. 0.73
   2 ?   -2.8   0.0       4.8   4.5e+03      20      31 ..     123     135 ..     123     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                      HTH_Tnp_ISL3 19 yilellles.rsvk..avArqlgvSwtTVwrildry 51
                                      +il +l+e+ r+++  ++A+++++S++TV+ +++++
  gi|344210075|ref|YP_004786251.1| 12 AILYALQEDaRNMSsgDIAERTDTSDSTVRKRINHL 47
                                      55555555555555337**************99986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.8
                      HTH_Tnp_ISL3  20 ilellles.rsvk 31 
                                       ++++ll++  +v+
  gi|344210075|ref|YP_004786251.1| 123 VAQALLDMgLTVA 135
                                       6889999988886 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   0.00025      0.23      15      47 ..      21      53 ..      12      59 .. 0.89
   2 ?   -1.7   0.0       3.1   2.9e+03      31      46 ..     117     132 ..     109     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGli 47
                                        ++s  ++a++  +s stv + + +Le  + i
  gi|344210075|ref|YP_004786251.1| 21 ARNMSSGDIAERTDTSDSTVRKRINHLESSEVI 53
                                      5689999*********************99887 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHHTTS CS
                              MarR  31 kstvtrvldrLekkGl 46 
                                        s +t v+ +L + Gl
  gi|344210075|ref|YP_004786251.1| 117 DSDITPVAQALLDMGL 132
                                       5678999999999997 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 ?   11.4   0.0   0.00025      0.23      20      52 ..      22      54 ..      10      61 .. 0.85
   2 ?   -3.2   0.0         9   8.5e+03       3      11 ..     123     131 ..     123     143 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglis 52
                                       +++  ++A++  ++ +tv + +++L+   +i+
  gi|344210075|ref|YP_004786251.1| 22 RNMSSGDIAERTDTSDSTVRKRINHLESSEVIK 54
                                      47999*************************998 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9
                                       HHHHHHHHH CS
                         HTH_Crp_2   3 lArfLlrla 11 
                                       +A+ Ll++ 
  gi|344210075|ref|YP_004786251.1| 123 VAQALLDMG 131
                                       678888873 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00025      0.24      28      51 ..      26      49 ..      12      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                            HTH_36 28 qetlakrlglsknTvsraikeLeq 51
                                        ++a+r+  s++Tv++ i+ Le 
  gi|344210075|ref|YP_004786251.1| 26 SGDIAERTDTSDSTVRKRINHLES 49
                                      569*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 926.14
//
Query:       gi|344210076|ref|YP_004786252.1|  [L=495]
Description: NADH-quinone oxidoreductase subunit 5-like protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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  119.2  17.4    1.9e-34  119.2  17.4    2.4  2  Proton_antipo_M  Proton-conducting membrane transporter
    3.1e-07   30.4   0.1    2.6e-06   27.4   0.1    2.7  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 !  119.2  17.4   2.2e-38   1.9e-34       1     226 [.     112     331 ..     112     339 .. 0.94
   2 ?    0.7   5.4     0.027   2.4e+02      77     163 ..     374     455 ..     347     464 .. 0.73

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 2.2e-38
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelgln 77 
                                       a++L+l+   + +++l +  Lig+ + + ++ +A+  +  ++ ++s +L +++ +l++ t  + ++ +  a   +l+
  gi|344210076|ref|YP_004786252.1| 112 ADHLALFGALWLAMGLLMAKLIGIVGGWDQAQAAATVARKYFIASSALLAVALTALWWTTDATTVTGVTAA-ADALG 187
                                       56777777788899999999********99*************************************9999.88899 PP

                   Proton_antipo_M  78 slelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirlllllavssneisqlllil 153
                                        +  l+++ +l++++++ sa++p+h Wl  + + aPtp sal+ A+  v+ag++ll+r+ +++  ++++++  ++++
  gi|344210076|ref|YP_004786252.1| 188 GPVWLVAAGALVLAAMIQSALLPFHGWLLSS-MTAPTPASALMhAG-FVNAGGILLTRFAPVIT-VDPALMLAIVAV 261
                                       999****************************.***********777.*****************.************ PP

                   Proton_antipo_M 154 aiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyer 226
                                       + +s++ g l+  +qtdiK  l+ S+++++G+m++++++ ++    aai+hl++h++ ka  Fl ag+ i ++
  gi|344210076|ref|YP_004786252.1| 262 GGASAIGGKLLKSVQTDIKGKLGCSTVGQMGFMIMQAGL-GFF--GAAITHLILHGFYKAYQFLSAGGQIEHT 331
                                       ***************************************.665..8********************9877665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.027
                   Proton_antipo_M  77 nslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirlllllavssneisqlllil 153
                                         ++ lll+++++++ l  +  +  h+ lp a   + +pv  +  a++  a+v+  +  + l+  +s++ + l l+ 
  gi|344210076|ref|YP_004786252.1| 374 VGSG-LLLTFFVVFTTLHAARSAVQHTSLPTAARYGAVPVVFFP-AIVIYAAVYTGV--SGLMP-VSPATTELTLLH 445
                                       3444.45555555555555666667*******999999998888.99******9988..77777.889999999999 PP

                   Proton_antipo_M 154 aiismllgsl 163
                                       +ii++++ ++
  gi|344210076|ref|YP_004786252.1| 446 GIIAVVFVGI 455
                                       9999888765 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 !   27.4   0.1   2.9e-10   2.6e-06      16      56 ..      58      98 ..      48      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.9e-10
                   Proton_antipo_N 16 fllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfay 56
                                      + +D+l++lm +v tf s +vh YS  Y+a+ + ++ Ffa 
  gi|344210076|ref|YP_004786252.1| 58 VAVDGLTVLMWVVATFFSGIVHSYSRRYLAGSRLKTGFFAT 98
                                      579***************************99999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 2776.33
//
Query:       gi|344210077|ref|YP_004786253.1|  [L=801]
Description: nucleoside-diphosphate-sugar pyrophosphorylase family protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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-264  879.1   0.0   3.1e-264  878.9   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 !  878.9   0.0  1.8e-268  3.1e-264       1     752 []      11     757 ..      11     757 .. 0.96

  Alignments for each domain:
  == domain 1  score: 878.9 bits;  conditional E-value: 1.8e-268
                           DUF2309   1 veeaaevipplwPlktfvahNplhgledlpfeeavaelaklfgarlylseeeyrealaegrideedLeaaeeeleee 77 
                                       +++aa ++ +lwP+++fv+ Npl g+ed+pf+eav ++a+l+g+r+y+s+e++r+al++g+id+e L+a+ +e + e
  gi|344210077|ref|YP_004786253.1|  11 IDTAATTVGSLWPIHSFVTANPLTGFEDQPFSEAVTQAADLLGGRGYPSAETFRAALQHGQIDPEILDAELSEAGYE 87 
                                       67899*****************************************************************6556555 PP

                           DUF2309  78 etlaelldaltged.........ldelvdeqlikllaaflDegqaawslpkrekglyaawrelakhdlslellllke 145
                                       ++++ lld+++  +         ++++vd++l+k+l+ flDeg a+ws+p+re+g+y+a+r +a+hd +++      
  gi|344210077|ref|YP_004786253.1|  88 NDPEVLLDRMATATdasksdsdtATDRVDQVLTKWLSTFLDEGSAHWSMPNREAGFYTAFRGVAEHDSEIP------ 158
                                       5555555555554445566667799**********************************************...... PP

                           DUF2309 146 lrkvlaelpedpeeaiaealeelgipeeeweaylealllalpGWagliryreeqpeaelqgeepaslvdllairLll 222
                                        + ++ +lpe+p++ai+++l+ +    ++w  ++e++l+alpGW+gli++r+++    +q+++p+sl+ +la rL+l
  gi|344210077|ref|YP_004786253.1| 159 DEGIITDLPETPTAAIEAVLAPYP--VSQWVPVFEEQLTALPGWTGLIKQRADD-GGVWQSAYPISLAGYLAARLAL 232
                                       789999**************9988..679************************9.799******************* PP

                           DUF2309 223 eaalleevakeklsleeleaaaaleelaeeergklwleAlErsyreellealaaeseseeaa...erpeaqavfCiD 296
                                         a+ +++a ++         + ++   ++e++ ++l+A+E++yr +l+e++aaes+s +++     p+aq+vfCiD
  gi|344210077|ref|YP_004786253.1| 233 LDAVGADIAPSN---------DSIDPDPAAELAGAFLRAWEATYRGDLVETVAAESQSLADSdksGCPDAQMVFCID 300
                                       *******77655.........589999*****************************998888767778********* PP

                           DUF2309 297 vRseslRRhLEevgpeveTlGfAGFFGvpiayqgldkeeeealcPvlltPkhlvkeeakeeeeaekakrkrrlkaal 373
                                       +Rse +RRh+E++g+ +eT+G+AGFFG+p++yqg+d++ + ++cP++l+P+h+v++++++++++++++r + +++++
  gi|344210077|ref|YP_004786253.1| 301 TRSEIIRRHIEAAGD-YETHGYAGFFGIPMEYQGYDTDVSVNACPPILDPQHHVTDVPTDDDTQASHDRLSGIRETA 376
                                       ***************.************************************************************* PP

                           DUF2309 374 ekllkelkrsllssfllvealGllyalkllaktlaprraarlkeklkakleekeetklkldkeseee......gltl 444
                                       ++++++++ ++++++ +ve++G  y+l+l+a+tl+p+r ++l +++++++ +++e    l +++++       glt+
  gi|344210077|ref|YP_004786253.1| 377 DEIIETVEANAATAYGYVETAGSGYGLALAARTLVPGRVHDLFDAVDDSVPDEHEFCDPLVHHQHTYagdlpvGLTT 453
                                       *******************************************************9999998887669********* PP

                           DUF2309 445 eeqvelveaaLraigLtenfAplVllvGHgSsseNNpheaaldCGACgGrsGgvnARvlAallNdpeVRegLaergi 521
                                       +e+ve++++a++++g+ e+f++lV+++GH+S+++NNp++++ldCGAC+G++Gg+nARvlA+++Nd eVR++L++rg+
  gi|344210077|ref|YP_004786253.1| 454 DEKVEYAATAFDLMGW-ETFSRLVVFTGHASETTNNPYDSSLDCGACAGNPGGPNARVLAKICNDDEVRAALRDRGF 529
                                       ****************.7*********************************************************** PP

                           DUF2309 522 eIPedTvFvaalhnTttDevelfdldllpashrealeklkadleeagelaaaeRarrlesaeakkekaeaeverrae 598
                                       eIPedTvF+a++hnTttDevel+d d +p+sh+++l++l+adl++a+e+aaaeRa+++     ++++  +e+erra+
  gi|344210077|ref|YP_004786253.1| 530 EIPEDTVFLAGEHNTTTDEVELYDSD-VPESHAADLDQLRADLATARENAAAERAESMGA---DTSSGVTETERRAA 602
                                       ***********************765.9******************************86...347899******** PP

                           DUF2309 599 dwsevRPEwglagnaafiigrReltrgldLdgraFLhsYdwrqDpdgklLeniltaplvVaqwInleYYfStvdnev 675
                                       dw+e+RPEwglagna f++g+Relt+++dL+graFLhsYdw++D+dg++Le+ilt+p+vV+qwIn +YYfStvdn+v
  gi|344210077|ref|YP_004786253.1| 603 DWAETRPEWGLAGNAGFVVGPRELTSDVDLGGRAFLHSYDWSTDADGEALEAILTGPMVVTQWINTQYYFSTVDNAV 679
                                       ***************************************************************************** PP

                           DUF2309 676 yGsGsKvlhnvvgriGVmeGnggDLrtGLplQsvhdgdr.eiHePlRLlvvieapreaierilarheavrelvdngW 751
                                       yGsGsKv+hn vg++GV++GnggDL+tGLplQs++++d+ ++H+PlRL++vi+ap ++++ +la+h+++++l+dn+W
  gi|344210077|ref|YP_004786253.1| 680 YGSGSKVTHNPVGNVGVYQGNGGDLMTGLPLQSLMAADDdPYHQPLRLSTVIHAPVDRVNGVLAEHPELADLLDNNW 756
                                       ************************************9999************************************* PP

                           DUF2309 752 l 752
                                       l
  gi|344210077|ref|YP_004786253.1| 757 L 757
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (801 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.34s 00:00:01.09 Elapsed: 00:00:00.53
# Mc/sec: 4562.16
//
Query:       gi|344210078|ref|YP_004786254.1|  [L=342]
Description: alkanal monooxygenase (FMN-linked) [Haloarcula hispanica ATCC 33960]
Scores for 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-33  114.4   2.0    7.7e-33  114.2   2.0    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 !  114.2   2.0   4.3e-37   7.7e-33      13     245 ..      13     250 ..       1     313 [. 0.76

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 4.3e-37
                    Bac_luciferase  13 galgaasaslrylvelaraaEelGfdavwvaehhggpgga...ldaftllaalaaaTerirlgtavtplytrhPavl 86 
                                        + +aa  ++ ++v+ a++aE+lG+ ++wvaehhg+   +     + +ll+ laa+T+ irlg++++ l  ++P+ +
  gi|344210078|ref|YP_004786254.1|  13 NDGTAAD-AYSNTVDAAQQAERLGYSRFWVAEHHGMGN-KlagTTPEVLLGNLAAETDSIRLGSGAVLLNHYSPFKV 87 
                                       4444444.99*************************844.36**99******************************** PP

                    Bac_luciferase  87 AqqaatLdhlsgGRfglglgt..ggpaveerrfGv..dhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalll 159
                                       A+ + +Ld l++GR++ glg+  g ++++ r+ G   + + + +  +E +e++   +++  +d  G+ +s    l +
  gi|344210078|ref|YP_004786254.1|  88 AELFGSLDGLAPGRIDAGLGRanG-SPAVDRALGTdrRVRNPDEDHAEKIEAVVSHLYDSYPD--GHAYS---DLEI 158
                                       *********************844.44455888998999999*********999999776665..44555...3678 PP

                    Bac_luciferase 160 prpgqgpiP.vyvaaaspaglelaarhadglllag.eppeeaaelierlragaaeagrdpa..dirvgisltvivad 232
                                       pr++ +  P  +v ++sp +++la++ +  + +a   +p  a + +e++r   +    + +  +++ ++++  ++a+
  gi|344210078|ref|YP_004786254.1| 159 PRSDAE-TPvPWVLGSSPSSAALAGELGLRYCFAAfIRPGLATRSFEEYRTHFESSELAGGvdEPQGMVAVNAVCAE 234
                                       888666.8989********************99999888888888888888777755544455************** PP

                    Bac_luciferase 233 teeeAraea...rali 245
                                       t++eA + +   +a +
  gi|344210078|ref|YP_004786254.1| 235 TDAEAARLRavaEASF 250
                                       *****99985443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); 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: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 2108.05
//
Query:       gi|344210079|ref|YP_004786255.1|  [L=343]
Description: Zn-dependent oxidoreductase/NADPH2:quinone reductase [Haloarcula hispanica ATCC 33960]
Scores for complete 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  108.6   0.4    2.7e-31  107.7   0.4    1.5  1  ADH_N          Alcohol dehydrogenase GroES-like domain
      2e-28   99.0   0.7    2.9e-28   98.5   0.7    1.2  1  ADH_zinc_N     Zinc-binding dehydrogenase
    3.2e-12   46.4   2.9    4.6e-12   45.9   2.9    1.3  1  Glu_dehyd_C    Glucose dehydrogenase C-terminus
    2.2e-05   25.5   0.5    4.4e-05   24.5   0.5    1.5  1  ADH_zinc_N_2   Zinc-binding dehydrogenase
    0.00064   20.4   2.4     0.0011   19.6   2.4    1.4  1  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
  ------ inclusion threshold ------
      0.041   13.2   0.1      0.073   12.4   0.1    1.4  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,


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 !  107.7   0.4   9.2e-35   2.7e-31       1     107 [.      24     133 ..      24     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 9.2e-35
                                       TTEEEEEEEEEEE-HHHHHHHTTS..TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHT CS
                             ADH_N   1 pgevlikvkaagiCgsDlhilkgg..kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCke 75 
                                       p++vl+ v+ +giCgsD+h++++g   ++ v+ pl+lGHE +Gev+evg++v++ + GdrV++ep ++c +Ca+Ck+
  gi|344210079|ref|YP_004786255.1|  24 PDDVLVAVRDVGICGSDVHYYEHGriGDYVVEDPLVLGHESAGEVVEVGENVTHHEPGDRVALEPGVPCRRCAHCKR 100
                                       689********************989999************************************************ PP

                                       T-GGG-TTBEETTTS.S-SSSBSEEEECGGGEE CS
                             ADH_N  76 geenlCeeakllgvs.ldGgfaeyvvvpekklv 107
                                       g+++lCee +++ +   dG+f+eyv  p+++++
  gi|344210079|ref|YP_004786255.1| 101 GDYHLCEEVTFMATPpHDGAFTEYVSWPADFAY 133
                                       **************99**********9998776 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.5   0.7   9.6e-32   2.9e-28       1     129 [.     175     303 ..     175     304 .. 0.97

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 9.6e-32
                                       HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaal 76 
                                       ++Gl+++++A+a+Ga  vi +d+ +ekl +a++ Gad ++n +e+dl+++++e t+g g+dvv+e++G++ ++++ +
  gi|344210079|ref|YP_004786255.1| 175 PIGLMVLEAARAAGAtDVILTDVVDEKLTFAEERGADLTVNVTETDLDAAVAEYTDGVGADVVVEASGAEPSIKSTI 251
                                       79****************************************888******************************** PP

                                       HCEEEEEEEEECSC.TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                        ADH_zinc_N  77 kllkpgGrlvvvGg.gkgeeefdlrnlllkeksilGsllgslreefkealdlla 129
                                       +++++gG++v+vG+ ++ e ++d+  l+ +e+ + Gs++++  +++ +a+dlla
  gi|344210079|ref|YP_004786255.1| 252 DVVRRGGTVVLVGLaSEAEVPIDVLELIDNEVDVHGSFRYK--NTYDAAVDLLA 303
                                       **************8888888********************..9**99**9987 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 !   45.9   2.9   1.6e-15   4.6e-12       4     209 ..     144     338 ..     141     341 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 1.6e-15
                       Glu_dehyd_C   4 gvLvEPisiveKaielaeasrsafewepesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelG 80 
                                       g L EP+s+   a       r  +  + +++l++GaG++GL+ l + +a   g ++v  +   d  d ++ + ee G
  gi|344210079|ref|YP_004786255.1| 144 GALCEPLSVGIHA------CRRGSVGTGDTVLITGAGPIGLMVLEAARA--AGATDVILT---DVVDEKLTFAEERG 209
                                       6677777775443......34445556789************9877775..566656444...4567789999**** PP

                       Glu_dehyd_C  81 atY.vdsretpvdeipeasee...mdlvvEaTGsakhafeaiealapnGvaaLlGvpedsevevdggelhrelvleN 153
                                       a   v+  et++d   +++++    d+vvEa G+ + +  +i+ ++  G ++L+G+ ++ ev +d+ el ++     
  gi|344210079|ref|YP_004786255.1| 210 ADLtVNVTETDLDAAVAEYTDgvgADVVVEASGAEPSIKSTIDVVRRGGTVVLVGLASEAEVPIDVLELIDN----- 281
                                       9753788999999887776533338****************************************9887654..... PP

                       Glu_dehyd_C 154 ka.lvGsvNanrrhfeaavdtLaalpeslldelvtkvvdldeleeAfed..ddetiKtv 209
                                       ++ + Gs     + ++aavd La  + + ++ ++  + +l+++++Af++  + + +K +
  gi|344210079|ref|YP_004786255.1| 282 EVdVHGSFR-YKNTYDAAVDLLADGEVD-VEGIIDFESELEDIDDAFRRamEPTVVKGM 338
                                       441667765.5688******99887665.699***************851144566655 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 !   24.5   0.5   1.5e-08   4.4e-05       2     123 ..     209     330 ..     208     335 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.5e-08
                                       T-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--.S-EEE-CHHHCTTT-EE CS
                      ADH_zinc_N_2   2 GAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsig.gpplsaallkpakkrkgrsv 73 
                                       GAd  ++ +++d+     + t+g g Dvv+++ g e  ++ +++v++ gG++v +g +    a+++   ++     v
  gi|344210079|ref|YP_004786255.1| 209 GADLTVNVTETDLDaavaEYTDGVGADVVVEASGAEPSIKSTIDVVRRGGTVVLVGlA--SEAEVPIDVLELIDNEV 283
                                       99999999988888889999**************88888*******777***999944..23333333333455556 PP

                                       EE--GGG...-.-HHHHHHHHHHHHHHH..----EEEEEEGGGHHHHHHHHH CS
                      ADH_zinc_N_2  74 kyeflfsmkasaqadileelaalieeGk..lrpvvdrvfpleeaaeAhryle 123
                                       +++  f     + +++ ++ ++l+++G+  ++  +d + +le++ +A+r+ +
  gi|344210079|ref|YP_004786255.1| 284 DVHGSF-----RYKNTYDAAVDLLADGEvdVEGIIDFESELEDIDDAFRRAM 330
                                       666666.....36677999*********555678999999********9865 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 !   19.6   2.4   3.8e-07    0.0011       1      89 [.     172     263 ..     172     285 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.8e-07
                                       --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHH....S-EEEEE-S--HHHH CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrdsllskdrkallasealtldlddliahl....dpdvvVEcasseava 73 
                                       G+G iG  vle+ ++  ++ ++ l  v+d++   +++r a+l+   + +dld+ +a+      +dvvVE+ + e   
  gi|344210079|ref|YP_004786255.1| 172 GAGPIGLMVLEAARAAGAT-DVILTDVVDEKLTFAEERGADLTVNVTETDLDAAVAEYtdgvGADVVVEASGAEPSI 247
                                       99***************98.***********88888999*****************88*9977*******9999999 PP

                                       TTHHHHHHTTEEEE-S CS
                     NAD_binding_3  74 elvlkaLkagkdvvta 89 
                                       +   +++++g  vv +
  gi|344210079|ref|YP_004786255.1| 248 KSTIDVVRRGGTVVLV 263
                                       9999*****9999975 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 ?   12.4   0.1   2.4e-05     0.073      35      77 ..     164     207 ..     155     231 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                                       TTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHHCHHH CS
                      2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkeeeeee 77 
                                       +g tv i G+G IG  v + ++a g+ +vi +d+  +k + +ee
  gi|344210079|ref|YP_004786255.1| 164 TGDTVLITGAGPIGLMVLEAARAAGAtDVILTDVVDEKLTFAEE 207
                                       689*******************9999899999999775553333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 2046.30
//
Query:       gi|344210080|ref|YP_004786256.1|  [L=383]
Description: mandelate racemase/muconate lactonizing family protein [Haloarcula hispanica ATCC 33960]
Scores for 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-62  209.3   0.2    7.3e-62  208.8   0.2    1.2  1  MR_MLE_C  Enolase C-terminal domain-like
    2.1e-21   76.3   0.0    4.4e-21   75.3   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 !  208.8   0.2   8.1e-66   7.3e-62       2     218 ..     129     355 ..     128     357 .. 0.94

  Alignments for each domain:
  == domain 1  score: 208.8 bits;  conditional E-value: 8.1e-66
                                       HHHHHHHHHHHHT-SEEEEETSSS........HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHG CS
                          MR_MLE_C   2 laeearelvaeqgfravKlkvggd........dvaedvervravreavgpgddvdlmvDanqawdlatAirvarele 70 
                                       +a++a+e  +e+g+ra+K++++++         v++ verv+a+r+avg+  d+ + vD++++++ ++A  ++++le
  gi|344210080|ref|YP_004786256.1| 129 VAAAAKE-DRERGYRAFKFNFAREfrpietpnAVDHAVERVAAIRDAVGD--DALVGVDFHGRVSKPMAADLVERLE 202
                                       4566666.6678********9999************************55..66**********************9 PP

                                       GGTESEEESSSSTTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHH CS
                          MR_MLE_C  71 eldllwlEEPvppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalae 146
                                       ++dl+++ +P+ pe+  ++ a +++ + ++pia+gE+ ysr+df++ll +++v i+qpdv++vgGi+e+rkva +ae
  gi|344210080|ref|YP_004786256.1| 203 QFDLMFIDQPLLPEH-DDSFASIAE-RtTVPIATGERFYSRYDFKRLLVDDGVSILQPDVTHVGGISEMRKVASMAE 277
                                       9************76.899*****5.559************************************************ PP

                                       HTT-EEEEBSCSSHHHHHHHHHHHHTTTTBEEEEEEGGGGH......TSGCSBSSSSEEETTEEECTSSSBTSSEB- CS
                          MR_MLE_C 147 afgvpvapHsgsgglglaaslhlaaaipnllileyfldael......leeelleeplevedGrvtvpdgpGlGveld 217
                                       af+v v+pH++ g++++aasl++  +++n+  +e++ld ++      l+    ++++++edG+v+ p+gpGlG++ld
  gi|344210080|ref|YP_004786256.1| 278 AFDVAVVPHCPLGPVAFAASLQVGFCAQNVVLHEQDLDLHDpttsqrLKVLEDPKTFQFEDGYVKRPTGPGLGIDLD 354
                                       **********889************************99999***9999999999********************** PP

                                       H CS
                          MR_MLE_C 218 e 218
                                       e
  gi|344210080|ref|YP_004786256.1| 355 E 355
                                       8 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 !   75.3   0.0   4.9e-25   4.4e-21      29     117 .]      16     108 ..      12     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 4.9e-25
                                       EEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHHHHCSS.....CHHHHHHHHHHH CS
                          MR_MLE_N  29 vlvkietseGvvGigeatsvggraetikaelddhlapllvgkdaanisdlaqllkravlg.....nmsAkaaidmAl 100
                                        l+k+et+eG+vG+ge+   g r et+ a++ + + ++l+g d+ + +  +++l++  +       msA a+id Al
  gi|344210080|ref|YP_004786256.1|  16 LLLKLETDEGIVGWGEPIVQG-RLETVRAAVTELIEAYLLGADPLRTEYHWRKLYQSGYFrggpiLMSALAGIDHAL 91 
                                       689******************.*************************************999*************** PP

                                       HHHHHHHTTSBHHHHTT CS
                          MR_MLE_N 101 wDlkakalnlpladLlG 117
                                       wD+k++  ++p+++LlG
  gi|344210080|ref|YP_004786256.1|  92 WDIKGRHYGAPVHELLG 108
                                       ****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2296.88
//
Query:       gi|344210081|ref|YP_004786257.1|  [L=257]
Description: 3-oxoacyl-ACP reductase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-74  249.0   1.3    4.9e-74  248.8   1.3    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    6.9e-60  201.9   2.8    8.2e-60  201.6   2.8    1.1  1  adh_short        short chain dehydrogenase
    4.1e-14   52.9   0.9    5.7e-14   52.4   0.9    1.2  1  KR               KR domain
     0.0011   19.3   0.1     0.0017   18.6   0.1    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.026   14.0   0.3      0.043   13.3   0.3    1.3  1  KdpD             Osmosensitive K+ channel His kinase sensor d
      0.063   12.7   0.6        0.1   12.1   0.6    1.4  1  Epimerase        NAD dependent epimerase/dehydratase family
      0.088   11.8   0.3       0.12   11.4   0.3    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
       0.14   12.4   2.0       0.33   11.2   1.7    1.7  1  DUF948           Bacterial protein of unknown function (DUF94


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 !  248.8   1.3   2.2e-77   4.9e-74       1     234 []      18     255 ..      18     255 .. 0.95

  Alignments for each domain:
  == domain 1  score: 248.8 bits;  conditional E-value: 2.2e-77
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE- CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnn 76 
                                       Gaa+g+G+++A  l e Ga+v+++d+n e+ +++++el  +++  + e+DVtde++vea+ve+v++++g +D+lvnn
  gi|344210081|ref|YP_004786257.1|  18 GAAQGLGKQMATGLTEMGADVAIADVNIEKaERTAAELDGQTDVVATEVDVTDEASVEAMVEDVTDRLGPIDVLVNN 94 
                                       9*****************************7777777877777778******************************* PP

                                       ----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSB.STTTT.HHHHHHHHHH CS
                      adh_short_C2  77 agiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaerv.vpnyn.aygaaKaale 149
                                       agi+++  +p++ets e+++r+++vnl ++fl+ak++ + ++++g g+ivn+ss+++  v vp+ +  y+++Ka++ 
  gi|344210081|ref|YP_004786257.1|  95 AGIVEN--SPAEETSIESWRRVVSVNLDGVFLCAKHVGQqMLERGeGRIVNVSSMSGFDVnVPQKQaSYNTTKAGVR 169
                                       ******..*******************************7778889*********998776888888********** PP

                                       HHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT.HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SE CS
                      adh_short_C2 150 altrylAvelgpkgiRvNavspgpikTlaasgikg.fdelleelearaplgrlgtpeevaeaalfLasdeasyitGq 225
                                        lt++lAve+g++g+RvNa++pg+++T++++++ + ++e++e + +++p+grlg+pee  e++++Lasd++sy+tG+
  gi|344210081|ref|YP_004786257.1| 170 MLTQSLAVEWGEQGVRVNAIAPGYMRTELVDEVLEeSPEMEETWLENTPMGRLGRPEELKELVVYLASDASSYMTGS 246
                                       *****************************8877654999************************************** PP

                                       EEEESTTGG CS
                      adh_short_C2 226 tlvvDgGlt 234
                                       t+v+DgG+t
  gi|344210081|ref|YP_004786257.1| 247 TVVMDGGYT 255
                                       ********8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.6   2.8   3.7e-63   8.2e-60       2     192 ..      13     204 ..      12     207 .. 0.95

  Alignments for each domain:
  == domain 1  score: 201.6 bits;  conditional E-value: 3.7e-63
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkl 78 
                                       +++vtGa++G+G+++a  l ++Ga+v+++d + ek+e++a+el  + ++++a +vDvtd+++vea+ve++ ++lg++
  gi|344210081|ref|YP_004786257.1|  13 TAIVTGAAQGLGKQMATGLTEMGADVAIADVNIEKAERTAAELDGQ-TDVVATEVDVTDEASVEAMVEDVTDRLGPI 88 
                                       79******************************************95.89**************************** PP

                                       SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGG..TSB-TTBHHHHHHH CS
                         adh_short  79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvag..kvpvagvaaYsAsK 153
                                       dvLvnNAGi +++p++e+s e w+rv++vNl gvfl++++v ++ml++ +GrIvnvsS+ g   +    +a+Y ++K
  gi|344210081|ref|YP_004786257.1|  89 DVLVNNAGIVENSPAEETSIESWRRVVSVNLDGVFLCAKHVGQQMLERGEGRIVNVSSMSGfdVNVPQKQASYNTTK 165
                                       *************************************************************52233457899***** PP

                                       HHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                         adh_short 154 aavagltrslakelaptgirvnavaPGlvdTdmakelre 192
                                       a+v++lt+sla e+ ++g+rvna+aPG+++T+++ e+ e
  gi|344210081|ref|YP_004786257.1| 166 AGVRMLTQSLAVEWGEQGVRVNAIAPGYMRTELVDEVLE 204
                                       *********************************988765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.9   2.6e-17   5.7e-14       3     174 ..      14     190 ..      12     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 2.6e-17
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                        ++tG++ gLG+++a+ l e ga   +         e+++++ ael   +++v + ++Dv+d+++vea++e+++++ 
  gi|344210081|ref|YP_004786257.1|  14 AIVTGAAQGLGKQMATGLTEMGADVAIADVNI----EKAERTAAELDG-QTDVVATEVDVTDEASVEAMVEDVTDRL 85 
                                       69********************9854443333....344456667766.789************************* PP

                                       S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--S....EEEEEEEHHH..HH--TT-HHHH CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesld....ffvlfSSiag..llgsagqanYa 150
                                       +pi   ++ Ag++++++ ee++ e++++v++  ++G+    + + ++ l+     +v +SS++g  +   ++qa+Y 
  gi|344210081|ref|YP_004786257.1|  86 GPIDVLVNNAGIVENSPAEETSIESWRRVVSVNLDGVFLCAKHVGQQMLErgegRIVNVSSMSGfdVNVPQKQASYN 162
                                       ************************************98877777776655222379*******95566678999998 PP

                                       HHHH....HHHHHHHHHHHHHHTEEEEE CS
                                KR 151 aaNa....flDalaeyrrsqglpavsin 174
                                       ++ a       +la ++ +qg ++ +i+
  gi|344210081|ref|YP_004786257.1| 163 TTKAgvrmLTQSLAVEWGEQGVRVNAIA 190
                                       7765222234556666666666666665 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 !   18.6   0.1   7.5e-07    0.0017      25      91 ..      36     109 ..      15     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.5e-07
                                       GEEEEEESSHHHHHHHHCHH.TTTCEEEEE--TTTHHHHHHHHHTTS.......SEEEE-SSGGGHHHHHHHHHH CS
                   Sacchrp_dh_NADP  25 aeitvadrskeklealaaka.lgvrfeaialdaenyeavLaallkeg.......dlvvnlsppissldvlkaCie 91 
                                       a++++ad + ek+e++aa++  ++++ a+++d+ ++++ ++a++++        d++vn ++ +++ +  ++ ie
  gi|344210081|ref|YP_004786257.1|  36 ADVAIADVNIEKAERTAAELdGQTDVVATEVDVTDEAS-VEAMVEDVtdrlgpiDVLVNNAGIVENSPAEETSIE 109
                                       379***************9988999*************.******999999999999999998888776666665 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   1.9e-05     0.043       3      93 ..      11      97 ..      10     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                              KdpD  3 GrlkiflGaapGvGktyamLeeaqelkeegvdvviglvethgrketeallegleviprkeveykgkeleeldldailar 81
                                      G+  i +Gaa+G Gk       a+ l+e g dv i+ v+ ++ ++t+a l+g + +  +ev++++++  e  ++ +  r
  gi|344210081|ref|YP_004786257.1| 11 GETAIVTGAAQGLGKQ-----MATGLTEMGADVAIADVNIEKAERTAAELDGQTDVVATEVDVTDEASVEAMVEDVTDR 84
                                      6778999********5.....58899***************************999999***99999999999999887 PP

                              KdpD 82 k.pevvlvDelah 93
                                        p  vlv + + 
  gi|344210081|ref|YP_004786257.1| 85 LgPIDVLVNNAGI 97
                                      4255577776665 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   0.6   4.5e-05       0.1       2      83 ..      15     107 ..      14     165 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.5e-05
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT.....-SE CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfkeeq.....pda 67 
                                       +VtGa+  +G++++  l e g +v   d + ++ ++ + e l        +e+d+td++++e++++++      +d+
  gi|344210081|ref|YP_004786257.1|  15 IVTGAAQGLGKQMATGLTEMGADVAIADVNIEKAERTAAE-LdgqtdvVATEVDVTDEASVEAMVEDVTdrlgpIDV 90 
                                       8**********************99999996555544433.3589999999********888777664212333788 PP

                                       EEE--S.---HHHHHHS CS
                         Epimerase  68 vihlAa.vggvaassed 83 
                                        ++ A+ v + +a+ ++
  gi|344210081|ref|YP_004786257.1|  91 LVNNAGiVENSPAEETS 107
                                       88888766666665444 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 ?   11.4   0.3   5.1e-05      0.12       1      67 [.      15      81 ..      15     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.1e-05
                         3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk..viegDvtdkdkleealegv 67
                                      +vtG+a  lG+++   L +++   +v ++D+++++  +  ++  + ++    e+Dvtd++++e+ +e+v
  gi|344210081|ref|YP_004786257.1| 15 IVTGAAQGLGKQMATGLTEMG--ADVAIADVNIEKAERTAAELDGQTDvvATEVDVTDEASVEAMVEDV 81
                                      69*******************..5******99998887666655555566889**********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 ?   11.2   1.7   0.00015      0.33      28      81 ..      45      99 ..      40     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                            DUF948 28 ldeaaatieelekqvdpilkevedlla.kvnelledvneklekvdplteavadlg 81
                                      +++a++t +el  q+d + +ev+ + +  v++++edv+++l  +d l+++++ + 
  gi|344210081|ref|YP_004786257.1| 45 IEKAERTAAELDGQTDVVATEVDVTDEaSVEAMVEDVTDRLGPIDVLVNNAGIVE 99
                                      67899******************998625677*****************998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); 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:                         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: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1594.63
//
Query:       gi|344210082|ref|YP_004786258.1|  [L=491]
Description: rhamnulokinase [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-23   82.3   0.0      5e-23   81.9   0.0    1.2  1  FGGY_C    FGGY family of carbohydrate kinases, C-terminal dom
    6.3e-18   65.2   0.0    8.6e-18   64.8   0.0    1.2  1  FGGY_N    FGGY family of carbohydrate kinases, N-terminal dom


Domain annotation for each model (and alignments):
>> 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 !   81.9   0.0   5.6e-27     5e-23       5     198 .]     255     443 ..     251     443 .. 0.87

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 5.6e-27
                            FGGY_C   5 lGTssflllvgtkpvisehglltpvagedgkpeyalegsiavagslvawlldnlglreeirdageveeslaelaaae 81 
                                        G + +l+++ ++pv+   ++ + v      +e ++ gs++ +++++++++ + ++r+++r+age    ++ l +a+
  gi|344210082|ref|YP_004786258.1| 255 TGSWFVLGVERDDPVRTDAAFEQAVS-----NELGVDGSVRLLKNINGFFMLE-ECRKAWREAGEP-LEYETLLSAA 324
                                       678888888*****************.....88***************66666.6**********8.5555566778 PP

                            FGGY_C  82 avadaggvvfvpafsglrapywdpdargti...tglsssttlahiarAaleavalqlrailealekdsgkpldrlav 155
                                        +a+++  +++++   +     +p+   ++   t++  +t+ ++i+r++l ++a +++  l+al++    p++ +++
  gi|344210082|ref|YP_004786258.1| 325 EEAPPRAALVDTDAETFGIDEPMPEQIRAYcrrTDQPVPTGQGSIVRCLLDSLAAKTALELDALAAVVDDPPSHIVL 401
                                       88888888888888777765444544444568999****************************************** PP

                            FGGY_C 156 dGGgskndllmqllAdilgvpVerpktaeatalGaAilAavaa 198
                                        GGg++n+l++qllAd++++pV  +++ eata+G+++ +avaa
  gi|344210082|ref|YP_004786258.1| 402 GGGGVRNELFCQLLADATNRPV-STGPVEATAVGNVLTQAVAA 443
                                       *********************8.5566*************995 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 !   64.8   0.0   9.6e-22   8.6e-18       4     245 .]       5     243 ..       3     243 .. 0.82

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 9.6e-22
                                       EEEEESSEEEEEEEETTS-EEEEEEEE--EB-SST..T--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE- CS
                            FGGY_N   4 glDcGttstkaivldekgkvvasaqaelelsspke..gwaeqdpeeiwqalaeairkvleqagisekqikaIgisgq 78 
                                       ++D+G+++  + + + +    a+++++   ++p e  g+  +d++++ + + + + ++ ++a    +    +gi + 
  gi|344210082|ref|YP_004786258.1|   5 AIDIGASGGTVFLGEVTESSFAVQEVHRFDNRPVErdGRYVWDVDALVDHIGDGLSAADDRA----DGLDTVGIDTW 77 
                                       67777777777765544444444444443333333335555555555555555555555555....77778888888 PP

                                       SS-EEEEETTTEESSEEE-TT--TTHHHHHHHHHTTCHCCHHHHHSS-SS.TTSHHHHHHHHHHHSCCHHCCHCEEE CS
                            FGGY_N  79 reglvllDkndkpLynailwkdrrtaeiveklkeegnekklyektglvls.tgftlsklkWlkenepevfekiekfl 154
                                       + +  ll  +++ L+  +++ d+++ ++ e++ e +++ +l+  tg++ + t +tl  l+ ++e epe++e+++  l
  gi|344210082|ref|YP_004786258.1|  78 GLDFGLL-ADGELLRDPVSYRDPESTATREQVFEAVGKRRLFDATGITNWnTPNTLWQLHTIAEREPERLEETDGLL 153
                                       8887766.678************************************9873679*********************** PP

                                       EHHHHHHHHHCT--EEEHHHHCTTTSEETTTTEE-HHHHHHTT--GGGS-EEE-TCCEEEEEECCCCCCTT.S-EEE CS
                            FGGY_N 155 liddyLiwrLtgqfvtdvtnasesmlfnikklewdeellailgipeelLPklvesseiigelkpelaaklGlkegvp 231
                                       ++ ++L  r+ g+ + +vt as++++++ +++ w   ll+ l +p +lLP+l e+++  g++ + +   l+  +  +
  gi|344210082|ref|YP_004786258.1| 154 MMPQLLSARIGGVPAGEVTIASTTQMVDPEERTWATDLLEELSVPTDLLPPLSEPGQCLGAVDDDVVSGLS-SPPEI 229
                                       *********************************************************************98.66778 PP

                                       EEEEEEHHHHHHHH CS
                            FGGY_N 232 vvggggDqqaaalG 245
                                       v ++ +D++aa+ G
  gi|344210082|ref|YP_004786258.1| 230 VTPASHDTAAAVAG 243
                                       9*********9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); 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: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 2734.27
//
Query:       gi|344210083|ref|YP_004786259.1|  [L=217]
Description: L-fuculose phosphate aldolase [Haloarcula hispanica ATCC 33960]
Scores for 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-50  170.8   0.3    3.5e-50  170.5   0.3    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 !  170.5   0.3   1.9e-54   3.5e-50       3     185 ..      15     188 ..      13     189 .. 0.93

  Alignments for each domain:
  == domain 1  score: 170.5 bits;  conditional E-value: 1.9e-54
                                       HHHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-TTHHHHHH CS
                       Aldolase_II   3 laeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkpssetplHla 79 
                                       ++e +r l + +l++gtgGn+S+r++ e+++ i psg+++ee+++ed+ vv++d g+vveg   + +ps e+p+Hla
  gi|344210083|ref|YP_004786259.1|  15 ICEYGRSLLEDDLTTGTGGNLSARLD-ENHIAISPSGIPYEEIEPEDVPVVRMD-GTVVEG---DVEPSTELPMHLA 86 
                                       8999*********************9.9*************************9.****66...679********** PP

                                       HHHH-TT-SEEEEE--HHHHHHHTCCSTSCHCCSSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHHHS-SEEEE CS
                       Aldolase_II  80 iykarpdaravvHtHspaavalsalagkeglppltqeaaklllgdevpvipyaapgteelgealaealkedakavll 156
                                       +y++rp ++ vvHtHsp+a++++ l  +e +p+ ++       g evpv++y+++ teelgea+++al+e+ +a ll
  gi|344210083|ref|YP_004786259.1|  87 VYRERPAVGGVVHTHSPYATTFASL--GEAIPASHYLLSF--TGTEVPVAEYRTHATEELGEAAVDALGESFNATLL 159
                                       ***********************98..8989866555554..4778***********************8779**** PP

                                       TTTEEEEEESSHHHHHHHHHHHHHHHHHH CS
                       Aldolase_II 157 rnHGlltvGetleeAvalaetleeaaeiq 185
                                       rnHG+lt+ e+l++A++ a ++e++a+i+
  gi|344210083|ref|YP_004786259.1| 160 RNHGVLTADESLDDAYTVALMVEYCARIH 188
                                       **************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1535.46
//
Query:       gi|344210084|ref|YP_004786260.1|  [L=386]
Description: multiple sugar ABC transporter ATP-binding protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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  109.9   0.0    2.5e-31  109.0   0.0    1.5  1  ABC_tran         ABC transporter
    3.1e-13   50.3   0.1    2.8e-12   47.3   0.1    2.6  2  OB_MalK          MalK OB fold domain
    1.3e-10   41.3   0.3      5e-10   39.4   0.1    2.2  1  TOBE_2           TOBE domain
      7e-09   36.1   0.1    2.4e-08   34.4   0.0    2.0  1  CysA_C_terminal  CysA C-terminal regulatory domain
    1.1e-08   35.3   0.0    0.00066   19.6   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00024   20.6   0.3    0.00057   19.4   0.3    1.6  1  SMC_N            RecF/RecN/SMC N terminal domain
    0.00039   20.4   0.0    0.00077   19.4   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
    0.00045   19.9   0.0    0.00098   18.8   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
     0.0027   17.9   0.0      0.017   15.3   0.0    2.2  2  AAA_33           AAA domain
     0.0036   17.1   1.0      0.048   13.4   0.7    2.5  2  Cytidylate_kin   Cytidylate kinase
     0.0041   17.4   0.0      0.013   15.8   0.0    1.8  2  AAA_22           AAA domain
  ------ inclusion threshold ------
       0.01   15.5   0.1      0.018   14.8   0.1    1.5  1  AAA_30           AAA domain
      0.017   14.7   0.1       0.61    9.6   0.0    2.4  2  AAA_25           AAA domain
      0.017   15.5   0.0      0.036   14.5   0.0    1.5  1  AAA_16           AAA ATPase domain
      0.025   15.0   0.1      0.079   13.4   0.1    2.0  1  AAA              ATPase family associated with various cellul
      0.027   15.0   0.0      0.052   14.0   0.0    1.4  1  AAA_23           AAA domain
      0.027   14.8   0.0        0.1   12.9   0.0    2.0  1  TOBE             TOBE domain
      0.046   14.1   0.6        3.4    8.2   0.1    3.2  3  DraK_HK_N        DraK Histidine Kinase N-terminal domain
       0.06   13.6   0.0       0.12   12.6   0.0    1.6  1  AAA_28           AAA domain
      0.064   13.2   0.0       0.15   12.0   0.0    1.6  1  SAM_LFY          Floricaula / Leafy protein SAM domain
      0.076   12.7   0.0       0.14   11.8   0.0    1.5  2  AAA_15           AAA ATPase domain
      0.099   13.2   0.0       0.21   12.2   0.0    1.6  1  AAA_18           AAA domain
       0.11   11.5   0.1       0.49    9.3   0.0    1.8  2  DUF3987          Protein of unknown function (DUF3987)
       0.12   12.5   0.2       0.36   10.9   0.2    2.0  1  MMR_HSR1         50S ribosome-binding GTPase
       0.14   12.6   0.1       0.29   11.5   0.1    1.7  1  RNA_helicase     RNA helicase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.0   0.0   3.5e-34   2.5e-31       2     136 ..      24     166 ..      23     167 .. 0.94

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 3.5e-34
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++vsl+++ ge +++vG++G+GKStL++++agl+++ eG+i++ +k +++  l    + i++++q+  l p++tv+e
  gi|344210084|ref|YP_004786260.1|  24 DDVSLDIRDGEFIVFVGPSGSGKSTLMRIVAGLETQSEGDIRIGDKVVNQ--LGPRARDIAMVFQNYALYPNMTVEE 98 
                                       89******************************************999999..99999******************** PP

                                       H..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n           s +eie+a+++     + d  ++++p +LSgGq+qrval ra++++p+++l+DEp 
  gi|344210084|ref|YP_004786260.1|  99 NmsfglkmstdMSADEIEEAVTSAAEMMDIDMLLDDKPGELSGGQQQRVALGRAIVRDPNVFLMDEPL 166
                                       ******99998777778888888888888999999999*****************************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 !   47.3   0.1   3.8e-15   2.8e-12       1      53 []     240     288 ..     240     288 .. 0.95
   2 ?   -1.0   0.0       4.6   3.3e+03      15      33 ..     334     354 ..     329     369 .. 0.68

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 3.8e-15
                           OB_MalK   1 GSPaMNflpatveedgvlvegggvtlplpeeqklalklyagkevilGiRPEhi 53 
                                       GSP+MNf+++tve +g ++ ++g++++l+e++  + +     e++lGiRPE++
  gi|344210084|ref|YP_004786260.1| 240 GSPSMNFFEGTVE-GG-TLRADGFDFDLTERM--QSAVGSRNELVLGIRPEDM 288
                                       9************.55.7**************..9999999**********96 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.6
                           OB_MalK  15 dg..vlvegggvtlplpeeqk 33 
                                       dg   + eg++v +++p++++
  gi|344210084|ref|YP_004786260.1| 334 DGqrPISEGQHVYVEIPDRDV 354
                                       455677889999999999883 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.1     7e-13     5e-10       1      76 []     281     357 ..     281     357 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 7e-13
                            TOBE_2   1 laiRPEklrlaaagg.anglsGtVedveylGsstryvvelaggql..vvvrqpnadrdsalapGdtVelswdpddav 74 
                                       l+iRPE+++l++++  ++ ++++V+ ve +Gs + ++++  +++    +++  ++  ++++ +G+ V ++++ +d++
  gi|344210084|ref|YP_004786260.1| 281 LGIRPEDMTLHDRANsGHEFEAVVDVVEPMGSISYVYLQARSQSHeqTFIVETDG--QRPISEGQHVYVEIPDRDVH 355
                                       79********94444347*******************998875440033333333..46****************** PP

                            TOBE_2  75 vl 76 
                                       ++
  gi|344210084|ref|YP_004786260.1| 356 LF 357
                                       98 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 !   34.4   0.0   3.4e-11   2.4e-08       1      43 []     245     290 ..     245     290 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 3.4e-11
                   CysA_C_terminal   1 NlFhGrvedGklriGglalpvP...elaga..dgqevvayVRPhDlei 43 
                                       N+F+G+ve+G+lr +g+++++    +   a     e v+++RP+D+++
  gi|344210084|ref|YP_004786260.1| 245 NFFEGTVEGGTLRADGFDFDLTermQ--SAvgSRNELVLGIRPEDMTL 290
                                       9*******************998663..3323567**********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 !   19.6   0.0   9.2e-07   0.00066       1      54 [.      35      76 ..      35      97 .. 0.84
   2 !   13.7   0.0   5.5e-05      0.04     234     298 ..     136     198 ..     107     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 9.2e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydp 54
                                      + v++Gp gsGKS+L+++  +l            e ++ g+ir+ ++  +   p
  gi|344210084|ref|YP_004786260.1| 35 FIVFVGPSGSGKSTLMRIVAGL------------ETQSEGDIRIGDKVVNQLGP 76
                                      689****************999............77777788777777666655 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 5.5e-05
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                       + elS G+++  al  a+ r++    ++l DEp ++L+ kl ++  + +++l++  ++  + +TH+
  gi|344210084|ref|YP_004786260.1| 136 PGELSGGQQQRVALGRAIVRDP---NVFLMDEPLSNLDAKLRAEMRTEINRLQNdLDVTTLYVTHD 198
                                       5688999999999999999999...89**********************999999**********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 !   19.4   0.3     8e-07   0.00057      25     205 ..      34     203 ..      23     218 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8e-07
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk.lkiekeevsis 100
                                       +f + vGp GSGKs l+  +    G +++++   +  ++++++    ++ + a   ++f+n       + +e++s  
  gi|344210084|ref|YP_004786260.1|  34 EFIVFVGPSGSGKSTLMRIV---AGLETQSEGDIRIGDKVVNQ-LGPRARDIA---MVFQNYALYpNMTVEENMSFG 103
                                       68999***********9866...56555544444456778877.555555555...555555555222344445555 PP

                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvk 177
                                        +++++ +   +i++   + +e++++    + ++ +LSgG+++ val    Ai  v+   ++l+De  ++LD+k ++
  gi|344210084|ref|YP_004786260.1| 104 LKMSTDMS-ADEIEEAVTSAAEMMDIDMLLDDKPGELSGGQQQRVALG--RAI--VRDPNVFLMDEPLSNLDAKLRA 175
                                       55554444.66888888888888777777777899*******977664..444..5666789*************** PP

                                       HHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 178 kvaellkeksknaQfivislreemleka 205
                                       ++ + +++ +++  +    ++++++e +
  gi|344210084|ref|YP_004786260.1| 176 EMRTEINRLQNDLDVTTLYVTHDQTEAM 203
                                       ***9999999886665444444443333 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.1e-06   0.00077      92     131 ..      25      65 ..      16      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-06
                                       HHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  92 elkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                       +++  ++d +++v+vG+SG GKStL+  +++ ++++ g+++
  gi|344210084|ref|YP_004786260.1|  25 DVSLDIRDgEFIVFVGPSGSGKSTLMRIVAGLETQSEGDIR 65 
                                       55556666699*****************9998888888876 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   1.4e-06   0.00098      14      39 ..      25      50 ..      21      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-06
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTll 39
                                      + +++i+  ++++++GpsGsGKSTl+
  gi|344210084|ref|YP_004786260.1| 25 DVSLDIRDGEFIVFVGPSGSGKSTLM 50
                                      566777744599************97 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.3e-05     0.017       2      20 ..      36      54 ..      35     110 .. 0.87
   2 ?   -0.5   0.0       1.7   1.2e+03      71     111 ..     277     325 ..     263     331 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-05
                            AAA_33  2 vllvGlpGsGKstlaerll 20
                                      +++vG++GsGKstl + ++
  gi|344210084|ref|YP_004786260.1| 36 IVFVGPSGSGKSTLMRIVA 54
                                      79************99765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                            AAA_33  71 rnvil.....datnls....rrerarflklarrlgvpvrivvvetdeetl 111
                                       + ++l     d+t+ +     +e+++++ +++ +g  ++ v++++  + +
  gi|344210084|ref|YP_004786260.1| 277 NELVLgirpeDMTLHDransGHEFEAVVDVVEPMG-SISYVYLQARSQSH 325
                                       55555555556664443322488899999999999.99999999876655 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.7   6.7e-05     0.048       5     122 ..      40     153 ..      36     201 .. 0.75
   2 ?   -2.0   0.0       3.4   2.4e+03     112     152 ..     335     374 ..     291     383 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.7e-05
                                       -STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHHHHHHTT--TT-HHHHHHHHHT--EEEEEEEEEETTEE-TTGGG CS
                    Cytidylate_kin   5 GPagsGKssvaralaeklglkyldtgalYRalalaalrrkvdlldeaalvelakevelsfeaekvllngedveeelr 81 
                                       GP+gsGKs++ r++a   gl+  + g + R+   ++ +      d+a +++  +     ++ e+ +  g +++++++
  gi|344210084|ref|YP_004786260.1|  40 GPSGSGKSTLMRIVA---GLETQSEGDI-RIGDKVVNQLGPRARDIAMVFQNYALYPN-MTVEENMSFGLKMSTDMS 111
                                       9*************9...5667777877.88888887878888888887765544333.344444455778999999 PP

                                       SHHHHHHHHHHTTSHHHHHHHHHHHHTT-B.SSBEEEEESSI CS
                    Cytidylate_kin  82 sdevekavSavaaipavRailvkklrelvk.karvvveGRDi 122
                                        de+e+av   a + ++   l +k  el   +++ v+ GR i
  gi|344210084|ref|YP_004786260.1| 112 ADEIEEAVTSAAEMMDIDMLLDDKPGELSGgQQQRVALGRAI 153
                                       999999999999999999999999888887778888888877 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.4
                                       SSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHH CS
                    Cytidylate_kin 112 karvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlk 152
                                        +r + eG  +  v +pd ++ +f  As e+  +R l +  
  gi|344210084|ref|YP_004786260.1| 335 GQRPISEGQHVY-VEIPDRDVHLFDPASGETIHQRQLGDDA 374
                                       455566666654.3468888888888888888888776654 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   1.8e-05     0.013       4      28 ..      32      56 ..      29      94 .. 0.85
   2 ?   -1.8   0.0         5   3.6e+03      92     117 ..     157     186 ..     110     201 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleq 28
                                      +  ++v +G+sG+GK+tl+r ++  
  gi|344210084|ref|YP_004786260.1| 32 DGEFIVFVGPSGSGKSTLMRIVAGL 56
                                      6789***************987765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5
                            AAA_22  92 ielliiDEaqh.lr...seealeeLrslln 117
                                       + +++ DE    l+   ++e+ +e+ +l+n
  gi|344210084|ref|YP_004786260.1| 157 PNVFLMDEPLSnLDaklRAEMRTEINRLQN 186
                                       335555553222444334555555555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   2.5e-05     0.018      20      47 ..      35      69 ..      29     213 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-05
                            AAA_30 20 vavltGpAGtGKttalkalreaweaa.g......g 47
                                      + v +Gp G+GK+t+++ ++ + +++ g      +
  gi|344210084|ref|YP_004786260.1| 35 FIVFVGPSGSGKSTLMRIVAGLETQSeGdirigdK 69
                                      7799****************999999445555542 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   0.00086      0.61      30      50 ..      30      50 ..      15      55 .. 0.91
   2 ?    2.6   0.1      0.12        90     100     188 ..     113     197 ..      93     203 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00086
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      ++ ge+++++G++g+GK+tl 
  gi|344210084|ref|YP_004786260.1| 30 IRDGEFIVFVGPSGSGKSTLM 50
                                      5689***************95 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.12
                            AAA_25 100 darllvldlagv.eslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg..densnsdvgalveale 173
                                       d+ + +++ a + ++++++ +d+ g+l  ++    ++++   +  r +v Dp  ++++   ++ +++  +++ + ++
  gi|344210084|ref|YP_004786260.1| 113 DEIEEAVTSAAEmMDIDMLLDDKPGELSGGQ----QQRV---ALGRAIVRDPNVFLMDEplSNLDAKLRAEMRTEIN 182
                                       4444445555555888888888888775554....2222...22467888888888877744444444599999999 PP

                            AAA_25 174 riarrtgaavllvhH 188
                                       r++  +++++l v H
  gi|344210084|ref|YP_004786260.1| 183 RLQNDLDVTTLYVTH 197
                                       999999999999999 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   0.0     5e-05     0.036      23      45 ..      32      54 ..      18      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrell 45
                                      ++e ++++G+sG+GKs+l+r ++
  gi|344210084|ref|YP_004786260.1| 32 DGEFIVFVGPSGSGKSTLMRIVA 54
                                      34899*************99776 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   0.1   0.00011     0.079       1      52 [.      36      87 ..      36     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                                      EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfke 52
                                      ++++Gp G GK++l++ va    ++   i   + + + +g ++++i+++f++
  gi|344210084|ref|YP_004786260.1| 36 IVFVGPSGSGKSTLMRIVAGLETQSEGDIRIGDKVVNQLGPRARDIAMVFQN 87
                                      579****************986666666776666666778888888888876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.3e-05     0.052      12      37 ..      25      51 ..      18      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.3e-05
                            AAA_23 12 dqeidF.skgltlItGpNGaGKTTild 37
                                      d+++d  +  + +++Gp G+GK+T+++
  gi|344210084|ref|YP_004786260.1| 25 DVSLDIrDGEFIVFVGPSGSGKSTLMR 51
                                      5666664456889************97 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00014       0.1       6      64 .]     299     356 ..     297     356 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                              TOBE   6 qlpgtVvvveplg..seveVrvdlggga.tLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                        +++ V+vvep g  s v+++++ + ++ t ++  ++++  +     G+ V+++i   +vhl
  gi|344210084|ref|YP_004786260.1| 299 EFEAVVDVVEPMGsiSYVYLQARSQSHEqTFIVETDGQRPIS----EGQHVYVEIPDRDVHL 356
                                       599**********55555555555555588888888888888....9999999887777775 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 ?    2.2   0.0      0.35   2.5e+02      13      46 ..      47      88 ..      45     122 .. 0.73
   2 ?   -1.2   0.0         4   2.8e+03      45      60 ..     199     221 ..     167     225 .. 0.54
   3 ?    8.2   0.1    0.0047       3.4      40      79 ..     338     375 ..     325     378 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.35
                                      HHHHHHHHHHHHHHHHTS---HHHHTTT-SS-S........E CS
                         DraK_HK_N 13 sraqrlasivdsrlaagepitaelLeeqvpgdr........y 46
                                      s + r+++ ++++ +++ +i ++++ +  p  r        y
  gi|344210084|ref|YP_004786260.1| 47 STLMRIVAGLETQSEGDIRIGDKVVNQLGPRARdiamvfqnY 88
                                      667899**************9999988766665555555554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4
                                       S........EEEEE-TT-.--B-S CS
                         DraK_HK_N  45 r........yvvVripggtpieaG 60 
                                       +        ++vV   g+   ++G
  gi|344210084|ref|YP_004786260.1| 199 QteamtmgdRLVVLNYGE-LQQVG 221
                                       222222222555555554.55666 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0047
                                       T-SS-SEEEEE-TT-.--B-S---.-SSEEEEEEE-TTS- CS
                         DraK_HK_N  40 qvpgdryvvVripggtpieaGedpvegrvisatargesge 79 
                                        + ++++v+V+ip++  +++  dp++g++i++++ g+  e
  gi|344210084|ref|YP_004786260.1| 338 PISEGQHVYVEIPDR-DVHLF-DPASGETIHQRQLGDDAE 375
                                       467888********8.69999.999********9998765 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   0.00016      0.12       2      25 ..      36      59 ..      35     121 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                            AAA_28  2 ivitGgestGKTtlleaLaargyp 25
                                      iv++G++++GK+tl++  a  +++
  gi|344210084|ref|YP_004786260.1| 36 IVFVGPSGSGKSTLMRIVAGLETQ 59
                                      9***************99954443 PP

>> SAM_LFY  Floricaula / Leafy protein SAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00021      0.15       4      63 ..      79     137 ..      76     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                           SAM_LFY   4 kgleelfeayGvryltvakiaelGftvstlvnmkeeelddmmkslseifrlellvGeryG 63 
                                       +++  +f++y + y  ++   ++ f  +   +m  +e+++ ++s +e++ +++l+ ++ G
  gi|344210084|ref|YP_004786260.1|  79 RDIAMVFQNYAL-YPNMTVEENMSFGLKMSTDMSADEIEEAVTSAAEMMDIDMLLDDKPG 137
                                       556678888876.444444457888888888***********************988866 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    0.0002      0.14      15      43 ..      24      53 ..      22     134 .. 0.85
   2 ?   -2.9   0.0       5.8   4.1e+03     323     364 ..     156     197 ..     147     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsileal 43
                                      +dv++d+ +  + v++G+ +sGKS+++++ 
  gi|344210084|ref|YP_004786260.1| 24 DDVSLDIRDGeFIVFVGPSGSGKSTLMRIV 53
                                      67899999988***************9875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.8
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +++++l++EP  +L  ++  ++   + +l nd +  +++ TH
  gi|344210084|ref|YP_004786260.1| 156 DPNVFLMDEPLSNLDAKLRAEMRTEINRLQNDLDVTTLYVTH 197
                                       677888888888888888888888888887777777777777 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   0.00029      0.21       1      25 [.      36      63 ..      36     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00029
                            AAA_18  1 IlltGtpGvGKttlakeLskrl.gf..g 25
                                      I+  G++G+GK+tl + ++ ++ ++   
  gi|344210084|ref|YP_004786260.1| 36 IVFVGPSGSGKSTLMRIVAGLEtQSegD 63
                                      8899************997665333551 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00068      0.49      38      62 ..      35      59 ..      34      66 .. 0.83
   2 ?   -0.8   0.0      0.81   5.8e+02      55      85 ..     161     191 ..     158     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00068
                           DUF3987 38 ytlvvapsGerKSpvdklvlrplee 62
                                      +++ v+psG++KS+++++v+ + ++
  gi|344210084|ref|YP_004786260.1| 35 FIVFVGPSGSGKSTLMRIVAGLETQ 59
                                      7899************999877655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.81
                           DUF3987  55 lvlrpleeieaelreeyeeelkeyeaekkaw 85 
                                       l+ +pl  ++a+lr+e++ e+++ +++ +++
  gi|344210084|ref|YP_004786260.1| 161 LMDEPLSNLDAKLRAEMRTEINRLQNDLDVT 191
                                       6778899999999999999998888877665 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   0.2    0.0005      0.36       2      21 ..      36      55 ..      35     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0005
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      +++vG + +GKStL++   g
  gi|344210084|ref|YP_004786260.1| 36 IVFVGPSGSGKSTLMRIVAG 55
                                      89*************98876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00041      0.29       1      20 [.      36      54 ..      36     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00041
                      RNA_helicase  1 iwlyGpsgeGKStlakeLak 20
                                      i+++Gpsg GKStl++  ++
  gi|344210084|ref|YP_004786260.1| 36 IVFVGPSGSGKSTLMRI-VA 54
                                      789************98.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); 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: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2426.56
//
Query:       gi|344210085|ref|YP_004786261.1|  [L=295]
Description: sugar ABC transporter permease [Haloarcula hispanica ATCC 33960]
Scores for complete 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   62.7  19.1    3.7e-17   62.7  19.1    2.2  2  BPD_transp_1     Binding-protein-dependent transport system i
  ------ inclusion threshold ------
       0.62    9.6  10.8        2.4    7.7   8.3    3.0  2  PMT_4TMC         C-terminal four TMM region of protein-O-mann
        2.9    7.9   5.8       0.35   10.9   0.7    2.2  2  TMEMspv1-c74-12  Plectrovirus spv1-c74 ORF 12 transmembrane p


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 ?   -3.6   4.0       1.3     8e+03      75      75 ..      59      59 ..      25     106 .. 0.46
   2 !   62.7  19.1   6.1e-21   3.7e-17      15     182 ..     120     286 ..     103     289 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.3
                      BPD_transp_1 75 a 75
                                       
  gi|344210085|ref|YP_004786261.1| 59 T 59
                                      1 PP

  == domain 2  score: 62.7 bits;  conditional E-value: 6.1e-21
                      BPD_transp_1  15 kldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralG 91 
                                       +  + +++ i   ++lP+++++++++ +f  l  l ++  +++++++  ++ +v+++++a+++ +p+ l+eaar++G
  gi|344210085|ref|YP_004786261.1| 120 PMERDVLVWILSSRMLPPIAVVLPFFIIFREL-NLFDTRVGMVLMYVSINLSLVVWVMKAFFDGIPETLEEAARVDG 195
                                       444555566666789*****999999887666.6778999************************************* PP

                      BPD_transp_1  92 asrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..lgtllleailgydyseisnggvlalviavl 166
                                       a+ +q frkvvlP+a+p i++ +i++f++++ + ++ + l+s  +  +++++ ++i ++ + +++  +++a +++++
  gi|344210085|ref|YP_004786261.1| 196 ATQFQGFRKVVLPAAKPGIFSVAIISFIFAWIELLFGLVLTSFEAvpVTLFVYSFIGSRSIEWGM--LAAASTAMIV 270
                                       *****************************************9999999**************999..9999999999 PP

                      BPD_transp_1 167 llnlvadilqrlldpr 182
                                       ++++++ +++++l+  
  gi|344210085|ref|YP_004786261.1| 271 PVVIFLIAVNKYLAAG 286
                                       9999999999998765 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 ?    1.4   0.1     0.035   2.1e+02     150     181 ..      17      48 ..       2      54 .. 0.71
   2 ?    7.7   8.3    0.0004       2.4      17     187 ..      52     237 ..      39     262 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.035
                          PMT_4TMC 150 slkkkklvklivvvvllvlviavFiffsplty 181
                                       +l+k+++ ++++vv  ++l++++Fi++ pl++
  gi|344210085|ref|YP_004786261.1|  17 RLDKDTRETIVTVVRHTILLTWSFIVLFPLYW 48 
                                       33334566677778888899999999999986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0004
                          PMT_4TMC  17 nalteshpyaSepyeWplllrgisywtkneekkqiyllGNpvlwwlstiallvfvllllalllrrqrgvkdleeeet 93 
                                        +l+++ + +S p +W++l +  +y+   +++  + ++ N +++++++++l++++++ +a++l+r     +  +   
  gi|344210085|ref|YP_004786261.1|  52 MSLKPPGTANSLPPDWIFLPTVYNYIQLIQDSGFVAAFANSLVMVSASVVLVLLIGVPAAYVLSRYDIPMER-DVLV 127
                                       567788999*******************99999************************999999887755554.6666 PP

                          PMT_4TMC  94 rllnsglflllgwalhylPfflmgRvlflhhYlpAllfail.....llaalldfllkslkkslkkk........... 154
                                       ++l s +++ +   +  lPff++ R l l+     ++  ++     l+ ++++ +++ + +    +           
  gi|344210085|ref|YP_004786261.1| 128 WILSSRMLPPI---AVVLPFFIIFRELNLFDTRVGMVLMYVsinlsLVVWVMKAFFDGIPE----Tleeaarvdgat 197
                                       66666655555...45579999999988887665555444400011334444444444444....144458888888 PP

                          PMT_4TMC 155 ......klvklivvvvllvlviavFif.fspltyGlpgts 187
                                             k+v  ++   +++++i++Fif +  l +Gl +ts
  gi|344210085|ref|YP_004786261.1| 198 qfqgfrKVVLPAAKPGIFSVAIISFIFaWIELLFGLVLTS 237
                                       8888876666666666666666666654778888887776 PP

>> TMEMspv1-c74-12  Plectrovirus spv1-c74 ORF 12 transmembrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   0.4         3   1.8e+04      10      17 ..      99     106 ..      98     107 .. 0.80
   2 ?   10.9   0.7   5.8e-05      0.35       8      24 ..     214     230 ..     208     232 .. 0.92

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 3
                   TMEMspv1-c74-12  10 SvvivLgi 17 
                                       Svv+vL i
  gi|344210085|ref|YP_004786261.1|  99 SVVLVLLI 106
                                       89999865 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 5.8e-05
                   TMEMspv1-c74-12   8 iFSvvivLgiFlyiGLs 24 
                                       iFSv i+  iF++i L+
  gi|344210085|ref|YP_004786261.1| 214 IFSVAIISFIFAWIELL 230
                                       9*************885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2097.21
//
Query:       gi|344210086|ref|YP_004786262.1|  [L=310]
Description: sugar ABC transporter permease [Haloarcula hispanica ATCC 33960]
Scores for complete 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-18   66.3  21.4    2.8e-18   66.3  21.4    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 ?   -2.8   5.1      0.26   4.6e+03      98     172 ..      21      99 ..      15     107 .. 0.60
   2 !   66.3  21.4   1.5e-22   2.8e-18       3     178 ..     106     299 ..     101     302 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.26
                      BPD_transp_1  98 frkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis....nggvlalviavlllnl 170
                                       +++  lP  +   +  +++ ++++ g++ l + l++ p l  +  ++   +++  +     ++ +++++i v++  l
  gi|344210086|ref|YP_004786262.1|  21 LWNDYLPYWFMAPMVAVMVMITFFPGAYDLYLSLIAEPTLDVFAADFVGLRNFETAFtrggAIHSFVITITVVVSAL 97 
                                       56666666666666666666777777777777777777766666666666666666666664444444444444444 PP

                      BPD_transp_1 171 va 172
                                       ++
  gi|344210086|ref|YP_004786262.1|  98 LL 99 
                                       44 PP

  == domain 2  score: 66.3 bits;  conditional E-value: 1.5e-22
                      BPD_transp_1   3 llGilaalnrnkkldkllrpliivllslPsfvlaillvlvf....................vilsilghlilp.vii 58 
                                       +l++l+a   +++ + + r+l+i+++++ ++ la +   ++                     +   l    l  vi+
  gi|344210086|ref|YP_004786262.1| 106 VLAALVAGVGSGRAKSFYRVLFIIPMAVAPVSLATIGRIMLnseigiipyvintgtpfaapNF---LSEIPLLtVIL 179
                                       44444444777999999***********999999999988899999999999****9965433...34444444999 PP

                      BPD_transp_1  59 llllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavllefl.gsw 134
                                       l ++ ++p++++i++a+l+s+pk l+ea+r++Ga+ w+++++v++P ++p+++   +++++ l+  + +++ l g++
  gi|344210086|ref|YP_004786262.1| 180 LDAWNWTPFMFIIFYAGLSSVPKTLIEASRVDGAPMWRRYVHVIIPYMKPVVFVATLIRLIDLFRTFGVVYGLtGGG 256
                                       99*****************************************************************9998650555 PP

                      BPD_transp_1 135 pGlgtllleailgydyseisnggvlalviavlllnlvadilqrl 178
                                       pG  t+l++++++ ++  ++  +++a++iav+ l+lv+ + + +
  gi|344210086|ref|YP_004786262.1| 257 PGTATQLVSINIYEQMFINN-QITVAAAIAVVYLVLVVALCNVI 299
                                       66555555544444444333.57777777777777776665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2214.05
//
Query:       gi|344210087|ref|YP_004786263.1|  [L=477]
Description: sugar ABC transporter substrate-binding protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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-25   89.4   3.2    6.1e-25   88.8   3.2    1.2  1  SBP_bac_1   Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.013   15.3   1.0      0.023   14.5   1.0    1.4  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


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 !   88.8   3.2   6.8e-29   6.1e-25       9     310 ..      90     384 ..      84     389 .. 0.87

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 6.8e-29
                                       HHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECT CS
                         SBP_bac_1   9 alqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapg 85 
                                       a++ +v   fe++ +gi+V+++  + +++++k ++++++G+g+ Dv+++ +  + ++ ++g+ +pldp+++++    
  gi|344210087|ref|YP_004786263.1|  90 AIKPAV-PVFEEL-TGIDVVWNVLPEQQFRTKRQTDVSTGAGQFDVFYM-DQVVNQFREEGWIQPLDPFFDDES-LF 162
                                       455555.669997.9**********************************.555569****************93.44 PP

                                       TCCTEEEEHHHHTHHHHCE.EE.....ES.EEEE.EEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCT.H CS
                         SBP_bac_1  86 vkdaadklsssvlpkilds.kv.....ly.vPly.aargliYNkdlfekagldppwtWdelveaakklkekgkkp.i 153
                                       ++d++d+++  + ++ +++ ++     +  +P+  +++  +Y+kdl++k +l++ +t +e+   a+ + e+     +
  gi|344210087|ref|YP_004786263.1| 163 DEDWYDPDD-LFEASRWQAhGGgysdtWTgMPITvEVQTQFYRKDLYDKHDLEVAETLEEFRQNAQTIHENESDVvG 238
                                       455555522.24455555544489**********55***************************************77 PP

                                       CCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT..HHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHH CS
                         SBP_bac_1 154 ggarggsasgtayyfalalakslggkvfdkdgg..gldnpegvtaatylvklyavanltkelkgkgaenkdgaaala 228
                                       ++ rg  + g + y +++++  +g+ ++++     gld+++  +aa+++v l       +++++ ga++++++++l+
  gi|344210087|ref|YP_004786263.1| 239 TVGRGDKGYGMNIYILNTFLREFGSSLWTEFPTdsGLDSDGVINAAEWYVSLL------QDYGPEGASTQTWSDVLS 309
                                       77777778899999****************99999999999999888888888......8***************** PP

                                       HHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE.EEEEEEEEBTTCSTHHHHHHH CS
                         SBP_bac_1 229 lfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi.lgayglaipkgsknpeaAkkF 304
                                        +++G+a+ +++  +          + ++  +++++ + +g+a +P   +g  +    ++ +  +k+++n e+A+ F
  gi|344210087|ref|YP_004786263.1| 310 TMQEGRAGHIVSDANL--------FWPGLTGSDSSVADTIGIAKVPSPADGQFSPnAFNWQISTSKNAQNSEQAFLF 378
                                       *********9876655........57899*************************9999999**************** PP

                                       HHHHTS CS
                         SBP_bac_1 305 ldflls 310
                                       + ++ s
  gi|344210087|ref|YP_004786263.1| 379 MVWASS 384
                                       ***988 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   1.0   2.6e-06     0.023       3      24 ..       5      25 ..       3      27 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.6e-06
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggca 24
                                      +RR+FLK+++++  + +l+gc+
  gi|344210087|ref|YP_004786263.1|  5 NRRTFLKATGVG-LLSGLAGCT 25
                                      8******66665.677788886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 3222.59
//
Query:       gi|344210088|ref|YP_004786264.1|  [L=344]
Description: alcohol dehydrogenase [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-33  114.2   3.2    2.5e-33  114.2   3.2    1.9  2  ADH_N          Alcohol dehydrogenase GroES-like domain
    4.7e-21   75.1   0.0    7.5e-21   74.5   0.0    1.3  1  ADH_zinc_N     Zinc-binding dehydrogenase
    4.4e-10   39.4   0.0    8.9e-10   38.4   0.0    1.5  1  Glu_dehyd_C    Glucose dehydrogenase C-terminus
    5.3e-05   24.3   0.0    9.4e-05   23.5   0.0    1.4  1  ADH_zinc_N_2   Zinc-binding dehydrogenase
    0.00067   20.2   0.0     0.0013   19.3   0.0    1.5  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.025   14.8   0.0      0.056   13.7   0.0    1.6  1  TrkA_N         TrkA-N domain
      0.038   14.3   0.1      0.067   13.5   0.1    1.4  1  NTP_transf_3   MobA-like NTP transferase domain
      0.047   13.6   0.1       0.13   12.1   0.1    1.8  2  Rossmann-like  Rossmann-like domain
       0.15   11.3   0.1       0.22   10.7   0.1    1.2  1  FAD_binding_3  FAD binding 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 !  114.2   3.2   1.3e-36   2.5e-33       2     105 ..      25     130 ..      24     134 .. 0.96
   2 ?   -2.0   0.0       1.6   3.3e+03      32      50 ..     230     248 ..     223     260 .. 0.75

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 1.3e-36
                                       TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-G CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegee 78 
                                       +evl++v a+++C +D+h+++g   + +++pl+lGHE +G+v+evg +v++++vGdrV+++p+++c+ C++Ck+ge+
  gi|344210088|ref|YP_004786264.1|  25 DEVLVQVGACSVCMTDYHMYHG--TFAAETPLVLGHEGAGTVAEVGADVEGFAVGDRVAINPTVPCNACSYCKKGET 99 
                                       89*******************9..7**************************************************** PP

                                       GG-TTBEETTTS....S-SSSBSEEEECGGG CS
                             ADH_N  79 nlCeeakllgvs....ldGgfaeyvvvpekk 105
                                       +lCe+++ +g      ldG+faeyv vp+ +
  gi|344210088|ref|YP_004786264.1| 100 HLCENNTSIGGAgdtiLDGAFAEYVRVPAIN 130
                                       ***9999999888**************9765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.6
                                       SEE---EEEEEEEEESTT- CS
                             ADH_N  32 plilGHEivGeveevgpev 50 
                                       p+ +G E++G v  + ++ 
  gi|344210088|ref|YP_004786264.1| 230 PVDVGAEAIGLVPTIKQAN 248
                                       7778999999998877654 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0   3.7e-24   7.5e-21       1     128 [.     173     301 ..     173     303 .. 0.93

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 3.7e-24
                                       HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaal 76 
                                       ++Gl+++q+ + +Ga  +++   ++e++ela++lGad+v++++e+d++e+i ++ g ++vdv  e++G   t+++a 
  gi|344210088|ref|YP_004786264.1| 173 PIGLLLLQAFRNAGAaPIVVSELDDERRELAADLGADAVVDPNEEDPEEAICAAAG-GPVDVGAEAIGLVPTIKQAN 248
                                       79*************7777789999*****************555**********5.5******************* PP

                                       HCEEEEEEEEECSCTSSEEE..EEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                        ADH_zinc_N  77 kllkpgGrlvvvGggkgeee..fdlrnlllkeksilGsllgslreefkealdll 128
                                       ++++ gG   ++G++ +e +  ++++++++ e+  +Gs+  + +e+f++a+ ll
  gi|344210088|ref|YP_004786264.1| 249 AVTASGGSTLIFGVPDQEATmeISPFDVFFDEVDYRGSFSLT-TEDFERAITLL 301
                                       **************9998887899999***************.9*****99886 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 !   38.4   0.0   4.5e-13   8.9e-10      29     208 ..     160     336 ..     141     339 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 4.5e-13
                       Glu_dehyd_C  29 wep.esalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYv.ds.retpvdei.peaseem 101
                                        +p +s+ ++GaG++GLL l +++    g   + v+   + +d + +l ++lGa  v d  +e+p + i ++a  ++
  gi|344210088|ref|YP_004786264.1| 160 IKPgDSVGIIGAGPIGLLLLQAFRN--AGAAPI-VVS--ELDDERRELAADLGADAVvDPnEEDPEEAIcAAAGGPV 231
                                       44436888***************95..566644.444..567788899*****97652541455666662456789* PP

                       Glu_dehyd_C 102 dlvvEaTGsakhafeaiealapnGvaaLlGvpeds.evevdggelhrelvleNkalvGsvNanrrhfeaavdtLaal 177
                                       d+  Ea G  + + +a    a+ G + + Gvp ++ ++e+   ++    + +     Gs    ++ fe a+  L   
  gi|344210088|ref|YP_004786264.1| 232 DVGAEAIGLVPTIKQANAVTASGGSTLIFGVPDQEaTMEISPFDV----FFDEVDYRGSFSLTTEDFERAITLLR-H 303
                                       ********************************8764666666554....45556678**************8775.5 PP

                       Glu_dehyd_C 178 peslldelvtkvvdldeleeAfed..ddetiKt 208
                                       ++   ++l+t++++ld+l +Afe+  + e +K 
  gi|344210088|ref|YP_004786264.1| 304 ERIDAETLITERIGLDDLPTAFERmgNAEGLKK 336
                                       666689****************96213445555 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 !   23.5   0.0   4.7e-08   9.4e-05       1     133 []     206     339 ..     206     339 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.7e-08
                                       TT-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHE.EEEEEEEE----.S-EEE-CHHHCTTT-E CS
                      ADH_zinc_N_2   1 lGAdevidyrtedfe....aatggegvDvvldtvggealleaslkvl.pggGrlvsiggpplsaallkpakkrkgrs 72 
                                       lGAd v+d  +ed e    aa+ g+ vDv  +++g   +++++ +v  +gg +l+  g p   a++   +++     
  gi|344210088|ref|YP_004786264.1| 206 LGADAVVDPNEEDPEeaicAAA-GGPVDVGAEAIGLVPTIKQANAVTaSGGSTLIF-GVPDQEATMEISPFDVFFDE 280
                                       8******999888887886555.788*********88898**99888555444544.33322233333333345566 PP

                                       EEE--GGG...-.-HHHHHHHHHHHHHHH--..--EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                      ADH_zinc_N_2  73 vkyeflfsmkasaqadileelaalieeGklr..pvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                       v+y   fs   +  +d +e+  +l+ ++++   + ++++ +l+++++A++++ ++    K+V+
  gi|344210088|ref|YP_004786264.1| 281 VDYRGSFS--LT-TED-FERAITLLRHERIDaeTLITERIGLDDLPTAFERMGNAEGLKKVVV 339
                                       66666664..33.667.************754499*****************98887777776 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 !   19.3   0.0   6.6e-07    0.0013       2      57 ..     166     217 ..     165     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.6e-07
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdnee 57 
                                       +giiGaG +g  l++ + +ag  +  iv + s   ++++ela++lg+++   +nee
  gi|344210088|ref|YP_004786264.1| 166 VGIIGAGPIGLLLLQAFRNAG--AAPIV-V-SELDDERRELAADLGADAVVDPNEE 217
                                       8********************..66677.6.67777788999999*9999888876 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   0.0   2.8e-05     0.056       3      46 ..     168     212 ..     166     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-05
                                       EES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEE CS
                            TrkA_N   3 iiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvv 46 
                                       iiG+G +G  l++ +++ g  ++vv + d+er e +++ g+++vv
  gi|344210088|ref|YP_004786264.1| 168 IIGAGPIGLLLLQAFRNaGAAPIVVSELDDERRELAADLGADAVV 212
                                       9****************66677****************9999876 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 ?   13.5   0.1   3.4e-05     0.067      30      81 ..     178     228 ..     169     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.4e-05
                                       HHHHHCTT.-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHH CS
                      NTP_transf_3  30 vldalraagvdevvvvggdeevlaalarlgvrvvededpgkgplaslaaalr 81 
                                       +l+a+r ag++++vv+  d+e ++ +a+lg++ v+d++ ++ p ++++aa+ 
  gi|344210088|ref|YP_004786264.1| 178 LLQAFRNAGAAPIVVSELDDERRELAADLGADAVVDPN-EEDPEEAICAAAG 228
                                       6899************999999**************95.8999999999984 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   0.1   6.7e-05      0.13      11      52 ..     164     205 ..     155     253 .. 0.85
   2 ?   -2.4   0.0         2   3.9e+03      55      80 ..     242     266 ..     231     269 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.7e-05
                     Rossmann-like  11 lsvGiisaGrvGtalgaaleraghvvvgisaisaasreraer 52 
                                        svGii+aG +G  l +a+  ag + + +s + +  re+a  
  gi|344210088|ref|YP_004786264.1| 164 DSVGIIGAGPIGLLLLQAFRNAGAAPIVVSELDDERRELAAD 205
                                       58*********************9999999998888888865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2
                     Rossmann-like  55 PdvpvlevedvaaraellllavPdae 80 
                                       P ++ ++    a     l++ vPd e
  gi|344210088|ref|YP_004786264.1| 242 PTIKQANA-VTASGGSTLIFGVPDQE 266
                                       44444444.23344566788899877 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00011      0.22       4      37 ..     166     199 ..     164     209 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSC CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttv 37 
                                       V I+GaGp Gl+l +  ++aG   ++v   +++ 
  gi|344210088|ref|YP_004786264.1| 166 VGIIGAGPIGLLLLQAFRNAGAAPIVVSELDDER 199
                                       89*********************99998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2471.43
//
Query:       gi|344210089|ref|YP_004786265.1|  [L=255]
Description: transcriptional regulator [Haloarcula hispanica ATCC 33960]
Scores for 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-29  101.1   0.0    3.9e-28   97.9   0.0    2.0  2  IclR            Bacterial transcriptional regulator
    8.4e-11   41.5   0.4    2.4e-10   40.1   0.1    1.8  2  HTH_IclR        IclR helix-turn-helix domain
    2.3e-07   30.6   0.0    3.6e-07   29.9   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
      1e-05   25.4   0.0    3.3e-05   23.7   0.0    1.8  1  HTH_11          HTH domain
    2.6e-05   24.0   0.1    6.5e-05   22.7   0.1    1.6  1  MarR_2          MarR family
    7.6e-05   22.7   0.1     0.0002   21.3   0.0    1.8  2  HTH_20          Helix-turn-helix domain
    0.00045   19.7   0.0     0.0008   18.9   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0005   19.9   0.1     0.0011   18.8   0.1    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0046   17.3   0.1     0.0085   16.4   0.1    1.4  1  Rrf2            Transcriptional regulator
     0.0062   16.7   0.1      0.013   15.7   0.1    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.028   14.6   0.0    1.3  1  HTH_34          Winged helix DNA-binding domain
      0.038   14.4   0.0       0.21   12.0   0.0    2.0  2  FaeA            FaeA-like protein
      0.044   13.7   0.0      0.073   13.0   0.0    1.4  1  MarR            MarR family
       0.13   12.1   0.0       0.29   11.0   0.0    1.6  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 ?    0.7   0.0      0.33   4.3e+02      58      77 ..      47      66 ..      32      69 .. 0.88
   2 !   97.9   0.0   3.1e-31   3.9e-28       7     127 ..     129     249 ..     126     251 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.33
                                      HHHHHHHHHTSEEEESSSST CS
                              IclR 58 eeLakvReqGyavdreEeee 77
                                      + L++ R+ Gy v+r E++e
  gi|344210089|ref|YP_004786265.1| 47 NHLSTLRAAGYVVKRAEKYE 66
                                      68999**********99875 PP

  == domain 2  score: 97.9 bits;  conditional E-value: 3.1e-31
                                       TSTT-EEEGGGSHHHHHHHHTS-HHHHHHHHHHHT---SSTTS--SHHHHHHHHHHHHHHTSEEEESSSSTTEEEEE CS
                              IclR   7 saiGtrlplyataiGKalLaaldeeeleallerlelkrlterTitdpeeLleeLakvReqGyavdreEeeegvrciA 83 
                                        + G+rlpl+  a GKalL+ l+ +++e++l ++el + t++T++dp+eL eeL +vR++G+a+ r+E++eg++ +A
  gi|344210089|ref|YP_004786265.1| 129 FHAGERLPLHVNAPGKALLSSLPSDRVESVLDERELVAPTDATLVDPDELIEELRRVRDDGIAFCRGEQYEGIIGVA 205
                                       689************************************************************************** PP

                                       EEEE-TTSSEEEEEEEEEETTTSHHHHHHHHHHHHHHHHHHHHH CS
                              IclR  84 apifdasgevvaAvsvsgptarlteeelkeellalvreaArkis 127
                                       ap+ d sg+ +aA+ + gp++rl+ ++l+e+++ +v  + ++i+
  gi|344210089|ref|YP_004786265.1| 206 APLPDVSGDRIAALGICGPVERLNGRYLREDITGQVLSTTKSIQ 249
                                       ***************************************99997 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 !   40.1   0.1   1.9e-13   2.4e-10       6      50 ..      16      60 ..      14      62 .. 0.96
   2 ?   -1.8   0.0       2.2   2.8e+03       9      31 ..      92     115 ..      91     117 .. 0.67

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.9e-13
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +aiL+al  a+++++++elA+  g++kS +h++L+tL   Gyv +
  gi|344210089|ref|YP_004786265.1| 16 VAILEALVDATGPVGVTELANLVGVSKSVAHNHLSTLRAAGYVVK 60
                                      69*****************************************86 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.2
                                       HCT-CTTBSS-.BHHHHHHHHTS- CS
                          HTH_IclR   9 Ldalaeapqel.tlselArrtglp 31 
                                       Ld la+a++e  tl  l + +g+p
  gi|344210089|ref|YP_004786265.1|  92 LDNLATATGETaTLFVLEETAGVP 115
                                       566888888854777777777766 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 !   29.9   0.0   2.8e-10   3.6e-07       3      45 ..      14      58 ..      12      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.8e-10
                                      HHHHHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  3 tRlkILklLae..gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      t + IL +L +  g+  v+ela+ +g+s+s    HL+ Lr aG+V
  gi|344210089|ref|YP_004786265.1| 14 TSVAILEALVDatGPVGVTELANLVGVSKSVAHNHLSTLRAAGYV 58
                                      5578****************************************9 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.6e-08   3.3e-05       4      46 ..      17      59 ..      16      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.6e-08
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46
                                      +ile L +a+gp+   eLA   +vS+++ ++++ +L+++g+ +
  gi|344210089|ref|YP_004786265.1| 17 AILEALVDATGPVGVTELANLVGVSKSVAHNHLSTLRAAGYVV 59
                                      599*************************************765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   5.1e-08   6.5e-05       6      55 ..      14      62 ..      10      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5.1e-08
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      +   +L aL ++ g+ + v+ela   g+sks ++++l  L aaG+v++r+
  gi|344210089|ref|YP_004786265.1| 14 TSVAILEALVDATGP-VGVTELANLVGVSKSVAHNHLSTLRAAGYVVKRA 62
                                      667899*******98.9*****************************9995 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.6e-07    0.0002      11      59 ..      14      63 ..       7      65 .. 0.89
   2 ?   -3.0   0.0       6.3     8e+03      22      36 ..     100     114 ..      92     117 .. 0.59

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.6e-07
                                      HHHHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20 11 vRrrilraL.araegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      +  +il aL    +++ ++ela ++++sk+ +++HL +L+ ag+v  + e
  gi|344210089|ref|YP_004786265.1| 14 TSVAILEALvDATGPVGVTELANLVGVSKSVAHNHLSTLRAAGYVVKRAE 63
                                      56789999988889999***************************987765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.3
                                       CTTB-HHHHHHHHTS CS
                            HTH_20  22 aegltaselaerldl 36 
                                       +e +t+  l e+ ++
  gi|344210089|ref|YP_004786265.1| 100 GETATLFVLEETAGV 114
                                       555566666665555 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 !   18.9   0.0   6.2e-07    0.0008       4      47 ..      14      58 ..      12      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.2e-07
                            HTH_24  4 tdrkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      t  +ILe+L +  +    +eLA  +g+S+s  + +l  L  +G++
  gi|344210089|ref|YP_004786265.1| 14 TSVAILEALVDaTGPVGVTELANLVGVSKSVAHNHLSTLRAAGYV 58
                                      56689988888788899***************************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 !   18.8   0.1   8.6e-07    0.0011      11      59 ..      16      65 ..       9      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.6e-07
                                      CCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                              TrmB 11 akvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrp 59
                                      + +  aL+ + gp  ++e+a+ +gv++s + + L+ L  +G+V ++ +++
  gi|344210089|ref|YP_004786265.1| 16 VAILEALVdATGPVGVTELANLVGVSKSVAHNHLSTLRAAGYVVKRAEKY 65
                                      677899**9***********************************998875 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   6.7e-06    0.0085      18      56 ..      21      59 ..       6      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.7e-06
                                      HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 18 akeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      a+ +  +pv ++e+a+ +++s+s++   l++Lr ag+v 
  gi|344210089|ref|YP_004786265.1| 21 ALVDATGPVGVTELANLVGVSKSVAHNHLSTLRAAGYVV 59
                                      44555669*****************************96 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   9.9e-06     0.013      19      54 ..      25      60 ..      17      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.9e-06
                                      HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                    Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyvey 54
                                        ++v++++la   +vs+s +   l+ L+ +Gyv+ 
  gi|344210089|ref|YP_004786265.1| 25 ATGPVGVTELANLVGVSKSVAHNHLSTLRAAGYVVK 60
                                      5689******************************75 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 ?   14.6   0.0   2.2e-05     0.028       4      79 ..      17      95 ..      15      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                            HTH_34  4 avlsyLas.vdeadfvelkealeatdgnLsvhlkkLekagYie..vdkefkgkkprtllriTpeGreafkkyvkaLksl 79
                                      a+l  L++ +  +  +el + ++++++    hl++L +agY++   +k   + +p  l + T++G++ +++ +++L++l
  gi|344210089|ref|YP_004786265.1| 17 AILEALVDaTGPVGVTELANLVGVSKSVAHNHLSTLRAAGYVVkrAEKYEASLRPLFLGERTRDGLSFYQAAKQQLDNL 95
                                      788899987888999***************************8224566667789999999999999999999988875 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.21       4      47 ..      17      60 ..      14      64 .. 0.90
   2 ?   -0.5   0.0       1.3   1.7e+03      26      33 ..      81      88 ..      78      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                      HHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEE CS
                              FaeA  4 eIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikr 47
                                       Ile l +  +p+  +e+A+ +g+s   a   L +L+++g + +
  gi|344210089|ref|YP_004786265.1| 17 AILEALVDATGPVGVTELANLVGVSKSVAHNHLSTLRAAGYVVK 60
                                      5899999999******************************8754 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.3
                                      TS-HHHHH CS
                              FaeA 26 glsaYQaR 33
                                      gls YQa 
  gi|344210089|ref|YP_004786265.1| 81 GLSFYQAA 88
                                      99****84 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.7e-05     0.073       2      50 ..      12      61 ..      11      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.7e-05
                                      -HHHHHHHH.HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  2 tltqfviLr.ilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      t+t + iL+ +++  gp  v+eLa+ +gvsks + + l +L  +G++ ++
  gi|344210089|ref|YP_004786265.1| 12 TQTSVAILEaLVDATGPVGVTELANLVGVSKSVAHNHLSTLRAAGYVVKR 61
                                      56666667514567899****************************99776 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00023      0.29      24      45 ..      29      50 ..      28      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                            HTH_10 24 vtlkeLAkelGIskstlsehLr 45
                                      v + eLA+  G+sks +++hL+
  gi|344210089|ref|YP_004786265.1| 29 VGVTELANLVGVSKSVAHNHLS 50
                                      5689****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1680.65
//
Query:       gi|344210090|ref|YP_004786266.1|  [L=334]
Description: HEAT domain-containing protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   50.8  10.4      8e-08   32.6   1.0    3.3  3  HEAT_2         HEAT repeats
      1e-08   35.5   8.6      0.016   15.7   0.2    4.8  5  HEAT_EZ        HEAT-like repeat
    1.6e-08   34.1   1.4       0.08   13.2   0.0    5.0  5  HEAT           HEAT repeat
     0.0002   21.5   0.0        0.5   10.4   0.0    2.6  2  Cnd1           non-SMC mitotic condensation complex subunit 1
     0.0048   15.5   0.1       0.94    8.0   0.1    2.6  3  Adaptin_N      Adaptin N terminal region
     0.0099   15.9   0.3      0.022   14.8   0.3    1.6  1  DZR            Double zinc ribbon
  ------ inclusion threshold ------
      0.011   15.5   4.7       0.02   14.6   4.7    1.5  1  zinc_ribbon_2  zinc-ribbon domain
       0.05   13.0   6.7       0.11   11.9   6.7    1.6  1  zf-ribbon_3    zinc-ribbon domain
      0.074   12.2   0.1        1.9    7.5   0.0    2.3  2  IFRD           Interferon-related developmental regulator (IF
       0.41   11.4   7.9         14    6.6   0.1    4.6  4  TPR_4          Tetratricopeptide repeat
       0.81   10.5  13.9         11    7.0   0.2    5.4  4  HEAT_PBS       PBS lyase 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 !   12.8   0.6   7.1e-05      0.12      18      88 .]      41     124 ..      13     124 .. 0.73
   2 !   32.6   1.0   4.9e-11     8e-08       2      81 ..     100     193 ..      99     200 .. 0.78
   3 !   26.4   1.1     4e-09   6.5e-06       2      67 ..     178     248 ..     177     272 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.1e-05
                            HEAT_2  18 raairaLgrignp......ealpaLvellededpavRraaaeaLgaigd..pe....alpaLkellddddd.dvvRe 81 
                                       +a +r+L   +++       +l  L+ +l+++++ +R + a+  + + +  p+    ++p L+e+l+d+++ ++vR+
  gi|344210090|ref|YP_004786266.1|  41 QACLRSLKAAADDqpklfdGVLTSLTVFLQNSERPTRLTTAKLFVTVSEsaPDsvvpVVPTLAERLADESEfYYVRA 117
                                       55556666444432334434477788888888888888888877666532233455579***********999**** PP

                            HEAT_2  82 aAaeaLa 88 
                                       + aeaL+
  gi|344210090|ref|YP_004786266.1| 118 RCAEALG 124
                                       *****96 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 4.9e-11
                            HEAT_2   2 daLlqalen.dpdpevrraairaLg..rignp......ealpaLvellededpavRraaaeaLg..aigdpe....a 63 
                                       ++L ++l++ +++++vr++ ++aLg    ++p      e+++ L+  le ++p+vR+  a+aL+  a+g+p+     
  gi|344210090|ref|YP_004786266.1| 100 PTLAERLADeSEFYYVRARCAEALGyvAVDHPdavvspEVVADLRIGLEFDKPEVREKLAKALAhvAMGRPDrlryQ 176
                                       67788885559999***********773445533444488***********************86678999966667 PP

                            HEAT_2  64 lpaLkellddddddvvRe 81 
                                       +++L+e l+ d+ ++vR 
  gi|344210090|ref|YP_004786266.1| 177 VDSLAEHLRADS-ELVRY 193
                                       8*******9875.56675 PP

  == domain 3  score: 26.4 bits;  conditional E-value: 4e-09
                            HEAT_2   2 daLlqalendpdpevrraairaLgrignp......ealpaLvellededpavRraaaeaLgaigdpealpaL 67 
                                       d L + l +  ++ vr++   aL  ig+       +a++aLv++lede+++vR  aaeaLg ++  ++++a 
  gi|344210090|ref|YP_004786266.1| 178 DSLAEHL-RADSELVRYHLSTALVVIGSAcperltDAREALVSCLEDESRYVRGRAAEALGLLAGTKSVEAF 248
                                       6788888.77788999999999996666555688899************************99877776665 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.015        25       5      49 ..      41      81 ..      38      84 .. 0.87
   2 !    8.5   0.0    0.0017       2.8      24      54 ..      93     125 ..      85     126 .. 0.80
   3 !   10.4   0.1   0.00045      0.74       3      53 ..     115     163 ..     114     165 .. 0.88
   4 !    8.0   0.2    0.0025       4.1       1      46 [.     152     193 ..     152     199 .. 0.86
   5 !   15.7   0.2     1e-05     0.016      10      54 ..     201     238 ..     192     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                           HEAT_EZ  5 raAawaLGrlaggepellqplvpeilpaLlalLnddsdeVRaaAa 49
                                       a+++ L      +++++++l + +l  L  +L++++ ++R ++a
  gi|344210090|ref|YP_004786266.1| 41 QACLRSL----KAAADDQPKLFDGVLTSLTVFLQNSERPTRLTTA 81
                                      6778888....667799***********************99998 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0017
                           HEAT_EZ  24 plvpeilpaLlalLnddsd..eVRaaAagaLgn 54 
                                       + v  ++p L+ +L d+s    VRa +a aLg 
  gi|344210090|ref|YP_004786266.1|  93 DSVVPVVPTLAERLADESEfyYVRARCAEALGY 125
                                       4455788888888889999*999********95 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00045
                           HEAT_EZ   3 vRraAawaLGrlaggepellqplvpeilpaLlalLnddsdeVRaaAagaLg 53 
                                       vR+ +a aLG +a+  p+++    pe+++ L  +L+ d++eVR++ a aL+
  gi|344210090|ref|YP_004786266.1| 115 VRARCAEALGYVAVDHPDAVV--SPEVVADLRIGLEFDKPEVREKLAKALA 163
                                       8*********99966666655..9*********************999996 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0025
                           HEAT_EZ   1 wrvRraAawaLGrlaggepellqplvpeilpaLlalLnddsd.eVRa 46 
                                       ++vR+  a aL+ +a g+p+ l+ +v+ +   L       ++ +VR+
  gi|344210090|ref|YP_004786266.1| 152 PEVREKLAKALAHVAMGRPDRLRYQVDSLAEHLR-----ADSeLVRY 193
                                       689********99***************999999.....55546676 PP

  == domain 5  score: 15.7 bits;  conditional E-value: 1e-05
                           HEAT_EZ  10 aLGrlaggepellqplvpeilpaLlalLnddsd.eVRaaAagaLgn 54 
                                       ++G   + +pe l ++ ++++ +L      d++  VR+ Aa aLg 
  gi|344210090|ref|YP_004786266.1| 201 VIG---SACPERLTDAREALVSCLE-----DESrYVRGRAAEALGL 238
                                       567...8899999999999999999.....999899********96 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         4   6.5e+03       9      29 ..      69      89 ..      61      90 .. 0.64
   2 !    9.3   0.0   0.00088       1.4       1      26 [.      98     125 ..      98     128 .. 0.87
   3 ?    4.1   0.0     0.043        71      14      28 ..     152     166 ..     150     168 .. 0.88
   4 ?    2.0   0.1       0.2   3.3e+02       4      30 ..     179     205 ..     177     206 .. 0.85
   5 !   13.2   0.0   4.9e-05      0.08       4      28 ..     216     240 ..     214     242 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4
                                      HT-SSHHHHHHHHHHHHHHHH CS
                              HEAT  9 lsDpspeVReaAakaLgalae 29
                                      l+ ++   R ++ak +++++e
  gi|344210090|ref|YP_004786266.1| 69 LQNSERPTRLTTAKLFVTVSE 89
                                      533333449999998887765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00088
                                       HHHHHHHHHT-..SSHHHHHHHHHHHHH CS
                              HEAT   1 llPlllkllsD..pspeVReaAakaLga 26 
                                       ++P+l + l D  +   VR+ +a+aLg 
  gi|344210090|ref|YP_004786266.1|  98 VVPTLAERLADesEFYYVRARCAEALGY 125
                                       5899*999999878888*********95 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.043
                                       HHHHHHHHHHHHHHH CS
                              HEAT  14 peVReaAakaLgala 28 
                                       peVRe  akaL+++a
  gi|344210090|ref|YP_004786266.1| 152 PEVREKLAKALAHVA 166
                                       9**********9875 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.2
                                       HHHHHHT-SSHHHHHHHHHHHHHHHHC CS
                              HEAT   4 lllkllsDpspeVReaAakaLgalaev 30 
                                        l + l+ +s  VR+    aL+ + + 
  gi|344210090|ref|YP_004786266.1| 179 SLAEHLRADSELVRYHLSTALVVIGSA 205
                                       688999*********999999998776 PP

  == domain 5  score: 13.2 bits;  conditional E-value: 4.9e-05
                                       HHHHHHT-SSHHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgala 28 
                                       +l+++l+D+s  VR  Aa+aLg la
  gi|344210090|ref|YP_004786266.1| 216 ALVSCLEDESRYVRGRAAEALGLLA 240
                                       6899******************887 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 !    8.5   0.0    0.0012       1.9      16      90 ..      92     170 ..      83     193 .. 0.80
   2 !   10.4   0.0   0.00031       0.5       7      86 ..     199     275 ..     190     312 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0012
                              Cnd1  16 pnlveylvepLrkrLkDedp..yVRktaaivvakL..ilndmvkekgflselaklleDenprVvanalaalteisek 88 
                                       p+ v ++v+ L +rL De++  yVR  +a ++  +   ++d v + +++++l+  le ++p+V++    al  ++  
  gi|344210090|ref|YP_004786266.1|  92 PDSVVPVVPTLAERLADESEfyYVRARCAEALGYVavDHPDAVVSPEVVADLRIGLEFDKPEVREKLAKALAHVAMG 168
                                       56677899999999999996669**9999999999866778999999999999999999999999988888887766 PP

                              Cnd1  89 se 90 
                                        +
  gi|344210090|ref|YP_004786266.1| 169 RP 170
                                       44 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00031
                              Cnd1   7 irtlgcirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalt 83 
                                       ++ +g+ + + l+++  e L ++L+De+ yVR  aa ++  L   + v+     ++l++   De + V + a++al+
  gi|344210090|ref|YP_004786266.1| 199 LVVIGSACPERLTDA-REALVSCLEDESRYVRGRAAEALGLLAGTKSVEAFP-EAQLEEFTVDE-EFVAERARFALS 272
                                       555555555555554.57899***************9998887766666555.45666666665.356666666666 PP

                              Cnd1  84 eis 86 
                                       ++ 
  gi|344210090|ref|YP_004786266.1| 273 QYR 275
                                       665 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.0    0.0088        14     213     281 ..      44     111 ..      25     135 .. 0.79
   2 !    8.0   0.1   0.00058      0.94     111     197 ..     135     221 ..     121     225 .. 0.79
   3 ?    3.1   0.0     0.017        28      99     138 ..     198     236 ..     192     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0088
                                       HHHHCC---SSHHHH..HHHHHHHCGGCGCSSCHHHHHHHHHCCHCCCCST.HHHCCHHCHHHHHHSSCC CS
                         Adaptin_N 213 iklltrlarqepeerskkellesllnllqssnnaVlletvnlivelapkne.livlavnaLvrllsskde 281
                                       ++ l++ a+ +p++   + +l+sl+  lq+s     l t++l+v+++++++ ++v +v  L + l ++ e
  gi|344210090|ref|YP_004786266.1|  44 LRSLKAAADDQPKLF--DGVLTSLTVFLQNSERPTRLTTAKLFVTVSESAPdSVVPVVPTLAERLADESE 111
                                       677788888888888..55999999999999999999999999988777666777777777776665554 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00058
                                       CHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SSHHH...HHHHHHHHHHHHCCCC CS
                         Adaptin_N 111 laedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdkdpgv...vlaAvalleeikkndr 184
                                       +++ ++ +++  l+ ++p vr k a a++++    pd lr q v+ + e l  ++ +v   +++A+ ++ +  +++r
  gi|344210090|ref|YP_004786266.1| 135 VSPEVVADLRIGLEFDKPEVREKLAKALAHVAMGRPDRLRYQ-VDSLAEHLRADSELVryhLSTALVVIGSA-CPER 209
                                       568889999999*****************************9.********666655511145566666666.8888 PP

                                       CCCHHHHHHHCCH CS
                         Adaptin_N 185 lllkllpklvrrL 197
                                       l +++ + lv++L
  gi|344210090|ref|YP_004786266.1| 210 L-TDAREALVSCL 221
                                       7.66666666666 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.017
                                       HHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHH CS
                         Adaptin_N  99 ALrvLssirvpelaedlapaikkllkdrspyvrkkAalai 138
                                       AL v++s +  e + d  +a+ ++l+d+s yvr  Aa a+
  gi|344210090|ref|YP_004786266.1| 198 ALVVIGSACP-ERLTDAREALVSCLEDESRYVRGRAAEAL 236
                                       5555555443.445677889999*************9765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.3   1.3e-05     0.022       9      37 ..     306     333 ..     302     334 .] 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                               DZR   9 ppdarfCseCgtklkavaaedrCpsCgek 37 
                                       p+++  C++Cg +l+ ++ +  Cp Cg++
  gi|344210090|ref|YP_004786266.1| 306 PEGDDGCPHCGLSLP-ESGPPLCPGCGTP 333
                                       778888999999996.7789999999987 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   4.7   1.2e-05      0.02       2      23 .]     312     334 .]     312     334 .] 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                     zinc_ribbon_2   2 CpnCGaelqd.nakFCpyCGtpl 23 
                                       Cp+CG  l++ + + Cp CGtpl
  gi|344210090|ref|YP_004786266.1| 312 CPHCGLSLPEsGPPLCPGCGTPL 334
                                       ********8648888*******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 ?   11.9   6.7   6.8e-05      0.11       5      26 .]     312     334 .]     310     334 .] 0.96

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.8e-05
                       zf-ribbon_3   5 CPnCGa.plssddnvCpyCGtkl 26 
                                       CP+CG  +++s+ + Cp CGt+l
  gi|344210090|ref|YP_004786266.1| 312 CPHCGLsLPESGPPLCPGCGTPL 334
                                       ******99*************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 ?    2.3   0.0     0.044        71     110     154 ..      85     127 ..      48     131 .. 0.76
   2 ?    7.5   0.0    0.0012       1.9     221     251 ..     211     241 ..     192     301 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.044
                              IFRD 110 itlgagdeseeileelkpvLkriikdssvslsakaaaieaLgllt 154
                                       +t+   +++ + +  ++p+L + + d+s  + ++a ++eaLg ++
  gi|344210090|ref|YP_004786266.1|  85 VTVS--ESAPDSVVPVVPTLAERLADESEFYYVRARCAEALGYVA 127
                                       5533..33334455567778888888887899**********876 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0012
                              IFRD 221 eealealvelLdssdvevriAAGeaiALlfE 251
                                        +a ealv++L+++++ vr  A ea++Ll  
  gi|344210090|ref|YP_004786266.1| 211 TDAREALVSCLEDESRYVRGRAAEALGLLAG 241
                                       45789***********************965 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0087        14      10      26 .]      15      31 ..      13      31 .. 0.93
   2 ?   -0.7   0.0         2   3.2e+03       6      15 ..     115     124 ..     111     133 .. 0.59
   3 ?    2.1   0.0      0.25   4.1e+02       6      18 ..     159     171 ..     157     172 .. 0.85
   4 ?    3.4   0.5     0.096   1.6e+02      13      24 ..     228     239 ..     224     240 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0087
                             TPR_4 10 allalGdldeAraller 26
                                      +ll++G+ ++A+++ler
  gi|344210090|ref|YP_004786266.1| 15 TLLEQGEKADALTALER 31
                                      699************98 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                             TPR_4   6 aLArallalG 15 
                                       ++Ar + alG
  gi|344210090|ref|YP_004786266.1| 115 VRARCAEALG 124
                                       5555555555 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.25
                             TPR_4   6 aLArallalGdld 18 
                                       a A a+ a G++d
  gi|344210090|ref|YP_004786266.1| 159 AKALAHVAMGRPD 171
                                       6799*******98 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.096
                             TPR_4  13 alGdldeArall 24 
                                        +G+++eA+ ll
  gi|344210090|ref|YP_004786266.1| 228 VRGRAAEALGLL 239
                                       588888888776 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 ?   -1.3   0.7       3.2   5.2e+03       7      27 .]      27      53 ..      22      53 .. 0.59
   2 ?    5.8   0.6     0.017        27       1      21 [.     115     143 ..     115     164 .. 0.71
   3 ?    2.8   0.0      0.16   2.6e+02       7      27 .]     197     223 ..     191     223 .. 0.73
   4 ?    7.0   0.2    0.0068        11       1      19 [.     228     246 ..     228     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.2
                                      HHHHHCTS......GGGHHHHHHHCTC CS
                          HEAT_PBS  7 kaLgqlgd......eeaipaLleaLqd 27
                                       aL +l        ++++  L++a +d
  gi|344210090|ref|YP_004786266.1| 27 TALERLSMagaadqQACLRSLKAAADD 53
                                      455554445555567777777777765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHCTS........GGGHHHH CS
                          HEAT_PBS   1 vRraAakaLgqlgd........eeaipaL 21 
                                       vR+++a+aLg +          +e+++ L
  gi|344210090|ref|YP_004786266.1| 115 VRARCAEALGYVAVdhpdavvsPEVVADL 143
                                       8*********9998887777774444444 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.16
                                       HHHHHCTS......GGGHHHHHHHCTC CS
                          HEAT_PBS   7 kaLgqlgd......eeaipaLleaLqd 27 
                                        aL  +g+      ++a +aL+ +L+d
  gi|344210090|ref|YP_004786266.1| 197 TALVVIGSacperlTDAREALVSCLED 223
                                       56666666777777899********98 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0068
                                       HHHHHHHHHHHCTSGGGHH CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaip 19 
                                       vR +Aa+aLg l  + +++
  gi|344210090|ref|YP_004786266.1| 228 VRGRAAEALGLLAGTKSVE 246
                                       8*********999866665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1927.13
//
Query:       gi|344210091|ref|YP_004786267.1|  [L=173]
Description: hypothetical protein HAH_5150 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   0.6      3e-15   56.4   0.0    1.9  2  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 !    2.3   0.1    0.0065   1.2e+02       3      42 ..       7      45 ..       5      63 .. 0.86
   2 !   56.4   0.0   1.7e-19     3e-15      84     189 .]      71     169 ..      63     169 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.0065
                           LUD_dom  3 efienleangaevyyaktaeealelilellkeksvvsegg 42
                                       f+++lea g++v  +++  ++ +++ e + e  v++   
  gi|344210091|ref|YP_004786267.1|  7 SFEDALEALGVTVSSTAE-SDLEAAVTEAVTEPAVGIALD 45
                                      58999*************.********9999998876654 PP

  == domain 2  score: 56.4 bits;  conditional E-value: 1.7e-19
                           LUD_dom  84 tadvgitganfaiAetGtlvlvdnegnrraltflpkvhivvvginkivpdledavkrlktaprnatrlqkktpyvsf 160
                                       +a +g+tga+ +i + G+lvl  +e+   +l++  + h++++  + i pd++ av+ l +      r +++   + +
  gi|344210091|ref|YP_004786267.1|  71 EATTGVTGAELGIGDYGSLVLSMTEEASELLSLFVERHVAILHEEDIQPDMDAAVAELDE------RFNETGGSAII 141
                                       799*********************************************************......77777788888 PP

                           LUD_dom 161 isgpsrtadielvlvygvhgpkrihvilv 189
                                        +gps tad    lv+g+hgpk++hvi+v
  gi|344210091|ref|YP_004786267.1| 142 ATGPSATADMG-ALVKGAHGPKEVHVIIV 169
                                       8********77.999************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1011.52
//
Query:       gi|344210092|ref|YP_004786268.1|  [L=728]
Description: 4Fe-S protein [Haloarcula hispanica ATCC 33960]
Scores for 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-42  143.7   0.2      1e-41  142.8   0.2    1.5  1  LUD_dom   LUD domain
    1.6e-08   34.9   3.0    3.5e-08   33.8   3.0    1.6  1  Fer4_8    4Fe-4S dicluster domain
      7e-08   32.5   3.7    0.00024   21.1   0.2    2.4  2  Fer4_10   4Fe-4S dicluster domain
    8.1e-07   29.1   3.3      2e-06   27.9   3.3    1.7  1  Fer4_9    4Fe-4S dicluster domain
    8.5e-07   29.4   2.1    1.6e-06   28.5   2.1    1.5  1  Fer4_17   4Fe-4S dicluster domain
      2e-06   28.3   5.6    4.7e-06   27.1   5.6    1.7  1  Fer4_7    4Fe-4S dicluster domain
     0.0001   22.5   1.0      0.013   15.7   0.1    2.5  2  Fer4_18   4Fe-4S dicluster domain
    0.00016   21.3  13.8    0.00021   21.0   3.5    2.4  2  Fer4      4Fe-4S binding domain
    0.00025   21.0   2.7    0.00025   21.0   2.7    2.5  2  Fer4_6    4Fe-4S binding domain
    0.00026   21.0   8.8     0.0014   18.7   8.8    2.1  1  Fer4_21   4Fe-4S dicluster domain
     0.0011   19.8   3.7       0.04   14.9   0.6    2.6  2  Fer4_16   4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
       0.01   15.9  15.3       0.04   14.0   4.3    2.5  2  Fer4_2    4Fe-4S binding domain
       0.03   14.8   3.2       0.03   14.8   3.2    2.4  2  Fer4_4    4Fe-4S binding domain
      0.041   14.8   5.9      0.041   14.8   5.9    2.5  2  Fer4_3    4Fe-4S binding domain
      0.052   13.3   3.4        0.1   12.4   0.2    2.4  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
       0.11   13.4   7.8       0.11   13.3   1.0    2.4  2  Fer4_22   4Fe-4S dicluster 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 !  142.8   0.2     9e-45     1e-41       1     166 [.      63     273 ..      63     300 .. 0.96

  Alignments for each domain:
  == domain 1  score: 142.8 bits;  conditional E-value: 9e-45
                           LUD_dom   1 leefienleangaevyyaktaeealelilellkeksv.......................vseggstdlgeigl... 51 
                                       l++++e +ean ++vy+a++a++a+++i+++++e+ +                       ++ +++tdlge+ l   
  gi|344210092|ref|YP_004786268.1|  63 LDQLTETVEANRGTVYIADDAADANDYIRDVVDERAAdrvvksksmtseeievnealeadGVDVVETDLGEWVLqva 139
                                       5799*******************************99**************************************** PP

                           LUD_dom  52 ........apalhsgreevldlfeekl............treareelrekfltadvgitganfaiAetGtlvlvdne 108
                                               apa+h+ re +++lf+e++            tr+ar++l e++ +a+vgitganf+ A+tGt+ lv++e
  gi|344210092|ref|YP_004786268.1| 140 deapshivAPAIHKSRESIAELFNERFepdepletaeelTRFARKKLGEQIIDAEVGITGANFVTADTGTMALVTSE 216
                                       ***************************************************************************** PP

                           LUD_dom 109 gnrraltflpkvhivvvginkivpdledavkrlktaprnatrlqkktpyvsfisgpsr 166
                                       gn+r ++ + ++h++v+g++k+ p++ d+  +++++ r++t+ q++t+yvs+ + p  
  gi|344210092|ref|YP_004786268.1| 217 GNARKTVAATDTHVAVAGVEKVIPTVGDLHPFIELIGRSGTG-QDITSYVSLLTPPVD 273
                                       ******************************************.*********988755 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   3.0   3.1e-11   3.5e-08       3      65 .]     317     384 ..     315     384 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 3.1e-11
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvlee.....eealwsCttcgaCtevCpvgi 65 
                                        +Ci+C+aC ++C  +++ + h +  +    + +  +++  e     ee  + Ct+c +C+++Cpvgi
  gi|344210092|ref|YP_004786268.1| 317 LYCIRCSACSNSCANFQSVGGHAFGGETYSGGIATGWEAGIEgldvaEEFNDLCTGCTRCVNACPVGI 384
                                       68***********99999886666555554442334444334466668899***************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 !   11.8   0.4   0.00018       0.2       7      31 ..     317     340 ..     311     352 .. 0.78
   2 !   21.1   0.2   2.2e-07   0.00024       7      24 ..     368     391 ..     363     411 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                           Fer4_10   7 dtCirCgkCvkaCPadltsvgakge 31 
                                         CirC +C ++C a+++svg+ ++
  gi|344210092|ref|YP_004786268.1| 317 LYCIRCSACSNSC-ANFQSVGGHAF 340
                                       57***********.87777766555 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 2.2e-07
                           Fer4_10   7 dtCirCgkCvkaCPadl......t 24 
                                       d C++C++Cv+aCP+ +      t
  gi|344210092|ref|YP_004786268.1| 368 DLCTGCTRCVNACPVGIdipwinT 391
                                       78*************776666431 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   3.3   1.8e-09     2e-06       1      49 [.     318     383 ..     318     384 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.8e-09
                            Fer4_9   1 kCtgCgaCveaC.pagvvvedaaerkarlraase................eaCigCgaCveaCpkg 49 
                                       +C++C aC ++C +++ v ++a++++                        + C+gC +Cv+aCp g
  gi|344210092|ref|YP_004786268.1| 318 YCIRCSACSNSCaNFQSVGGHAFGGETYSGGIATgweagiegldvaeefnDLCTGCTRCVNACPVG 383
                                       6***********9666666666666666555544667778888888889999************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 !   28.5   2.1   1.5e-09   1.6e-06       2      61 .]     319     385 ..     318     385 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.5e-09
                           Fer4_17   2 CiqCgyClpeCpsyea.......ydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgld 61 
                                       Ci+C++C ++C  ++         +++   ++  +++g+ +   +ee  +lC++C +C+ +CP g+d
  gi|344210092|ref|YP_004786268.1| 319 CIRCSACSNSCANFQSvgghafgGETYSGGIATGWEAGIEGLDVAEEFNDLCTGCTRCVNACPVGID 385
                                       *************999666443222245578888888766666677999**************9987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   5.6   4.2e-09   4.7e-06       2      52 .]     319     384 ..     318     384 .. 0.64

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4.2e-09
                            Fer4_7   2 CigCgaCvaaC...............pvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       Ci C aC + C                ++ i +  e+  +g + +e   + C+gC++Cv++CP+g+
  gi|344210092|ref|YP_004786268.1| 319 CIRCSACSNSCanfqsvgghafggetYSGGIATGWEAGIEGLDVAEEFNDLCTGCTRCVNACPVGI 384
                                       ***********544444444433333122222222334446577788899**************96 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.027        30      54      96 ..     312     330 ..     279     339 .. 0.63
   2 !   15.7   0.1   1.1e-05     0.013      58      77 ..     367     386 ..     342     389 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.027
                           Fer4_18  54 kekgagdcidcescvkvcPtgidirkGlqleciscllcidacd 96 
                                       + +++  ci c++c + c                         
  gi|344210092|ref|YP_004786268.1| 312 QLRETLYCIRCSACSNSC------------------------A 330
                                       344444555555555555........................4 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.1e-05
                           Fer4_18  58 agdcidcescvkvcPtgidi 77 
                                       +  c+ c  cv+ cP+gidi
  gi|344210092|ref|YP_004786268.1| 367 NDLCTGCTRCVNACPVGIDI 386
                                       445****************9 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   2.7     0.016        18       7      18 ..     318     329 ..     316     329 .. 0.93
   2 !   21.0   3.5   1.9e-07   0.00021       5      21 ..     367     383 ..     364     384 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.016
                                       TSSS-THHHHHS CS
                              Fer4   7 kCigCGaCvevC 18 
                                        Ci+C aC + C
  gi|344210092|ref|YP_004786268.1| 318 YCIRCSACSNSC 329
                                       5*********99 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 1.9e-07
                                       TTTSSS-THHHHHSTTT CS
                              Fer4   5 eekCigCGaCvevCPvg 21 
                                        ++C+gC +Cv++CPvg
  gi|344210092|ref|YP_004786268.1| 367 NDLCTGCTRCVNACPVG 383
                                       599*************8 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.8     0.079        88       9      19 ..     319     329 ..     318     334 .. 0.91
   2 !   21.0   2.7   2.2e-07   0.00025       6      22 ..     367     383 ..     362     384 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.079
                            Fer4_6   9 CigCgdCvrvC 19 
                                       Ci C +C + C
  gi|344210092|ref|YP_004786268.1| 319 CIRCSACSNSC 329
                                       *********99 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.2e-07
                            Fer4_6   6 pdkCigCgdCvrvCPeg 22 
                                        d+C+gC +Cv++CP g
  gi|344210092|ref|YP_004786268.1| 367 NDLCTGCTRCVNACPVG 383
                                       69*************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 !   18.7   8.8   1.2e-06    0.0014       7      53 ..     318     382 ..     314     386 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
                           Fer4_21   7 kCigCgkCliaCedtshqai....................eidaktvlkvvedeCvGCnlCssvCPv 53 
                                        Ci C  C  +C +   q +                     i++  v++  +d C+GC+ C++ CPv
  gi|344210092|ref|YP_004786268.1| 318 YCIRCSACSNSCAN--FQSVgghafggetysggiatgweaGIEGLDVAEEFNDLCTGCTRCVNACPV 382
                                       5***********96..888877755665555544444333233334447789**************9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.042        47       2      12 ..     319     329 ..     288     333 .. 0.79
   2 !   14.9   0.6   3.5e-05      0.04       2      15 ..     370     383 ..     369     406 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.042
                           Fer4_16   2 CgtCgkCaevC 12 
                                       C++C +C ++C
  gi|344210092|ref|YP_004786268.1| 319 CIRCSACSNSC 329
                                       67777777766 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.5e-05
                           Fer4_16   2 CgtCgkCaevCPtn 15 
                                       C++C++C+++CP++
  gi|344210092|ref|YP_004786268.1| 370 CTGCTRCVNACPVG 383
                                       ************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 ?    7.0   3.2    0.0062         7      10      20 ..     319     329 ..     313     331 .. 0.88
   2 ?   14.0   4.3   3.6e-05      0.04       8      21 ..     368     381 ..     365     382 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0062
                            Fer4_2  10 CigCgaCvsaC 20 
                                       Ci+C+aC ++C
  gi|344210092|ref|YP_004786268.1| 319 CIRCSACSNSC 329
                                       ********99* PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.6e-05
                            Fer4_2   8 drCigCgaCvsaCP 21 
                                       d C+gC  Cv+aCP
  gi|344210092|ref|YP_004786268.1| 368 DLCTGCTRCVNACP 381
                                       78************ PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   2.8     0.072        81       4      14 ..     319     329 ..     314     333 .. 0.93
   2 ?   14.8   3.2   2.7e-05      0.03       2      17 .]     368     383 ..     367     383 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.072
                            Fer4_4   4 CigCgsCvaaC 14 
                                       Ci+C +C ++C
  gi|344210092|ref|YP_004786268.1| 319 CIRCSACSNSC 329
                                       **********9 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.7e-05
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       + C+gC +Cv+aCP+g
  gi|344210092|ref|YP_004786268.1| 368 DLCTGCTRCVNACPVG 383
                                       67************86 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   4.1     0.066        74       1      11 [.     319     329 ..     319     331 .. 0.95
   2 ?   14.8   5.9   3.7e-05     0.041       1      14 [.     370     383 ..     370     384 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.066
                            Fer4_3   1 CtgCgaCvevC 11 
                                       C+ C+aC ++C
  gi|344210092|ref|YP_004786268.1| 319 CIRCSACSNSC 329
                                       *********** PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.7e-05
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       CtgC +Cv++CPvg
  gi|344210092|ref|YP_004786268.1| 370 CTGCTRCVNACPVG 383
                                       *************9 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 ?    0.7   0.4      0.37   4.2e+02      11      37 ..     306     330 ..     300     337 .. 0.79
   2 ?   12.4   0.2     9e-05       0.1      24      55 ..     370     398 ..     359     402 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.37
                                       ---HHHHHHHHTT----TT-HHHHCST CS
                           Fer4_20  11 glteeealeeAsRClqCkkapcvkgCP 37 
                                       +++++e l+e   C++C  + c+++C 
  gi|344210092|ref|YP_004786268.1| 306 EMRDDEQLRETLYCIRC--SACSNSCA 330
                                       56677888999999999..77888885 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 9e-05
                                       ----TT-HHHHCSTT---HHHHHHHHHTT-HH CS
                           Fer4_20  24 ClqCkkapcvkgCPveidipefikkiaegnle 55 
                                       C  C  + cv++CPv idip +i+++ +++++
  gi|344210092|ref|YP_004786268.1| 370 CTGC--TRCVNACPVGIDIP-WINTVVRDRIN 398
                                       9999..89***********9.99999887765 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.9      0.14   1.6e+02       2      13 ..     319     330 ..     308     335 .. 0.79
   2 ?   13.3   1.0    0.0001      0.11      80      96 .]     368     384 ..     360     384 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.14
                           Fer4_22   2 ClsCgaCtlvCp 13 
                                       C++C+aC+  C+
  gi|344210092|ref|YP_004786268.1| 319 CIRCSACSNSCA 330
                                       777888877775 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.0001
                           Fer4_22  80 sgCvGCgRCieacpvki 96 
                                         C+GC RC++acpv+i
  gi|344210092|ref|YP_004786268.1| 368 DLCTGCTRCVNACPVGI 384
                                       68************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (728 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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):              16  [number of targets reported over threshold]
# CPU time: 0.77u 0.33s 00:00:01.10 Elapsed: 00:00:00.54
# Mc/sec: 4043.62
//
Query:       gi|344210093|ref|YP_004786269.1|  [L=432]
Description: hypothetical protein HAH_5152 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   21.6   0.0    0.00041   20.6   0.0    1.4  1  DUF362    Domain of unknown function (DUF362)
    0.00042   19.6   0.0    0.00065   18.9   0.0    1.2  1  Lar_N     Lactate racemase N-terminal domain


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 !   20.6   0.0   4.6e-08   0.00041      20     160 ..      84     224 ..      74     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.6e-08
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DUF362  20 pevvravvellkeagagkiivgdspglyv.srgkahrevaeeagydelaegadiadglegedevvvpvkgkhlkkel 95 
                                       p++v++v++++ +ag  +++v+ + g +  ++g+  r  ++e g++e a g++i+   +     vv+v g++  +++
  gi|344210093|ref|YP_004786269.1|  84 PTIVAGVADAVSDAG-YEPFVFPAMGSHGgATGEGQRTMLNELGVTESAIGCEIRSTMD-----VVEV-GRTPDRDV 153
                                       899**********99.68********7542445559999********999**9865443.....3333.55445555 PP

                                       xx.xxx.xxxxxxxxxxxxxxxxxx.xx..xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DUF362  96 ki.aka.vleaDviInlpklKgHal.ag..vtgalKn.lfGcisgsgkaeiHskrdsekfaekiadlakal 160
                                        + a + ++ aD+iI + ++K H    g   +g  K   +G+  ++g +  H++  +++f ++i +++  l
  gi|344210093|ref|YP_004786269.1| 154 PVvADDtAVAADAIIPINRVKPHTDfDGpvESGLSKMlVIGMGKQRGAQIAHKWAVDWSFRRMIPEITGQL 224
                                       551555789**************9853355344556669999999999****8884677999999998773 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 !   18.9   0.0   7.3e-08   0.00065      93     196 ..     103     209 ..      81     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.3e-08
                             Lar_N  93 ilvAtGlHrkqteeelkkilGeevvkrikvvnhdaedksslvklGtts.kGtpveinklvaeadlviltGfiepHy. 167
                                       +  A G+H  +t e  + +l  e+   ++ +  + + + ++v++G+t+ +  pv+   +++ ad +i ++ ++pH  
  gi|344210093|ref|YP_004786269.1| 103 VFPAMGSHGGATGEGQRTMLN-ELGVTESAIGCEIRSTMDVVEVGRTPdRDVPVVADDTAVAADAIIPINRVKPHTd 178
                                       45699*********9999998.77888888888999***********73589***********************64 PP

                             Lar_N 168 faGf..sGGrKsilpGvasretimanHkavl 196
                                       f G   sG +K +++G+++++  +  Hk ++
  gi|344210093|ref|YP_004786269.1| 179 FDGPveSGLSKMLVIGMGKQRGAQIAHKWAV 209
                                       7674448889999999999999999998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2610.55
//
Query:       gi|344210094|ref|YP_004786270.1|  [L=444]
Description: hydroxypyruvate reductase; glycerate kinase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-70  236.4   1.1    3.8e-70  236.0   1.1    1.2  1  DUF4147   Domain of unknown function (DUF4147)
    1.9e-25   89.1   7.7    1.9e-25   89.1   7.7    2.1  2  MOFRL     MOFRL family


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 !  236.0   1.1   4.3e-74   3.8e-70       2     229 .]      17     250 ..      16     250 .. 0.95

  Alignments for each domain:
  == domain 1  score: 236.0 bits;  conditional E-value: 4.3e-74
                                       HHHHHHHHHHTTSHHHHHHTTHHHH--..............-SEEEEEESTTHHHHHHHHH....HHHGEEEEEEET CS
                           DUF4147   2 lraifeaaveavdpeklvkralslkee.......eldlskkkrvvvvgaGKAaaamaaalee...ealksgvvvvkk 68 
                                       + +++eaa++a+ p+ ++++a+s++ e       ++dl+++++vvvvg GKAa ++ +ale+   ++l++g vvvk+
  gi|344210094|ref|YP_004786270.1|  17 ALDCIEAAIDAAAPDVATRSAVSREGEtltigetTYDLDSYSDVVVVGGGKAAGGVTRALESilgDRLSGGHVVVKQ 93 
                                       5689******************9944456666679**************************98888899******84 PP

                                       T-----TT-EEEEE-SSS--HHHHHHHHHHHHHHSS--TT-EEEEEE-TTHHHHS--B-TT--HHHHHHHHHHHHHC CS
                           DUF4147  69 ghaeekerievleaahplPdeesveaarkilelaeklkeddlvlvliSGGgSAllaaPaegitledkqaltkaLlas 145
                                         a+++++++   ++hplP+++ vea+++ile++++++ed+lvl++++GG+SAll+aPa ++tle +q++t++Ll+ 
  gi|344210094|ref|YP_004786270.1|  94 --AADTDTVRSSVGDHPLPSDRNVEATTDILETVDDADEDTLVLFVLTGGASALLSAPAGELTLEALQTTTDRLLSG 168
                                       ..478899999****************************************************************** PP

                                       T--HHHHHHHHHTTBSSTTTHHHHHHTTSEEEEEEE--STT--TTTGGG-TTS-----HHHHHHHHHHTT---..-H CS
                           DUF4147 146 GasIqelNtVRkhlsaikGGrLaraaaparvvsLilSDVvgddldvIASGPtvpdsstfadalailekykleeklpe 222
                                       G++I+e+N+VRkhls++kGG++ar aapa+v  L+lSDVvg+d ++I+SGP vpd++t++dala++++y+l+   p+
  gi|344210094|ref|YP_004786270.1| 169 GVAIEEINAVRKHLSDLKGGQIARRAAPATVAGLLLSDVVGNDRSTIGSGPSVPDETTYEDALAVFDRYDLT--PPP 243
                                       ***********************************************************************9..7** PP

                                       HHHHHH. CS
                           DUF4147 223 svrelLe 229
                                       +vr++Le
  gi|344210094|ref|YP_004786270.1| 244 AVRKHLE 250
                                       *****96 PP

>> MOFRL  MOFRL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2       0.5   4.5e+03       6      29 ..      47      75 ..      44      99 .. 0.44
   2 !   89.1   7.7   2.2e-29   1.9e-25       2     109 .]     334     433 ..     333     433 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.5
                                      EE--B----S-.....----HHHHHHHHH CS
                             MOFRL  6 gGEttvtvkgk.....GkGGrnqelalal 29
                                       GEtt  + +        GG++   + ++
  gi|344210094|ref|YP_004786270.1| 47 IGETTYDLDSYsdvvvVGGGKAAGGVTRA 75
                                      57777777433455553344444333333 PP

  == domain 2  score: 89.1 bits;  conditional E-value: 2.2e-29
                                       EEEEEE--B----S-.----HHHHHHHHHHH...HTTT-TTEEEEEEETTS--SSSS--EEEEETTHHHHHHHTT-- CS
                             MOFRL   2 vllsgGEttvtvkgk.GkGGrnqelalalalelkelegaeevvllsagtDGiDGptdaaGaivdaetleraeaagld 77 
                                       vll+gGEttvtv+g+ G+GG+nqe++ + al     ++  ++v+++++tDG DG++ +aGai+da+++++ e+    
  gi|344210094|ref|YP_004786270.1| 334 VLLAGGETTVTVTGDgGQGGPNQEFVRSGAL-----DHGGDAVIAAVDTDGEDGSSVVAGAIADATVIDDRER---- 401
                                       89***********9999**************.....335789**************************98776.... PP

                                       HHHHHHTT-HHHHHHHTT-EE-----S----E CS
                             MOFRL  78 akeaLanndsyeffeklgallktgpTgtNVnD 109
                                       a+eaL +nd+ ++++++ga+++tgpTgtNVnD
  gi|344210094|ref|YP_004786270.1| 402 AREALLANDAGSYLSAVGATVETGPTGTNVND 433
                                       79*****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); 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: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 2468.64
//
Query:       gi|344210095|ref|YP_004786271.1|  [L=356]
Description: putative glycosyl hydrolase family 88 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-57  195.7   0.0    1.4e-57  195.4   0.0    1.1  1  Glyco_hydro_88   Glycosyl Hydrolase Family 88
  ------ inclusion threshold ------
      0.076   11.5   0.0       0.11   10.9   0.0    1.2  1  Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127


Domain annotation for each model (and alignments):
>> Glyco_hydro_88  Glycosyl Hydrolase Family 88
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.4   0.0   1.5e-61   1.4e-57      29     337 ..      27     352 ..       3     355 .. 0.84

  Alignments for each domain:
  == domain 1  score: 195.4 bits;  conditional E-value: 1.5e-61
                                       HHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHCCCTTS-...........................CTTSGGGTGHH CS
                    Glyco_hydro_88  29 wtnGvflsglleayeatgdkeyldyakawadslideggk...........................telelDdidig 78 
                                       w  Gv+++gll+  +     + +d++++ + ++ d+g+                             +   ++ +ig
  gi|344210095|ref|YP_004786271.1|  27 WITGVAINGLLAEGSEQSVTAAKDLVDRAVATQDDNGQLgygpsypievfshgreyeasweltvkkCMNTNNTTAIG 103
                                       6666666666655554444455555544444433333335555555556666666666666666545556678899* PP

                                       HHHHHHHHHH-THHHHHHHHHHHHHHHHCS-B.TTS.B.S...BTTSTTEEETHHHHHHHHHHHHHHHHHCGTHHHH CS
                    Glyco_hydro_88  79 llllllyeltkderykeaaeeladyvlakpprtseGgfwh...kkkepeqlWlDgLfMaipllaklskvtgepkyld 152
                                       +  l+ ye t+dery  aa+  ++  l+   rt+ Gg  h   +    + lW+D  +M +p+  ++++   ep+  d
  gi|344210095|ref|YP_004786271.1| 104 HGVLDFYERTGDERYLDAARGEYE-WLQSVDRTETGGIPHhdpEVAGIKSLWIDSVYMMCPFFSRYAEAADEPAAHD 179
                                       ************************.788************6665566789*************************** PP

                                       HHHHHHHHHHHHHBETTTSEB-SEEETTTTSTTS.--BHHHHHHHHHHHHHHHHHS-TT-TTHHHHHHHHHHHHHHH CS
                    Glyco_hydro_88 153 eaikqflltarhlfdpetGlyyhgwdesgtedwakefWaRgngWalaglaevlelLpekekarqelinllrdlvkal 229
                                       ea+ q+l +a+hl dp tGl++h w e + + +  +fWaRgngWa+a+++e+l+ Lp ++ +r++l + +rd++++l
  gi|344210095|ref|YP_004786271.1| 180 EAVTQYLVHAEHLRDPRTGLFRHIWVETPDHYPQGAFWARGNGWAAAAAVEILDRLPDDHDQREDLVERFRDHCESL 256
                                       ******************************999999***************************************** PP

                                       HCTS-TTSSEBSBTT-TTTTSSBEHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHCEE-TTS-EEE-SEE CS
                    Glyco_hydro_88 230 aklqdeeglWhqilddgskesylEtSatalfvygLakgvnkglldkkkykkvaqkawkallkkaveedGqllvkqvs 306
                                         lqd +g+Wh ++dd +    lE+S+t +f+y+  +g++ glld+ +y+++a  a++a+    v+++G    ++ +
  gi|344210095|ref|YP_004786271.1| 257 LPLQDGSGFWHNLVDDTD--TPLESSGTLMFAYAFNRGIELGLLDESQYRDSADDALDAVTHV-VDDEGA---VGRV 327
                                       ******************..*******************************************.******...5555 PP

                                       TS--SCTCHHHHTS-EESS-HHHHHHHHHHH CS
                    Glyco_hydro_88 307 vgtgiggddyYksvdvnsiedygvgafllal 337
                                       +g + gg     + + + + +yg+g++l+a+
  gi|344210095|ref|YP_004786271.1| 328 AGPP-GG----PEAPLTVT-PYGQGWYLMAA 352
                                       6666.56....57787777.*********96 PP

>> Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   1.3e-05      0.11      60     161 ..      22     133 ..       4     147 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHHH.HHHH--HHHHHHHHHHHHHHHHHCH...SSS-B-GCCTHH...SSEETTEESH...----HHH CS
                   Glyco_hydro_127  60 gdlgkwleavall.lastkdkelekrldrlvdelakaQq...edGYlsavtelk...neakkeawap...dshelYn 126
                                        d   w+ +va   l +++ ++  + ++ lvd+  + Q+   + GY  +++       ++ + +w     +++++ n
  gi|344210095|ref|YP_004786271.1|  22 LDGKSWITGVAINgLLAEGSEQSVTAAKDLVDRAVATQDdngQLGYGPSYPIEVfshGREYEASWELtvkKCMNTNN 98 
                                       55567888887542677778888888888999888889833333444444444466544555555556655888888 PP

                                       HHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHH CS
                   Glyco_hydro_127 127 lgkliegavayyqatgkeklldvatrladyleevl 161
                                          +  g ++ y+ tg+e+ ld+a    ++l++v+
  gi|344210095|ref|YP_004786271.1|  99 TTAIGHGVLDFYERTGDERYLDAARGEYEWLQSVD 133
                                       88888899999999999999999988888886554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2387.99
//
Query:       gi|344210096|ref|YP_004786272.1|  [L=385]
Description: hypothetical protein HAH_5155 [Haloarcula hispanica ATCC 33960]
Scores for 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-29   99.8  22.2    5.8e-10   39.6   1.9    5.5  5  VCBS             Repeat domain in Vibrio, Colwellia, Bradyrhi
      3e-22   78.4  30.3      0.018   15.2   0.0    7.3  7  FG-GAP           FG-GAP repeat
    4.2e-08   32.8   7.6       0.22   10.9   0.0    6.1  7  TcdB_toxin_midN  Insecticide toxin TcdB middle/N-terminal reg
    3.4e-06   26.8   5.1        6.2    6.6   0.0    6.3  7  PliI             Periplasmic lysozyme inhibitor of I-type lys
    5.5e-05   22.4   7.2        1.3    8.0   0.2    5.1  5  Itfg2            Integrin-alpha FG-GAP repeat-containing prot
    0.00024   21.1   2.6        3.8    7.6   0.0    5.0  5  BBS2_Mid         Ciliary BBSome complex subunit 2, middle reg


Domain annotation for each model (and alignments):
>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   1.5   2.8e-10   8.4e-07       1      61 []      31     117 ..      31     117 .. 0.88
   2 !   39.6   1.9   1.9e-13   5.8e-10       1      60 [.     106     168 ..     106     169 .. 0.88
   3 !   12.5   0.3   5.9e-05      0.18      36      60 ..     198     222 ..     184     223 .. 0.79
   4 !   20.6   5.0   1.7e-07    0.0005       1      60 [.     212     263 ..     212     264 .. 0.90
   5 !   33.6   0.1   1.5e-11   4.4e-08       1      60 [.     306     369 ..     299     370 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 2.8e-10
                              VCBS   1 DldgDGrlDlvvandgg...........................lrvyrnngdGtftdvtktslggsgggtgvavgD 50 
                                       Dl g+Gr+D++v+++gg                           ++++++++ G ++  t  + ++ + g+g +++D
  gi|344210096|ref|YP_004786272.1|  31 DLTGNGRPDIIVTGMGGnptisvagnriqvpthgplsrvtprleTNIFWYENPG-WERHTLATETDLHPGVGTDLAD 106
                                       99***********96555899999999*****************9999999776.77777766666777899***** PP

                              VCBS  51 lDgDGdlDllv 61 
                                       +DgDG  Dl+v
  gi|344210096|ref|YP_004786272.1| 107 IDGDGNVDLVV 117
                                       *********98 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 1.9e-13
                              VCBS   1 DldgDGrlDlvvan.dgglrvyrnngdGtftdvtkt..slggsgggtgvavgDlDgDGdlDll 60 
                                       D+dgDG  Dlvv++  g+ +vy++++  + td++++  +++    ++ + v+D+D+DGd++l+
  gi|344210096|ref|YP_004786272.1| 106 DIDGDGNVDLVVGQgFGRSNVYWYEQPESPTDPWQQhlISDRFEKYHDLLVADVDNDGDAELI 168
                                       9************768**********9999999998434444888889************996 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 5.9e-05
                              VCBS  36 slggsgggtgvavgDlDgDGdlDll 60 
                                       +++++ ++ g+av+D+DgDG  +++
  gi|344210096|ref|YP_004786272.1| 198 IIDEDIRIEGLAVADIDGDGTKEVV 222
                                       5555667779**********99987 PP

  == domain 4  score: 20.6 bits;  conditional E-value: 1.7e-07
                              VCBS   1 DldgDGrlDlvvandgglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDll 60 
                                       D+dgDG  ++v+++    +vy+++ +G++      ++ ++++ t v+v+DlD DG ++++
  gi|344210096|ref|YP_004786272.1| 212 DIDGDGTKEVVAGT----NVYHHD-NGDWVR---SDVCTGWDDTRVTVADLDQDGTPEII 263
                                       9***********87....89***9.788875...47899999****************98 PP

  == domain 5  score: 33.6 bits;  conditional E-value: 1.5e-11
                              VCBS   1 DldgDGrlDlvva......n.dgglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDll 60 
                                       Dl g+G++D++v+      n +    v++n gdG f+d t +s+ +    + + ++D++gDG+lD++
  gi|344210096|ref|YP_004786272.1| 306 DLTGNGYPDIYVGemslgeNaSPEQLVFENLGDGEFRDHTVVSGIP---THEAQLVDMNGDGKLDIV 369
                                       99***********99887643566999*********9977654444...45799***********97 PP

>> FG-GAP  FG-GAP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0     2e-05     0.061       3      25 ..      25      48 ..      24      60 .. 0.76
   2 !   12.8   4.8   3.3e-05     0.099       5      28 ..     102     121 ..      98     127 .. 0.81
   3 !    7.8   2.8    0.0012       3.7       5      19 ..     154     168 ..     152     169 .. 0.90
   4 !   13.1   1.6   2.7e-05     0.081       4      24 ..     207     225 ..     206     234 .. 0.80
   5 !   14.2   0.0   1.2e-05     0.036       5      33 ..     249     278 ..     247     282 .. 0.74
   6 !   15.2   0.0     6e-06     0.018       4      24 ..     301     319 ..     299     328 .. 0.84
   7 !   12.8   0.0   3.3e-05     0.098       6      19 ..     356     369 ..     353     375 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                                      SSEEEESTSSSSS-EEEEEE.TT- CS
                            FG-GAP  3 yslavgDvNGDGyaDLavGA.pes 25
                                      +sl ++D+ G G +D++v+  +++
  gi|344210096|ref|YP_004786272.1| 25 SSLETTDLTGNGRPDIIVTGmGGN 48
                                      68999**************53223 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.3e-05
                                       EEEESTSSSSS-EEEEEETT-ETC CS
                            FG-GAP   5 lavgDvNGDGyaDLavGApeskgg 28 
                                         ++D++GDG  DL+vG     g+
  gi|344210096|ref|YP_004786272.1| 102 TDLADIDGDGNVDLVVG----QGF 121
                                       5689*************....554 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0012
                                       EEEESTSSSSS-EEE CS
                            FG-GAP   5 lavgDvNGDGyaDLa 19 
                                       l v+Dv++DG a+L+
  gi|344210096|ref|YP_004786272.1| 154 LLVADVDNDGDAELI 168
                                       789*********997 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 2.7e-05
                                       SEEEESTSSSSS-EEEEEETT CS
                            FG-GAP   4 slavgDvNGDGyaDLavGApe 24 
                                       +lav+D++GDG  +++ G  +
  gi|344210096|ref|YP_004786272.1| 207 GLAVADIDGDGTKEVVAG--T 225
                                       69**********999999..3 PP

  == domain 5  score: 14.2 bits;  conditional E-value: 1.2e-05
                                       EEEESTSSSSS-EEEEEETT.-ETCSTT..BE CS
                            FG-GAP   5 lavgDvNGDGyaDLavGApe.skggayg..Ga 33 
                                       ++v+D+++DG +++++   e +++ ++   G+
  gi|344210096|ref|YP_004786272.1| 249 VTVADLDQDGTPEIILS--EgDSPTYGThpGR 278
                                       89**************9..5455555544565 PP

  == domain 6  score: 15.2 bits;  conditional E-value: 6e-06
                                       SEEEESTSSSSS-EEEEEETT CS
                            FG-GAP   4 slavgDvNGDGyaDLavGApe 24 
                                       sl ++D+ G Gy+D+ vG  e
  gi|344210096|ref|YP_004786272.1| 301 SLQTADLTGNGYPDIYVG--E 319
                                       899***************..3 PP

  == domain 7  score: 12.8 bits;  conditional E-value: 3.3e-05
                                       EEESTSSSSS-EEE CS
                            FG-GAP   6 avgDvNGDGyaDLa 19 
                                        ++D+NGDG+ D++
  gi|344210096|ref|YP_004786272.1| 356 QLVDMNGDGKLDIV 369
                                       579*********98 PP

>> TcdB_toxin_midN  Insecticide toxin TcdB middle/N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.016        49      30      63 ..      26      58 ..       4      73 .. 0.73
   2 !    6.2   0.0     0.002       6.1      25      46 ..      96     117 ..      84     131 .. 0.79
   3 ?   -1.4   0.0      0.44   1.3e+03      31      55 ..     154     181 ..     139     189 .. 0.76
   4 ?    3.1   0.1     0.018        55      31      45 ..     208     222 ..     199     232 .. 0.81
   5 !    7.3   0.1   0.00089       2.7      18      56 ..     236     274 ..     231     294 .. 0.81
   6 ?   -1.0   0.0      0.32   9.5e+02      31      45 ..     302     316 ..     285     322 .. 0.85
   7 !   10.9   0.0   7.5e-05      0.22      16      52 ..     344     376 ..     334     384 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.016
                   TcdB_toxin_midN 30 nlslaDldGdGladlvltipsag.tgavqkatsll 63
                                       l+  Dl G+G +d+++t+ + + t  v  a++++
  gi|344210096|ref|YP_004786272.1| 26 SLETTDLTGNGRPDIIVTGMGGNpTISV--AGNRI 58
                                      48899**********9998887744444..55544 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.002
                   TcdB_toxin_midN  25 svedtnlslaDldGdGladlvl 46 
                                         +++   laD+dGdG  dlv+
  gi|344210096|ref|YP_004786272.1|  96 LHPGVGTDLADIDGDGNVDLVV 117
                                       56778889***********986 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.44
                   TcdB_toxin_midN  31 lslaDldGdGladlvltipsag...tga 55 
                                       l +aD+d dG a+l+ ++  ++   +++
  gi|344210096|ref|YP_004786272.1| 154 LLVADVDNDGDAELIGLSQDSEtvfYYD 181
                                       6789999999999888777766555555 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.018
                   TcdB_toxin_midN  31 lslaDldGdGladlv 45 
                                       l +aD+dGdG+ ++v
  gi|344210096|ref|YP_004786272.1| 208 LAVADIDGDGTKEVV 222
                                       579********9965 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.00089
                   TcdB_toxin_midN  18 irvgtstsvedtnlslaDldGdGladlvltipsagtgav 56 
                                       +r++  t  +dt +++aDld dG+++++l    + t++ 
  gi|344210096|ref|YP_004786272.1| 236 VRSDVCTGWDDTRVTVADLDQDGTPEIILSEGDSPTYGT 274
                                       788999999*****************9988766665554 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 0.32
                   TcdB_toxin_midN  31 lslaDldGdGladlv 45 
                                       l+ aDl G+G +d+ 
  gi|344210096|ref|YP_004786272.1| 302 LQTADLTGNGYPDIY 316
                                       788*********974 PP

  == domain 7  score: 10.9 bits;  conditional E-value: 7.5e-05
                   TcdB_toxin_midN  16 etirvgtstsvedtnlslaDldGdGladlvltipsag 52 
                                       +t+ +g +t+      +l+D++GdG++d+v ++ +++
  gi|344210096|ref|YP_004786272.1| 344 HTVVSGIPTHE----AQLVDMNGDGKLDIVGKSYGPA 376
                                       56666665554....467**********998776655 PP

>> PliI  Periplasmic lysozyme inhibitor of I-type lysozyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.091   2.7e+02      60      78 ..      25      43 ..      20      49 .. 0.88
   2 ?    3.5   0.1     0.019        56      63      79 ..     103     119 ..      99     127 .. 0.86
   3 !    6.6   0.0    0.0021       6.2      32      80 ..     126     172 ..     119     185 .. 0.84
   4 !    5.6   0.2    0.0042        12      54      78 ..     200     224 ..     177     241 .. 0.82
   5 ?    2.2   0.0     0.049   1.5e+02      62      78 ..     249     265 ..     244     272 .. 0.88
   6 ?   -1.9   0.0       0.9   2.7e+03      61      83 ..     301     323 ..     293     334 .. 0.87
   7 ?    2.7   0.1     0.034     1e+02      55      76 ..     342     369 ..     320     379 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.091
                                      EEEEEE-SSSSSS-EEEEE CS
                              PliI 60 eevkladvngdkkkelvvl 78
                                       +++++d+ g+++++++v+
  gi|344210096|ref|YP_004786272.1| 25 SSLETTDLTGNGRPDIIVT 43
                                      57899************97 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.019
                                       EEE-SSSSSS-EEEEEE CS
                              PliI  63 kladvngdkkkelvvlk 79 
                                        lad++gd++ +lvv +
  gi|344210096|ref|YP_004786272.1| 103 DLADIDGDGNVDLVVGQ 119
                                       68************965 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0021
                                       EEEE--SSTTSTTSSEEEEEEEEESSEEEEEEEE-SSSSSS-EEEEEEE CS
                              PliI  32 vrlykkaepdtdldefvaGlvlsRdGsveevkladvngdkkkelvvlkr 80 
                                       v  y+  +p+ ++d + + l+  R    +++ +adv++d+  el+ l +
  gi|344210096|ref|YP_004786272.1| 126 VYWYE--QPESPTDPWQQHLISDRFEKYHDLLVADVDNDGDAELIGLSQ 172
                                       44444..9999999999***************************97655 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.0042
                                       EESSEEEEEEEE-SSSSSS-EEEEE CS
                              PliI  54 sRdGsveevkladvngdkkkelvvl 78 
                                         d  +e + +ad++gd++ke+v  
  gi|344210096|ref|YP_004786272.1| 200 DEDIRIEGLAVADIDGDGTKEVVAG 224
                                       556678889************9965 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.049
                                       EEEE-SSSSSS-EEEEE CS
                              PliI  62 vkladvngdkkkelvvl 78 
                                       v++ad++ d+++e++ +
  gi|344210096|ref|YP_004786272.1| 249 VTVADLDQDGTPEIILS 265
                                       899***********986 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 0.9
                                       EEEEE-SSSSSS-EEEEEEE-SS CS
                              PliI  61 evkladvngdkkkelvvlkrsaG 83 
                                       ++++ad+ g++ +++ v + s G
  gi|344210096|ref|YP_004786272.1| 301 SLQTADLTGNGYPDIYVGEMSLG 323
                                       57899*********999988877 PP

  == domain 7  score: 2.7 bits;  conditional E-value: 0.034
                                       ESSEEEE......EEEE-SSSSSS-EEE CS
                              PliI  55 RdGsvee......vkladvngdkkkelv 76 
                                       Rd +v++      ++l+d+ngd+k ++v
  gi|344210096|ref|YP_004786272.1| 342 RDHTVVSgiptheAQLVDMNGDGKLDIV 369
                                       55555555555569**********9998 PP

>> Itfg2  Integrin-alpha FG-GAP repeat-containing protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.039   1.2e+02     254     279 ..      23      48 ..      21      60 .. 0.86
   2 !    7.4   0.1   0.00064       1.9      84     124 ..     104     144 ..     102     147 .. 0.82
   3 !    8.0   0.2   0.00043       1.3      67     101 ..     135     173 ..     124     190 .. 0.72
   4 !    4.4   0.1    0.0055        16      82      98 ..     208     224 ..     204     236 .. 0.87
   5 ?    1.6   0.1     0.038   1.1e+02      82     101 ..     249     268 ..     245     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.039
                             Itfg2 254 qlfaLekLDvtgdgreEvvaCaWDGq 279
                                       +l +Le  D+tg+gr ++++ +  G+
  gi|344210096|ref|YP_004786272.1|  23 KLSSLETTDLTGNGRPDIIVTGMGGN 48 
                                       699****************9887775 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00064
                             Itfg2  84 iaDidgDgkvElvvgytDrvvrayrWeeseeeeeslskklv 124
                                       +aDidgDg+v+lvvg      ++y +e++e+ ++  +++l+
  gi|344210096|ref|YP_004786272.1| 104 LADIDGDGNVDLVVGQGFGRSNVYWYEQPESPTDPWQQHLI 144
                                       68*************99888888877777777777777765 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00043
                             Itfg2  67 lkpvfsqhlpant....kvvliaDidgDgkvElvvgytD 101
                                        +  ++qhl+++     + +l+aD+d+Dg  El+    D
  gi|344210096|ref|YP_004786272.1| 135 PTDPWQQHLISDRfekyHDLLVADVDNDGDAELIGLSQD 173
                                       55567888887642222679*************854444 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.0055
                             Itfg2  82 vliaDidgDgkvElvvg 98 
                                       + +aDidgDg+ E+v+g
  gi|344210096|ref|YP_004786272.1| 208 LAVADIDGDGTKEVVAG 224
                                       5699**********998 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.038
                             Itfg2  82 vliaDidgDgkvElvvgytD 101
                                       v +aD+d+Dg+ E++++  D
  gi|344210096|ref|YP_004786272.1| 249 VTVADLDQDGTPEIILSEGD 268
                                       679************98776 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.5   1.5e+03      80     103 ..      24      47 ..      21      51 .. 0.79
   2 ?    2.7   0.0     0.042   1.3e+02       4     100 ..     104     119 ..      97     127 .. 0.63
   3 !    5.4   0.1    0.0061        18       2      26 ..     154     178 ..     153     182 .. 0.87
   4 !    7.6   0.0    0.0013       3.8       2      20 ..     208     226 ..     207     233 .. 0.91
   5 ?   -0.5   0.0      0.42   1.3e+03       3      18 ..     250     265 ..     245     270 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.5
                          BBS2_Mid  80 vvalaaydingdgtkelivgwsnG 103
                                       + +l + d++g+g  ++iv+   G
  gi|344210096|ref|YP_004786272.1|  24 LSSLETTDLTGNGRPDIIVTGMGG 47 
                                       567889999999999999876665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.042
                          BBS2_Mid   4 ladvdgdgeneLvvgsddfeirvfkeeelvaeitetekvvslarlekerfayaleNGtvgvyekkerlWrvksknev 80 
                                       lad+dgdg+ +Lvvg                                                              
  gi|344210096|ref|YP_004786272.1| 104 LADIDGDGNVDLVVG-------------------------------------------------------------- 118
                                       455555555555555.............................................................. PP

                          BBS2_Mid  81 valaaydingdgtkelivgw 100
                                                           
  gi|344210096|ref|YP_004786272.1| 119 -------------------Q 119
                                       ...................4 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0061
                          BBS2_Mid   2 laladvdgdgeneLvvgsddfeirv 26 
                                       l++advd+dg++eL+  s+d e   
  gi|344210096|ref|YP_004786272.1| 154 LLVADVDNDGDAELIGLSQDSETVF 178
                                       789************9999998665 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0013
                          BBS2_Mid   2 laladvdgdgeneLvvgsd 20 
                                       la+ad+dgdg++e+v+g++
  gi|344210096|ref|YP_004786272.1| 208 LAVADIDGDGTKEVVAGTN 226
                                       899**************98 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 0.42
                          BBS2_Mid   3 aladvdgdgeneLvvg 18 
                                       ++ad+d+dg+ e++ +
  gi|344210096|ref|YP_004786272.1| 250 TVADLDQDGTPEIILS 265
                                       5777888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2675.51
//
Query:       gi|344210097|ref|YP_004786273.1|  [L=429]
Description: UDP-glucose 6-dehydrogenase/nucleotide sugar dehydrogenase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-43  147.8   0.0    4.2e-43  147.1   0.0    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    3.1e-23   81.8   0.0    5.2e-23   81.1   0.0    1.4  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    9.2e-18   64.6   0.0    2.7e-17   63.1   0.0    1.8  1  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
     0.0036   17.8   0.0        1.7    9.3   0.0    3.3  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0071   16.5   0.0      0.037   14.2   0.0    2.1  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0076   16.1   0.0      0.012   15.6   0.0    1.3  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.021   14.5   0.0    1.3  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.014   14.8   0.0      0.088   12.2   0.0    2.2  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.015   15.6   0.0        1.2    9.4   0.0    2.6  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.023   15.0   0.1       0.18   12.1   0.0    2.5  2  TrkA_N          TrkA-N domain
       0.09   12.8   0.0       0.63   10.0   0.0    2.4  3  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
       0.17   12.5   0.0       0.72   10.4   0.0    2.1  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.1   0.0   2.8e-46   4.2e-43       1     183 [.       4     180 ..       4     184 .. 0.96

  Alignments for each domain:
  == domain 1  score: 147.1 bits;  conditional E-value: 2.8e-46
                                       SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC- CS
                    UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveea 77 
                                       m+++v GlGY+G+ ta ++a+ gh+v+g D d++  ++l++g+  + e +Le++v++a+        + ++ ++  a
  gi|344210097|ref|YP_004786273.1|   4 MRVCVHGLGYIGMATASLFANNGHDVVGFDTDDRVRSQLKRGEPDVSEDQLESYVRAAI-----DSGLTISDEPVPA 75 
                                       89*********************************************************.....455678888999* PP

                                       SEEEE-----B-TTTTCB-THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-TTCEEEEE--- CS
                    UDPG_MGDP_dh_N  78 dvifiaVgTPskkkgkaaDlkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkkgvdfdvvsnPE 154
                                         ++i+V+TP +k+  +aDl+yv++a++++++ l+ ++vvv++STvp+ t+  +v +il +   + g+d+++ + PE
  gi|344210097|ref|YP_004786273.1|  76 AYHIICVPTPYDKSAGSADLRYVKEASQTVSSLLRPNDVVVLESTVPPSTTATVVAPILSQSGLEPGEDIGLGYVPE 152
                                       *************99************************************************************** PP

                                       ---TTSHHHHHHS-S-EEEEESSCHHHHH CS
                    UDPG_MGDP_dh_N 155 flregsavkdllnpdrvviGveekkaeaa 183
                                        +++g+a+ +l  +dr+++G ++ +++ a
  gi|344210097|ref|YP_004786273.1| 153 TMLPGNAITELRSNDRILGGYDSASTA-A 180
                                       *********************999988.4 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 !   81.1   0.0   3.5e-26   5.2e-23       2      93 ..     201     286 ..     200     287 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 3.5e-26
                      UDPG_MGDP_dh   2 tAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaeel 78 
                                       tAE++Kl++Naf++++I+++N la +++ +g++v++ ie ++++pr    +l+pg+GvGG+clp+D+ +L a++++ 
  gi|344210097|ref|YP_004786273.1| 201 TAEFVKLVQNAFRDVNIAYANALALIARDYGVNVRDAIELANSHPR--VDILNPGPGVGGHCLPVDPFFLGANSDN- 274
                                       9*********************************************..59********************999977. PP

                      UDPG_MGDP_dh  79 gleaelleavrevNe 93 
                                          ++l++++r+vN+
  gi|344210097|ref|YP_004786273.1| 275 ---TDLIDTARQVNQ 286
                                       ...799*******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 !   63.1   0.0   1.8e-20   2.7e-17       1     104 [.     309     415 ..     309     416 .. 0.83

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 1.8e-20
                                       EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGG...BTCCEEES-CHHHHTT-SEEEE-S CS
                    UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaele...ekgvevvdsleealkgadaivilt 74 
                                       ailG+a+K ++dD+R+Sp l+i++++  ++ e    +P  ++  + +  +    ++   +++l++al+gada+v++t
  gi|344210097|ref|YP_004786273.1| 309 AILGVAYKGNVDDTRNSPGLEIARTIVGAESEAPSLEPDRQDTTSLRLCDpyvSNSRYDLEPLSDALDGADAAVLAT 385
                                       8*************************9988855555555555555555555552223335689************** PP

                                       --GGGGGS-HHHHHHCCSS-EEEESSS-CC CS
                    UDPG_MGDP_dh_C  75 ehdefkeldlaklkelmkpavvfDgrnvld 104
                                       +hdef +l+ +++ +l+ ++v+fD+  vld
  gi|344210097|ref|YP_004786273.1| 386 AHDEFADLSPERVGSLLDTRVIFDTLDVLD 415
                                       **************************9998 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 !    9.3   0.0    0.0012       1.7       2      58 ..       6      57 ..       5      62 .. 0.84
   2 ?    4.3   0.0     0.042        62      18      81 ..      66     133 ..      57     140 .. 0.77
   3 ?   -0.1   0.0      0.96   1.4e+03      55      91 ..     371     407 ..     360     411 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneea 58
                                      +++ G G +g a as ++++g   h++v +   + +++++  ++ +++v++ + e  
  gi|344210097|ref|YP_004786273.1|  6 VCVHGLGYIGMATASLFANNG---HDVV-G-FDTDDRVRSQLKRGEPDVSEDQLESY 57
                                      55669****************...****.8.89999999999999999999555554 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.042
                                       HHHTTS...-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE..-S-HHHHHHHHHHC CS
                     F420_oxidored  18 llaaga...qpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvl..avkpedveevlsel 81 
                                       l+ +++   ++++i+ + ++  ++a ++  ++  ++++ + + +++ +dvvvl  +v+p+ ++ v++ +
  gi|344210097|ref|YP_004786273.1|  66 LTISDEpvpAAYHIICVPTPYDKSAGSADLRYVKEASQ-TVSSLLRPNDVVVLesTVPPSTTATVVAPI 133
                                       55555555556778877777778888888888777777.9************98889**9999999988 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.96
                                       HHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEE CS
                     F420_oxidored  55 neeaaeeadvvvlavkpedveevlselakdalkgklv 91 
                                        ++a++ ad  vla     ++++  e   ++l  +++
  gi|344210097|ref|YP_004786273.1| 371 LSDALDGADAAVLATAHDEFADLSPERVGSLLDTRVI 407
                                       57999*********99999988877775555555555 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 !   14.2   0.0   2.5e-05     0.037       2     102 ..       6     131 ..       5     140 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.............EEE-SSHHHHHHHC......... CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.............akaaesieelvasl......... 56 
                                       + + GlG +G+  a+ ++++g++v++++ +     +l   +             a            +         
  gi|344210097|ref|YP_004786273.1|   6 VCVHGLGYIGMATASLFANNGHDVVGFDTDDRVRSQLKRGEpdvsedqlesyvrA------------Aidsgltisd 70 
                                       6788************************876666665555576665555444330............2333444455 PP

                                       .....SEEEE-SSSHHHHHHHHHS..........HCCC--TT-EEEE-S---HHHHHHHHH CS
                     NAD_binding_2  57 .....dvvitmvkagkavdevieg..........llealkkgdilidgstsspedtrelak 102
                                               i++v+   +  +   +          + + l+++d+++  st+ p++t  + +
  gi|344210097|ref|YP_004786273.1|  71 epvpaAYHIICVPTPYDKSAGSADlryvkeasqtVSSLLRPNDVVVLESTVPPSTTATVVA 131
                                       5555555566666543333322222344445666888889999999999999998877655 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 !   15.6   0.0   7.7e-06     0.012       2      41 ..       6      48 ..       5     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.7e-06
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH...HHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdisee...alekalek 41
                                      v v G G +G   a++fa++g++Vv +d++++   +l++++  
  gi|344210097|ref|YP_004786273.1|  6 VCVHGLGYIGMATASLFANNGHDVVGFDTDDRvrsQLKRGEPD 48
                                      8899***********************9965411145554444 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.4e-05     0.021       1      98 [.       6     104 ..       6     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHH.HHHHCEEEEETTCEEEEEECEEECCH..SCCCCS-ESEEEE CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsrrlea.lkknGlrltseggeeilrppealsae..ekselepidlviv 74 
                                       +++ G+G iG   a   a++g+dv+  + ++r+ + lk+   ++++++     ++++a+++    + e  p+ + i+
  gi|344210097|ref|YP_004786273.1|   6 VCVHGLGYIGMATASLFANNGHDVVGFDTDDRVRSqLKRGEPDVSEDQ--LESYVRAAIDSGltISDEPVPAAYHII 80 
                                       689****************************99986777777777777..555555555555545567789****** PP

                                       -SSGGGHHHHHHHHGGGECTCEEE CS
                              ApbA  75 tvKayqteealeeikplldpntvv 98 
                                       +v++  +++a ++  +++++ + +
  gi|344210097|ref|YP_004786273.1|  81 CVPTPYDKSAGSADLRYVKEASQT 104
                                       *****9999999877777766544 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 ?   12.2   0.0   5.9e-05     0.088      37      75 ..       4      42 ..       2      61 .. 0.80
   2 ?   -1.1   0.0      0.69     1e+03      79     111 ..      99     131 ..      81     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.9e-05
                                      SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCH CS
                      2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeee 75
                                      ++v++ GlG IG a+a +++  g +v+++d+  + +++ 
  gi|344210097|ref|YP_004786273.1|  4 MRVCVHGLGYIGMATASLFANNGHDVVGFDTDDRVRSQL 42
                                      689***************************998866633 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.69
                                       TCEECSHHHHHHH-SEEEE-S--STTTTTSBSH CS
                      2-Hacid_dh_C  79 gvelvsleellaesDivslhlpltpetrhlina 111
                                       +   +++  ll+  D+v+l   + p+t+  + a
  gi|344210097|ref|YP_004786273.1|  99 KEASQTVSSLLRPNDVVVLESTVPPSTTATVVA 131
                                       34456899999********99999999887765 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   0.0   0.00079       1.2       5      36 ..      12      43 ..      10      70 .. 0.85
   2 ?    3.2   0.0     0.068     1e+02      13      36 ..     238     261 ..     237     285 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00079
                                      SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8  5 GlsGlvaAylLakagfdvlllekrdrlGGraa 36
                                      G  G+++A+l a++g+dv+ +++ dr+  +++
  gi|344210097|ref|YP_004786273.1| 12 GYIGMATASLFANNGHDVVGFDTDDRVRSQLK 43
                                      788*********************99866655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.068
                                       HHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8  13 ylLakagfdvlllekrdrlGGraa 36 
                                        +La+ + +v++l  ++++GG++ 
  gi|344210097|ref|YP_004786273.1| 238 IELANSHPRVDILNPGPGVGGHCL 261
                                       568888889*************97 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00012      0.18       2      40 ..       7      45 ..       6      55 .. 0.86
   2 ?   -1.3   0.0       1.7   2.6e+03      63      76 ..     378     391 ..     374     426 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                      EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHT CS
                            TrkA_N  2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelree 40
                                       + GlG +G++ a  + ++g+dvv+ d+d+++  +l++ 
  gi|344210097|ref|YP_004786273.1|  7 CVHGLGYIGMATASLFANNGHDVVGFDTDDRVRSQLKRG 45
                                      689***************6669*******9998888765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.7
                                       ESEEEE-SSSHHHH CS
                            TrkA_N  63 adaviaatgddean 76 
                                       ada + at +de+ 
  gi|344210097|ref|YP_004786273.1| 378 ADAAVLATAHDEFA 391
                                       56666666666544 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   0.00042      0.63       2      39 ..       6      43 ..       5      64 .. 0.89
   2 ?   -1.7   0.0       1.7   2.5e+03      59     105 ..     270     317 ..     265     337 .. 0.69
   3 ?   -2.4   0.0       2.7   4.1e+03      63      84 ..     371     392 ..     368     406 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00042
                                      EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHH CS
                    NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeelieein 39
                                      ++v G G  G a A ++a+ngh+v+ +  ++ +  +++
  gi|344210097|ref|YP_004786273.1|  6 VCVHGLGYIGMATASLFANNGHDVVGFDTDDRVRSQLK 43
                                      89************************999988777765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.7
                                       EES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE..---S CS
                    NAD_Gly3P_dh_N  59 attdlaealkgadiivlvvPsqalrevlkklkgllkkkailvs..liKG 105
                                       a++d ++ ++ a+ +   +P+ ++ + +++l +l  +k+i++   + KG
  gi|344210097|ref|YP_004786273.1| 270 ANSDNTDLIDTARQVNQRMPHYVVDRLAEELGPLD-DKTIAILgvAYKG 317
                                       66777777777778888888888888888887744.4444443235566 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.7
                                       HHHHHTT--EEEE---HHHHHH CS
                    NAD_Gly3P_dh_N  63 laealkgadiivlvvPsqalre 84 
                                       l +al+gad  vl+  +  +++
  gi|344210097|ref|YP_004786273.1| 371 LSDALDGADAAVLATAHDEFAD 392
                                       678999*******999987765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00048      0.72       1      38 [.       5      42 ..       5      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00048
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrll 38
                                      +v v G Gyig+  A+ +a+ g++V  ++  d+++++l
  gi|344210097|ref|YP_004786273.1|  5 RVCVHGLGYIGMATASLFANNGHDVVGFDTDDRVRSQL 42
                                      67899***********************9999999665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); 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:                        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 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 2646.21
//
Query:       gi|344210098|ref|YP_004786274.1|  [L=454]
Description: export protein [Haloarcula hispanica ATCC 33960]
Scores for 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-79  264.9   3.3    8.2e-79  264.9   3.3    2.1  3  Polysacc_synt_3  Polysaccharide biosynthesis protein
    7.8e-34  117.3   4.0    7.8e-34  117.3   4.0    3.1  4  Polysacc_synt    Polysaccharide biosynthesis protein
      5e-06   26.6  16.9      5e-06   26.6  16.9    2.8  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 !  264.9   3.3   1.4e-82   8.2e-79       1     292 [.       2     294 ..       2     295 .. 0.99
   2 ?   -1.0   0.1      0.14   8.2e+02     254     275 ..     354     375 ..     313     381 .. 0.72
   3 ?   -3.0   0.5      0.56   3.4e+03      84      91 ..     414     421 ..     384     441 .. 0.49

  Alignments for each domain:
  == domain 1  score: 264.9 bits;  conditional E-value: 1.4e-82
                   Polysacc_synt_3   1 vLARLLspedFGvvaialvvislanlfvdmGlssaliqke.dlteedlstvftfnlvlgllialvlfllapliasfy 76 
                                       vLARLL p +FG+v++a +vi  +  ++++Gl+ ali ++ ++ +++l+tv +++ v gl+i  ++f++apli +f+
  gi|344210098|ref|YP_004786274.1|   2 VLARLLDPRAFGIVGLASLVIVGLRRVSKLGLDDALIYNKdENVDRYLNTVLVMKGVRGLVIGGLVFVAAPLIGQFF 78 
                                       8************************************999788999******************************* PP

                   Polysacc_synt_3  77 nqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllsslls 153
                                        +p l+ ++r +a+  ++ g+++    +++++l+F k f++++ + +v++iva++ Al+  +vwAL++  ++ ++ +
  gi|344210098|ref|YP_004786274.1|  79 SEPALISIVRAMAIGSVVMGFQNPAIVYFKKDLNFHKEFAYEVGAEAVYFIVAFAYALVNPTVWALAFAYIARNVAR 155
                                       ***************************************************************************** PP

                   Polysacc_synt_3 154 lvllwlaskwrprlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaeits 230
                                       + l++l +++rp ++f+++ ++e++ +g+++++s++lny++++ d++++G++l+sa+LG+Y+ a+rl+++p +e+t 
  gi|344210098|ref|YP_004786274.1| 156 FGLSYLLHEYRPWPSFDTDLAREMIDYGKWITGSSILNYISNEGDDIFVGWLLGSATLGFYQFAYRLSNAPATEVTH 232
                                       ***************************************************************************** PP

                   Polysacc_synt_3 231 viakVlfPalSrlqddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqWleav 292
                                       vi++V+fPa+S++qdd ++lr+ +++++rl++++v P+avg+avvae++v  +lG+qWl++v
  gi|344210098|ref|YP_004786274.1| 233 VISRVTFPAYSKIQDDMEALRAGFYRTIRLSTFLVAPMAVGIAVVAEPFVLAFLGEQWLPMV 294
                                       ************************************************************98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.14
                   Polysacc_synt_3 254 ylkvlrlialivlPiavglavv 275
                                         +v+ +  +i++P+ ++la++
  gi|344210098|ref|YP_004786274.1| 354 AATVVGVYVFIMMPLDMYLAAA 375
                                       3445555556666666666655 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.56
                   Polysacc_synt_3  84 vlrvlalv 91 
                                       +++++ lv
  gi|344210098|ref|YP_004786274.1| 414 IVEFAVLV 421
                                       22222222 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.3   4.0   1.3e-37   7.8e-34      25     274 .]       2     246 ..       1     246 [. 0.95
   2 ?   -3.7   5.9         1     6e+03      79     127 ..     262     313 ..     256     366 .. 0.68
   3 ?   -1.8   0.2      0.26   1.6e+03     151     169 ..     355     374 ..     343     390 .. 0.62
   4 ?   -4.4   3.8       1.6   9.6e+03     140     174 ..     399     434 ..     395     439 .. 0.64

  Alignments for each domain:
  == domain 1  score: 117.3 bits;  conditional E-value: 1.3e-37
                     Polysacc_synt  25 ylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslillnvllvllvlvllfllllliaaf 101
                                       +lar+l+p  fG+v la  +++ l  ++ lGl+ al+  ++++ + ++l ++++ + + +l++  l+f++++li +f
  gi|344210098|ref|YP_004786274.1|   2 VLARLLDPRAFGIVGLASLVIVGLRRVSKLGLDDALIYNKDENVD-RYLNTVLVMKGVRGLVIGGLVFVAAPLIGQF 77 
                                       89******************************************9.5****************************** PP

                     Polysacc_synt 102 lglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaavlgavlaal 178
                                       +++p+l ++++++a+  +++ + +  ++ + ++l++ k +a ++ +e + ++++ + a+  +  ++a+++++ + ++
  gi|344210098|ref|YP_004786274.1|  78 FSEPALISIVRAMAIGSVVMGFQNPAIVYFKKDLNFHKEFAYEVGAEAVYFIVAFAYALVNPT-VWALAFAYIARNV 153
                                       ******************9*********************************88888888888.************* PP

                     Polysacc_synt 179 vggivslavlrkkf..rprfvilslklvrellsfsapltisslaillytyidsillglllgaeavGiYnaayqllva 253
                                       ++  ++l +l +++  +p+f +    l re++ ++ ++t+ss+++++++  d i+ g+llg+ ++G+Y++ay+l++a
  gi|344210098|ref|YP_004786274.1| 154 AR--FGLSYLLHEYrpWPSFDTD---LAREMIDYGKWITGSSILNYISNEGDDIFVGWLLGSATLGFYQFAYRLSNA 225
                                       **..8888888899444666666...*************************************************** PP

                     Polysacc_synt 254 isgllapivtaalfPvfselq 274
                                       +   ++  +++++fP+ s++q
  gi|344210098|ref|YP_004786274.1| 226 PATEVTHVISRVTFPAYSKIQ 246
                                       ******************986 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1
                     Polysacc_synt  79 lnvllvllvlvllflllll.iaaflglpel..avlylilalmllllvgvasf 127
                                       l+++lv  ++v +++++ + + aflg++ l  +++++ila+++l+  ++asf
  gi|344210098|ref|YP_004786274.1| 262 LSTFLVAPMAVGIAVVAEPfVLAFLGEQWLpmVLPMQILAIYGLIRGYIASF 313
                                       7788888888888888855045599998872245556666666655555555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.26
                     Polysacc_synt 151 srvilvliavflfld.ivaa 169
                                       + v+ v ++++++ld ++aa
  gi|344210098|ref|YP_004786274.1| 355 ATVVGVYVFIMMPLDmYLAA 374
                                       44566667777777643333 PP

  == domain 4  score: -4.4 bits;  conditional E-value: 1.6
                     Polysacc_synt 140 yaavsqvveqlsrvilvliavflfld.ivaavlgav 174
                                       +a+v +v+e +s++  v +av+ +    ++av +++
  gi|344210098|ref|YP_004786274.1| 399 AAVVLWVQEMISVIPIVEFAVLVVVGaATYAVSVLL 434
                                       577888888888888776665554432555555544 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 ?   -0.8   7.0      0.25   1.5e+03      35     124 ..      61     150 ..      51     163 .. 0.69
   2 ?   -3.5   0.1       1.7     1e+04     125     133 ..     268     276 ..     255     290 .. 0.49
   3 !   26.6  16.9   8.4e-10     5e-06       2     141 ..     297     435 ..     296     437 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.25
                   Polysacc_synt_C  35 lvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrllgikl..ellrrllkpllaalvmgivvylll 109
                                       lvig l  + +  +li +f    a+i++v a+++++v++ +    ++ +k   ++ + +   + a +v +iv+++ +
  gi|344210098|ref|YP_004786274.1|  61 LVIGGL--VFVAAPLIGQFFSEPALISIVRAMAIGSVVMGFQNPAIVYFKKdlNFHKEFAYEVGAEAVYFIVAFAYA 135
                                       555555..556678888887788999999999999999988888888888887778888888888888888866444 PP

                   Polysacc_synt_C 110 llllgllllaal.all 124
                                       l++++++ la +  ++
  gi|344210098|ref|YP_004786274.1| 136 LVNPTVWALA-FaYIA 150
                                       4444444333.33444 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.7
                   Polysacc_synt_C 125 lavlvgalv 133
                                       + ++vg++v
  gi|344210098|ref|YP_004786274.1| 268 APMAVGIAV 276
                                       222222222 PP

  == domain 3  score: 26.6 bits;  conditional E-value: 8.4e-10
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavln.lyal 77 
                                       ++ila++ ++ +++  ++s+  ++g q++++k  ++++ +  i  ++   +fgi G+a+  v  ++++++ + +y++
  gi|344210098|ref|YP_004786274.1| 297 MQILAIYGLIRGYIASFGSVWRATGNQDYLVKLQALTIGLIAIPIYPAATEFGIAGVAATVVGVYVFIMMPLdMYLA 373
                                       89******************************************************666666666555554449999 PP

                   Polysacc_synt_C  78 rrllgikl.ellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllll 141
                                          +  +l  l   +  pl  a++m++vv++++ ++  ++    +++++ v+vga+ Y++ +ll+
  gi|344210098|ref|YP_004786274.1| 374 AAAVEGSLqRLAIEFAYPLPGAAAMAAVVLWVQEMISVIPI---VEFAVLVVVGAATYAVSVLLM 435
                                       999999997667777799**********7766666655554...47888888********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2872.72
//
Query:       gi|344210099|ref|YP_004786275.1|  [L=379]
Description: group 1 glycosyl transferase [Haloarcula hispanica ATCC 33960]
Scores for complete 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  112.3   0.0    7.3e-32  110.3   0.0    1.8  2  Glycos_transf_1  Glycosyl transferases group 1
    3.9e-27   95.3   0.0    6.8e-27   94.5   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.7e-15   57.4   0.0    4.2e-15   56.2   0.0    1.6  2  Glyco_transf_4   Glycosyltransferase Family 4
    4.2e-11   43.5   0.1    7.6e-11   42.7   0.1    1.4  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.7e-05   25.1   0.0    4.2e-05   23.9   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
    0.00071   19.6   0.0     0.0011   19.0   0.0    1.2  1  Glyco_trans_4_2  Glycosyl transferase 4-like


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 ?   -0.8   0.0      0.33   9.7e+02      76     117 ..      85     129 ..      78     138 .. 0.74
   2 !  110.3   0.0   2.4e-35   7.3e-32      10     164 ..     201     353 ..     194     361 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.33
                                       GEEECCHSSSHHHHHHCESEEEEEESS...BSS-HHHHHHHHTT- CS
                   Glycos_transf_1  76 iflgevsredleellknadifvlpsis...EgfGivllEAmaagl 117
                                       ++lg  +++ l++ ++ a+i++l + +       +v++E +a+g+
  gi|344210099|ref|YP_004786275.1|  85 QYLGDTEPDILISEKTDANILCLGAKRvaeSTTTVVPTEHIAFGM 129
                                       677777778888888889999999999995445566777777775 PP

  == domain 2  score: 110.3 bits;  conditional E-value: 2.4e-35
                                       TTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSH CS
                   Glycos_transf_1  10 gknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredl 86 
                                        ++ +  ++l+vgr  ++K++++ +++f++++++  p+++ viaG g+e +++++l  el+l + + + g+v+  + 
  gi|344210099|ref|YP_004786275.1| 201 IEDPDTDVLLFVGRHHPQKDLKTWLRSFKRVNDT-LPDTRAVIAGRGSETETVRELTVELGLTEVTSIPGYVD--NP 274
                                       5677899************************998.**************************************..** PP

                                       HHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHH CS
                   Glycos_transf_1  87 eellknadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdgetGllvkpnnaealaeairklledeelr 162
                                         ++++a++f+l+s+ Eg+++vl+EAma+g+p+++++  +gp+e+++dge G l + ++++++a a  ++l+++  +
  gi|344210099|ref|YP_004786275.1| 275 YRFMNQASLFLLSSQFEGLPTVLIEAMACGCPIVSTDcPSGPREILADGEYGRLTPVGDVDSIATAALEMLDNPTPA 351
                                       *************************************************************************9555 PP

                                       HH CS
                   Glycos_transf_1 163 er 164
                                       + 
  gi|344210099|ref|YP_004786275.1| 352 AV 353
                                       44 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 !   94.5   0.0   2.3e-30   6.8e-27       3     134 .]     208     347 ..     206     347 .. 0.92

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 2.3e-30
                                       EEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---..HHHHHHH.T.T-T.TEEEE---THHHHHHHH-SE CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgprpeeleela.a.gleerveftGfvedlaellaaadv 75 
                                       v+lfvGr  +++k ++  l+ ++++ +   d r vi+G+g++ e ++el+ + gl+e  ++ G+v++  +++++a++
  gi|344210099|ref|YP_004786275.1| 208 VLLFVGRH-HPQKDLKTWLRSFKRVNDTlpDTRAVIAGRGSETETVRELTvElGLTEVTSIPGYVDNPYRFMNQASL 283
                                       89******.567**************88745*******998556888766458**999*******99********** PP

                                       EEE--..---SHHHHHHHHTT-EEEE-TGG.GTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  76 fvaPs..egfglkllEamaaglpvVatdvg.giaevv..gengllvppgdpealaeailrLled 134
                                       f++ s  eg++ +l+Eama+g+p+V+td++ g++e++  ge g l p gd++++a a l++l++
  gi|344210099|ref|YP_004786275.1| 284 FLLSSqfEGLPTVLIEAMACGCPIVSTDCPsGPREILadGEYGRLTPVGDVDSIATAALEMLDN 347
                                       *****999*********************889***99***********************9986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0   1.4e-18   4.2e-15       1     168 [.      21     185 ..      21     187 .. 0.84
   2 ?   -2.2   0.0       1.2   3.5e+03     130     166 ..     231     271 ..     206     273 .. 0.56

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 1.4e-18
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrl.lrslaflrrlrrllkrekpDvv 76 
                                       vGG+e ++++++++La rG++V++v+++++g+l+ +v    +v  + l   + +   + a+l +l++ l   +pD++
  gi|344210099|ref|YP_004786275.1|  21 VGGAEQVTVNIVNGLAGRGYDVELVVSHPGGELRTAV--ADSVAVIELADVRIPgIGIGAHLHKLAQYLGDTEPDIL 95 
                                       7***********************************6..3333333333333330345678899************* PP

                    Glyco_transf_4  77 Hahspaalgaallalrr.rlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrery 152
                                        +    a +++l a r  ++   +V t H  +      +  +++sr +r++ ++l+ +a+ +iavS+ +ad l e+ 
  gi|344210099|ref|YP_004786275.1|  96 ISEKTDANILCLGAKRVaESTTTVVPTEHIAF---GMMPDESLKSRGVRKVAAQLYPAANDLIAVSDGVADSLGEKT 169
                                       99998888877666555878888888889888...56678999999******************************* PP

                    Glyco_transf_4 153 gvppekitVipnGvDl 168
                                        v++ +i V++n+v +
  gi|344210099|ref|YP_004786275.1| 170 AVDRGDISVLHNPVEI 185
                                       *************986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                    Glyco_transf_4 130 l...lrradrvia....vSeatadelrerygvppekitVipnGv 166
                                       +   l  +++via     +e++++  +e +g+ +  +t ip  v
  gi|344210099|ref|YP_004786275.1| 231 VndtLPDTRAVIAgrgsETETVRELTVE-LGLTE--VTSIPGYV 271
                                       1344788888888555556666666666.66665..77666655 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 !   42.7   0.1   2.6e-14   7.6e-11       1     159 [.      22     181 ..      22     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 2.6e-14
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvv 77 
                                       gG+++++ +++ +La rG++V++++++p ++ + +++d v v+ l   r p + +  a+l+ l+++l   +  pd++
  gi|344210099|ref|YP_004786275.1|  22 GGAEQVTVNIVNGLAGRGYDVELVVSHPGGELRTAVADSVAVIELADVRIP-GIGIGAHLHKLAQYL--GDTEPDIL 95 
                                       8******************************************99877777.68999**********..******** PP

                   Glyco_trans_4_4  78 hahsptaglaarlarrrr..giplvvtlh...glllrrgsgavrrlyralerrllrradavlvvseaeaeelra.lg 148
                                       +++   a+++++ a+r +   + +v t h   g  +    + + r +r +   l+  a  +++vs+++a+ l +   
  gi|344210099|ref|YP_004786275.1|  96 ISEKTDANILCLGAKRVAesTTTVVPTEHiafGMMP--DESLKSRGVRKVAAQLYPAANDLIAVSDGVADSLGEkTA 170
                                       *****9999999888444224556666675333322..35677777778889**********************666 PP

                   Glyco_trans_4_4 149 vpadrvvvvpn 159
                                       v++ ++ v++n
  gi|344210099|ref|YP_004786275.1| 171 VDRGDISVLHN 181
                                       *********99 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 !   23.9   0.0   1.4e-08   4.2e-05       3      76 ..     285     361 ..     280     377 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.4e-08
                   Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltdda.egleelftpgkevilfe..dleelaekiryllanpeerraiaeaarer 76 
                                       L  s+ e++ ++l Ea+acG++++++d  +g++e++ +g+ + l    d++++a +  ++l+np  ++ +  +a  +
  gi|344210099|ref|YP_004786275.1| 285 LLSSQFEGLPTVLIEAMACGCPIVSTDCpSGPREILADGEYGRLTPvgDVDSIATAALEMLDNPTPAAVLQDRAADF 361
                                       55566699999***************999***********99999999**************998888777777655 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 !   19.0   0.0   3.8e-07    0.0011      11      89 ..      26     105 ..      18     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.8e-07
                   Glyco_trans_4_2  11 vhtlrlakeLakrgyeVhvitpkkga.kdeleaegihvhrlkvdrkgpleyl.k.afklkklikkikPDvvhahyak 84 
                                        +t++++++La rgy+V+++ +++g   +  +a+ ++v++l  d+++p   + + + kl++ + + +PD+++   + 
  gi|344210099|ref|YP_004786275.1|  26 QVTVNIVNGLAGRGYDVELVVSHPGGeLRTAVADSVAVIELA-DVRIPGIGIgAhLHKLAQYLGDTEPDILISEKT- 100
                                       57999*****************7776477788999******8.99995555525467*************976554. PP

                   Glyco_trans_4_2  85 pygll 89 
                                       + ++l
  gi|344210099|ref|YP_004786275.1| 101 DANIL 105
                                       34444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); 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:                         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: 00:00:00.40
# Mc/sec: 2841.83
//
Query:       gi|344210100|ref|YP_004786276.1|  [L=73]
Description: hypothetical protein HAH_5159 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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: 00:00:00.44
# Mc/sec: 499.92
//
Query:       gi|344210101|ref|YP_004786277.1|  [L=332]
Description: hypothetical protein HAH_5160 [Haloarcula hispanica ATCC 33960]
Scores for 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-64  217.8   6.7    2.4e-64  217.6   6.7    1.0  1  DUF1616   Protein of unknown function (DUF1616)


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 !  217.6   6.7   1.3e-68   2.4e-64       4     293 .]      25     329 ..      19     329 .. 0.93

  Alignments for each domain:
  == domain 1  score: 217.6 bits;  conditional E-value: 1.3e-68
                           DUF1616   4 lalllllailvpvlnetplRivlglplvLflPGYaliaaLFPe..............krdidgieRlaLSfglSiai 66 
                                        ++++++ +  p+   tp+R+ lg++++++lPGY++ + LFP+              +  i+  e ++L +glSiai
  gi|344210101|ref|YP_004786277.1|  25 SMAAVIISLRRPNAVPTPIRVTLGFLFIFVLPGYTVLTSLFPAiysqsamadeqritHYPISFAEGVVLTVGLSIAI 101
                                       3344555556688999****************************************9999***************** PP

                           DUF1616  67 vpliglvlnvtpwgirlepilvslslftlllalvAivrRsrlpeeerfsvplralieslkeeleeksesrldkalnv 143
                                       vpl  lvln+ +w i +++ +v+++++t +++ +Ai+ R  + +++   vp+++l++ l  ++++k++  ++ a +v
  gi|344210101|ref|YP_004786277.1| 102 VPLSVLVLNFVAWPIGPVSTVVTVAALTAVMSGIAIIHR--IVDSQSAGVPIERLTSILTGSFQSKPT--IRSAAEV 174
                                       **************************************9..67777778*****99999999999765..89***** PP

                           DUF1616 144 lLvvsivlavaalgyavvaPkegekfTelyllgedgd..elvaenypteltagesqevivgieNhEheevnYtvvvl 218
                                       + v+ ++l+++ +g a+++ + ge++Tel++l+e+ +  +l+a++ypt+l++ge++e++v + NhE+++v+Ytvv +
  gi|344210101|ref|YP_004786277.1| 175 ITVCLLLLSAGIAGAALTQTNGGEQYTELSILTEEAEtgNLTADGYPTSLQVGEQTELVVSVGNHEGQTVQYTVVTR 251
                                       **********************************9877899************************************ PP

                           DUF1616 219 lqev.tdeeevevlerteldrrevtladnetweqelevepea..tgenlrleflLYkdevpeeptteeayrslhlwV 292
                                       lq v t+  e +v++ t++d+ +v++ d++  +q + ++ ++  + ++ rl++lLYk+ +p++pt e+ayr++h+w+
  gi|344210101|ref|YP_004786277.1| 252 LQSVsTSGGERTVTRATTIDTLSVNVGDGDVSRQAMPITANTvaDADRHRLVVLLYKGAPPANPTLENAYRDVHIWI 328
                                       ***99888999999*****************9999999888766899*****************************9 PP

                           DUF1616 293 n 293
                                       n
  gi|344210101|ref|YP_004786277.1| 329 N 329
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); 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:                         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 0.29s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2316.15
//
Query:       gi|344210102|ref|YP_004786278.1|  [L=606]
Description: hypothetical protein HAH_5161 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 3670.87
//
Query:       gi|344210103|ref|YP_004786279.1|  [L=473]
Description: sulfatase [Haloarcula hispanica ATCC 33960]
Scores for 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-37  127.3   0.8    1.1e-36  126.8   0.8    1.2  1  Sulfatase     Sulfatase
    0.00028   20.6   0.7     0.0021   17.7   0.7    2.3  1  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 !  126.8   0.8   1.2e-40   1.1e-36       1     305 [.       5     336 ..       5     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 126.8 bits;  conditional E-value: 1.2e-40
                                       EEEEEEEESSE-TTGSGGGTTTSCSSHHHHHHH..HTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT CS
                         Sulfatase   1 pnvvliladdlgagdlglyggktattpnldrla..eeglrftnfysaaplcspsraalltgryphnsgvasntevgg 75 
                                       pn++++++d+++a+  +     + ttpn++r+a  + g  ftn ++ a  + ps a++ltg yp  +g +  +    
  gi|344210103|ref|YP_004786279.1|   5 PNIIWLTLDSVRADRTSMAPEARDTTPNMQRIAnlADGQAFTNCITHAMWSLPSDASMLTGTYPSYHGTGLWN---- 77 
                                       8*******************************************************************55444.... PP

                                       HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC..CTTTSEEEETSSSCHHTCCCCCCCCCECTCCC.... CS
                         Sulfatase  76 gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyk..nrgfdrflgfptgsaalkdpekseyngevlrv.... 146
                                       + lp++ +t++e + + GY+t    + + + ++ +s  +  +rgfd+f    + s+ l++ + ++    +l +    
  gi|344210103|ref|YP_004786279.1|  78 EVLPEEIPTVAERFSDLGYHT---AGVSQNAYCSDS--TglSRGFDQFDL-VNKSDFLSTVGVRTLLKYAL-Klrth 147
                                       99*******************...333334444444..145889997655.33356555555444443222.25778 PP

                                       ......TTTTCSHHHHHHHHHHHHH..HCCCTSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCH....... CS
                         Sulfatase 147 ......ppeggysddrlldealefl..larndkpfflylatlapHappeapdeyakkyatffddgseaar....... 208
                                             ++++   d   ld a + l   +  ++pff++++tl+ H p+  p  + ++   f+d++++++        
  gi|344210103|ref|YP_004786279.1| 148 sggytlSTDQHRTDYLALDLAKRRLrsFQGSEEPFFMFVHTLGAHLPYAPPLSFRDT---FTDTLEQTTDeaietav 221
                                       8889996666666666666666666644555**************965555555554...45555554335568888 PP

                                       ......................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSC CS
                         Sulfatase 209 ......................qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrgg 263
                                                              l++ y++ ++y+D+ +g+++++L  +  l +t++v+t+Dhg+ l+e   +  +g
  gi|344210103|ref|YP_004786279.1| 222 evssnhyrstasgcdfsdrtdnALAAMYDGLMSYTDWYVGQFFEYL-NSLDLGPTVFVVTGDHGDLLGE---DDVLG 294
                                       9999999999999999999**9************************.888899**************66...66666 PP

                                       TTCSSSHHHHBEEEEEEETTTSHCEEECSEEEGGGHHHHHHH CS
                         Sulfatase 264 kganayeggtrvPllvwwpgekaprvseelvshiDlfptild 305
                                        + + ++g ++vP++v++ + +a    ++l  hiD++  +l 
  gi|344210103|ref|YP_004786279.1| 295 HQLSLHDGLVNVPMVVHGLQSLADLPADTLLQHIDVMQALLL 336
                                       6669*********************************99885 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.7   2.4e-07    0.0021       2     233 ..       8     284 ..       7     286 .. 0.53

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.4e-07
                                       EEEEETT-BTTHHHHHGS...TSHHHHHHHH..HSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTT CS
                      Phosphodiest   2 lvislDGlradlldrlae...llpnlaaLak..egvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrkt 73 
                                       + ++lD++rad  +   e   ++pn++++a+   g  ++n+++++   + p+ as++TG+yP+ HG      +++ +
  gi|344210103|ref|YP_004786279.1|   8 IWLTLDSVRADRTSMAPEardTTPNMQRIANlaDGQAFTNCITHA-MWSLPSDASMLTGTYPSYHGTG---LWNEVL 80 
                                       568899999877665434467**********99999999988876.579*****************63...465666 PP

                                       TEEEEEETTTTGG..........................GGGCTTS-HHHHHHHTH......TTCEEEESE.TTTTS CS
                      Phosphodiest  74 geyvvfvtededa..........................prwwqgepiwdtaakar......glkaaalfw.pgsev 117
                                        e  + v e+ ++                           ++++++ +++t+           l++++ ++   ++ 
  gi|344210103|ref|YP_004786279.1|  81 PEEIPTVAERFSDlgyhtagvsqnaycsdstglsrgfdqFDLVNKSDFLSTVGVRTllkyalKLRTHSGGYtLSTDQ 157
                                       66555555544445556666665555555555555554422233333333333333333333444444444223444 PP

                                       EBTTCT.SC..........TBHHSBTCT.CSTTS....................CHHHHHHHHHHHHHHHCHTHSHH CS
                      Phosphodiest 118 dystyyylvs.........etppryleddfnakv....................pledkvdkavlqtwldaafakvv 165
                                       ++++y +l +         +            ++                    +++d++++ +  +  d+ + + +
  gi|344210103|ref|YP_004786279.1| 158 HRTDYLALDLakrrlrsfqG------------SEepffmfvhtlgahlpyapplSFRDTFTDTLE-QTTDE-AIETA 220
                                       44433333334333333331............333333333333333333333366666664233.33332.33445 PP

                                       HHHCTSSESEEEEEECCCHHHHHHH-TTSHHHHHHH.HHHHHHHHHHHHHHHHTTGTTTEEEEEEES-- CS
                      Phosphodiest 166 lekelekpdlllvyleetDtvgHkfGpdspevedal.rrvDkaigdLlealderglsaetniilvSDHG 233
                                       +e ++  ++ ++   +  D+  + +     ++ d l ++ D ++g+++e+l    l + t +++++DHG
  gi|344210103|ref|YP_004786279.1| 221 VEVSSNHYRSTASGCDFSDRTDNAL----AAMYDGLmSYTDWYVGQFFEYLNSLDL-GPTVFVVTGDHG 284
                                       5555556666666666666666666....244444414456666666666666655.334466666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3323.67
//
Query:       gi|344210104|ref|YP_004786280.1|  [L=328]
Description: hypothetical protein HAH_5163 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00083   18.8   0.4     0.0011   18.4   0.4    1.2  1  Sulfatase  Sulfatase
     0.0065   16.6   0.0      0.011   15.8   0.0    1.3  1  PglZ       PglZ domain


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 !   18.4   0.4   1.2e-07    0.0011     146     271 ..     152     285 ..      94     306 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-07
                                       C..........TTTTCSHHHHHHHHHHHHHHCCCTSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCH.... CS
                         Sulfatase 146 v..........ppeggysddrlldealefllarndkpfflylatlapHappeapdeyakkyatffddgseaar.... 208
                                       +          ++ ++   ++++d+a++   ar+++   +++++l+pH+ p+  + y+++       + e ++    
  gi|344210104|ref|YP_004786280.1| 152 KflhvhnhdydDYFPEAPPQVMTDYAIDT--ARTTEFERMVVHYLQPHT-PYIAEAYEENRP-----LLEVEAdpwt 220
                                       044444444444445678899********..566888899********9.456666655533.....3333334556 PP

                                       ..........HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSCTTCSSSHH CS
                         Sulfatase 209 ..........qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrggkganayeg 271
                                                 ++ e yl+ ++ v d i+ +l+ +      d   vv+t+Dhg+  +e++ + +++    a+++
  gi|344210104|ref|YP_004786280.1| 221 ameqgtasvtEVKELYLDNLRFVLDSIELLLQNI------DAEKVVITADHGELFGEMGLYGHPEGF--AHPN 285
                                       6778999999************************......5556999******99885555554443..5544 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.2e-06     0.011     127     173 ..     224     271 ..     208     274 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-06
                              PglZ 127 dkasteqksfeaveeslkelkelvksllee.ngykvlltaDHGfiyqr 173
                                         ++++ +++e+    l ++ + ++ ll++ ++ kv++taDHG ++ +
  gi|344210104|ref|YP_004786280.1| 224 QGTASVTEVKELYLDNLRFVLDSIELLLQNiDAEKVVITADHGELFGE 271
                                       55678889999999999999999******99*************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 2233.24
//
Query:       gi|344210105|ref|YP_004786281.1|  [L=466]
Description: hypothetical protein HAH_5164 [Haloarcula hispanica ATCC 33960]
Scores for 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-16   58.8   9.1      7e-15   55.4   0.2    3.6  3  Pectate_lyase_3  Pectate lyase superfamily protein
    6.6e-06   26.1  12.5     0.0014   18.5   9.3    3.0  2  Beta_helix       Right handed beta helix region
  ------ inclusion threshold ------
      0.026   14.2   0.2      0.069   12.9   0.2    1.7  1  End_N_terminal   N terminal extension of bacteriophage endosi


Domain annotation for each model (and alignments):
>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.2   1.2e-18     7e-15       3     119 ..       4     120 ..       2     168 .. 0.79
   2 !    5.3   0.5    0.0026        16     148     215 .]     208     283 ..     170     283 .. 0.62
   3 ?    0.2   0.3     0.091   5.4e+02     117     170 ..     318     367 ..     284     383 .. 0.59

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 1.2e-18
                                       EGGGGT---EEEEE-HHHHHHHH......HTSS-EEE-SEEEEESS-E.........EE-SSEEEEES-TTTEEEEE CS
                   Pectate_lyase_3   3 nVkdyGakgDGvtDdtaaiqkaiscasatttgavVYfPaGtYlvsspi.........ilksgvqLvGdgngrpvlka 70 
                                       +V+d Ga+gDG+tDdtaai++a    +a + g++VYfPaGtYlv s            + ++ +  G++ g +vl+ 
  gi|344210105|ref|YP_004786281.1|   4 DVTDHGAVGDGSTDDTAAIRAAA---DAASPGGTVYFPAGTYLVGSNSpfpldypmdGSWDNLTWKGESFGSTVLQM 77 
                                       8**********************...8889999*************9999999998888899999999999999999 PP

                                       -TT-SS--SEEES-TTT-..-EEEEEEEEEEEGGGG-SS---SSEEE.ES CS
                   Pectate_lyase_3  71 aaafvgaglidgdpyvsggsealiatnnfyrqirnlkiditavapga.tg 119
                                        ++  + +++ + +  +g   +++      +   +l++d+++ ++++  g
  gi|344210105|ref|YP_004786281.1|  78 VGGQSRWHMMFRARSSDG--SQMTG-----VRFEQLTMDMNGSQQSGaPG 120
                                       999888888888888866..22222.....24788888888884444333 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0026
                                       ---SS--EEEE.ES-EEES-SS-SEEES-EEEEEES-EEE-...S--SEEE-T.T-E...EEEEEEEEESSSE.EEE CS
                   Pectate_lyase_3 148 ifiengsggfl.ndlvfsglgdigiavgnqqftvrnitfnn...attgievlw.gwg...wtlknvkinnceg.Gid 215
                                        +++++   ++ +  +  glg+  i  gn + ++rn ++ +   +t+gi+++  + +     l++v i+nc+g Gid
  gi|344210105|ref|YP_004786281.1| 208 TTADYQTV-IVeRSYFSAGLGAVKIDPGNLKTVLRNTYIAGgsrTTRGIKTNNdNYDcgsLELEDVVIENCGGpGID 283
                                       33333222.3323344445788888889*************9999999999875544314455599******99986 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.091
                                       E..ES-EEEEEEEEEEES-SSEEE-SSS---TT---SS--EEEEES-EEES-SS-S CS
                   Pectate_lyase_3 117 a..tgihwqtaqatslenvefemseasgtkhqgifiengsggflndlvfsglgdig 170
                                          +g++  t+   s++nv  ++       +  +f +++s+g +++++ +g+++ig
  gi|344210105|ref|YP_004786281.1| 318 IyaEGVDLGTSGTISVHNVSPNN------DGIALFFDESSSGSIEEVRHDGTSGIG 367
                                       13345555555555555552222......234577777777777777777777666 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 !   13.7   0.2   7.3e-06     0.043      73     145 ..     126     205 ..      87     219 .. 0.75
   2 !   18.5   9.3   2.4e-07    0.0014      13     149 ..     158     330 ..     155     356 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.3e-06
                                       -TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT......--SEE---TT.---EEES-EEES-SSEEE CS
                        Beta_helix  73 alfgasnnlienneitdnggsGiylnyssnntienNiidnna......gsGividdss.snvtvtnNtitnnkgaGi 142
                                        ++g++  +++++ i +  + G++l +    ++++++++ ++      g+++ +++ss ++++++ + i +++g  i
  gi|344210105|ref|YP_004786281.1| 126 VYDGSGTFTMRDCVIKNSLNFGVQLGDDIAGDFKYCQFSRCGdpdvsaGHALNLNQSSkQTTNISWCLIEDSAGTDI 202
                                       345888889999999999999**9999999999********999999999999999999888899999999876555 PP

                                       E-T CS
                        Beta_helix 143 avv 145
                                       ++ 
  gi|344210105|ref|YP_004786281.1| 203 DIG 205
                                       544 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.4e-07
                                       EESEEEES-......SS-SEEE-SSS-...EEES-EEES-SS-SEEE-TT.....-S-EEES-EEE---SEEE-TT. CS
                        Beta_helix  13 iknntisns......ggyGiylrgssn..vvienneiannsgsGiyilgs.....snntisnntisdnngggialf. 75 
                                       +k +++s++       g+++ l++ss+  + i+ + i+++ g+ i+i  +     + ++++++++s +  g+++++ 
  gi|344210105|ref|YP_004786281.1| 158 FKYCQFSRCgdpdvsAGHALNLNQSSKqtTNISWCLIEDSAGTDIDIGDDttadyQTVIVERSYFSAGL-GAVKIDp 233
                                       7899999999999999999999999998877888999999999999999999999**************.******7 PP

                                       --S--EEES-EEES-SS-..SEE-TT.-S-...-EEES-EEESTT--SEE---TT---EEES-EEES-S........ CS
                        Beta_helix  76 gasnnlienneitdnggs..Giylny.ssn...ntienNiidnnagsGividdsssnvtvtnNtitnnk........ 138
                                       g+ +++++n  i   +++  Gi +n+ +++   + +e+ +i+n++g Gi +  +++++   n +++ n+        
  gi|344210105|ref|YP_004786281.1| 234 GNLKTVLRNTYIAGGSRTtrGIKTNNdNYDcgsLELEDVVIENCGGPGIDLGGGGHGTLTLNQVAVRNVendgmrsf 310
                                       77777777777777743355**99954555666**********************7777777777777776667777 PP

                                       .........SEEEE-TT-SS CS
                        Beta_helix 139 .........gaGiavvgsss 149
                                                 +G+++ +s++
  gi|344210105|ref|YP_004786281.1| 311 ggysgmgiyAEGVDLGTSGT 330
                                       77665555555555555555 PP

>> End_N_terminal  N terminal extension of bacteriophage endosialidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   1.2e-05     0.069       1      26 [.      10      35 ..      10      48 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                                      ---EEEEE-HHHHHHHHHHS-TTS-E CS
                    End_N_terminal  1 akGDGvtdDtdalsevlaaapvgkki 26
                                      a+GDG tdDt+a+ ++  aa+ g  +
  gi|344210105|ref|YP_004786281.1| 10 AVGDGSTDDTAAIRAAADAASPGGTV 35
                                      89***********9998776555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2957.57
//
Query:       gi|344210106|ref|YP_004786282.1|  [L=267]
Description: hypothetical protein HAH_5165 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00011   21.7   0.2    0.00013   21.5   0.2    1.1  1  Sulfatase  Sulfatase


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 !   21.5   0.2   7.2e-09   0.00013     155     283 ..     107     235 ..      45     253 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 7.2e-09
                                       HHHHHHHHHHHHCCCTSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCH......HHHHHHHHHHHHHHHHH CS
                         Sulfatase 155 drlldealefllarndkpfflylatlapHappeapdeyakkyatffddgseaar......qlleaylnsveyvDdli 225
                                       +++++ al+ +   +  ++ l++++++pH+p +   ++ +  +++ d+ +   r        ++ay + + yv +++
  gi|344210106|ref|YP_004786282.1| 107 EAVTEAALDKI-G-QYPNKRLVIHYMQPHHP-YIGTDIDGFEQKRVDMREYVRRssvdtdTIRAAYQDNLQYVLKHV 180
                                       34444444443.1.1245679********85.5555555555556666555555788888***************** PP

                                       HHHHHHHHHTTTGGGEEEEEEESSSSCCCG.........HHTTSSSCTTCSSSHHHHBEEEEEEETT CS
                         Sulfatase 226 grvlaaLeenglldntlvvftSDhgaslee.........sngplrggkganayeggtrvPllvwwpg 283
                                       +r++++L  +g+   t  v+ +Dhg++l+e          ++p r +      ++ ++vP  v +++
  gi|344210106|ref|YP_004786282.1| 181 QRLVEEL--EGK---T--VISADHGEALGErlspfpvswFGHPIRVYT-----DELVQVPWHVVSNE 235
                                       *******..443...4..679*******99777766555333333333.....35555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1811.44
//
Query:       gi|344210107|ref|YP_004786283.1|  [L=461]
Description: hypothetical protein HAH_5166 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-11   44.9   6.1    9.7e-11   41.9   2.9    3.3  2  Pectate_lyase_3  Pectate lyase superfamily protein
     0.0003   20.7   3.7     0.0003   20.7   3.7    2.7  2  Beta_helix       Right handed beta helix region
  ------ inclusion threshold ------
       0.13   12.2   0.3       0.64    9.9   0.0    2.1  2  ChlamPMP_M       Chlamydia polymorphic membrane protein middl


Domain annotation for each model (and alignments):
>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   2.9   1.6e-14   9.7e-11       3     210 ..      74     287 ..      72     289 .. 0.77
   2 ?    0.1   0.1       0.1     6e+02     118     152 ..     347     385 ..     280     429 .. 0.50

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.6e-14
                                       EGGGGT---EEEEE-HHHHHHHH......HTSS-EEE-SEEEEESS-E.........EE-SSEEEEES-TTTEEEEE CS
                   Pectate_lyase_3   3 nVkdyGakgDGvtDdtaaiqkaiscasatttgavVYfPaGtYlvsspi.........ilksgvqLvGdgngrpvlka 70 
                                       +V +yGa+ DG tDdtaai++ai   +a +  ++V fP+G  l+s+           + +++v+L G  +  + l  
  gi|344210107|ref|YP_004786283.1|  74 DVVEYGASVDGETDDTAAIKRAI---DAAAPDGIVEFPPGEVLISPQRdlpgaitldQRQQNVTLRGPEQETARLVM 147
                                       899********************...8888999*************9999*******************99999999 PP

                                       -TT-SS--SEEES-TT.T-..-EEEEEEEEEEEGGGG-SS---SSEEE..ES-EEEEEEEEE.EES-SSEEE-SSS- CS
                   Pectate_lyase_3  71 aaafvgaglidgdpyv.sggsealiatnnfyrqirnlkiditavapga..tgihwqtaqats.lenvefemseasgt 143
                                       a+   ++g+ +g  ++ ++gse+ +        +  l+id ++ ++++  t+i+ + a+++  + +++++++ +s  
  gi|344210107|ref|YP_004786283.1| 148 AP--GQDGVHYGLHITpRTGSEDDEI------RLEHLTIDLNSDKQSGvgTAIRTNGADGQLaMRDCVVTSTRNS-- 214
                                       88..7777777777773224433333......3889999999998888456666554444434788888887777.. PP

                                       --TT---SS--EEEEES-EEES-SS-SEEES........-EEEEEES-EEE-S--SEEE-T..T-EEEEEEEEEESS CS
                   Pectate_lyase_3 144 khqgifiengsggflndlvfsglgdigiavg........nqqftvrnitfnnattgievlw..gwgwtlknvkinnc 210
                                          g+ +  g    ++ ++f+ +gd  +a          + q +++n++++n ++g++++   +++  l+ v++++c
  gi|344210107|ref|YP_004786283.1| 215 ---GVKMVGGMDADIRYCTFKDNGDESYAHAitpnqtaqKTQTVIKNVYCTN-QRGVSIDVgtDENKDLQTVRVEEC 287
                                       ...899999988888888888888888877668989999999999******9.666555441055555555666555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.1
                                       ES-EEEEEEEEEEES-SSEEE-SSS....---TT---SS CS
                   Pectate_lyase_3 118 tgihwqtaqatslenvefemseasg....tkhqgifien 152
                                        g++ +  +  +l +v +++ ++++    +   gi++e+
  gi|344210107|ref|YP_004786283.1| 347 PGLDLPNRSTLQLNEVAIKNVDKNNvergNDRGGIRTEK 385
                                       333333333333333333333333222212222333333 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 !   20.7   3.7     5e-08    0.0003      43     149 ..     186     303 ..     151     312 .. 0.48
   2 ?    2.8   0.5     0.016        93      13      79 ..     336     415 ..     329     438 .. 0.54

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5e-08
                                       S-SS-SEEE-TT.-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-....SEE-TT...-S--EEES-EEE CS
                        Beta_helix  43 nnsgsGiyilgs.snntisnntisdnngggialfgasnnlienneitdnggs....Giylny...ssnntienNiid 111
                                       +  g+ i+++g+     +++++++   ++g+++ g+    i+++++ dng+      i+ n+    ++++i+n + +
  gi|344210107|ref|YP_004786283.1| 186 SGVGTAIRTNGAdGQLAMRDCVVTSTRNSGVKMVGGMDADIRYCTFKDNGDEsyahAITPNQtaqKTQTVIKNVYCT 262
                                       23334444444444555555555555555666666666666666666665543333332222332222333333333 PP

                                       STT--SEE---TT......---EEES-EEES-SSEEEE-TT-SS CS
                        Beta_helix 112 nnagsGividdss......snvtvtnNtitnnkgaGiavvgsss 149
                                       n    G++id +       ++v+v+ ++i+n+   +++v  +++
  gi|344210107|ref|YP_004786283.1| 263 NQ--RGVSIDVGTdenkdlQTVRVEECIIKNSF-GALKVDPTAA 303
                                       33..34444444444566666666666666665.5555555554 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.016
                                       EESEEEES-SS-SEEE-SSS-.........EEES-EEES.-SS-SEEE-TT-S-EEES-EEE---....SEEE-TT- CS
                        Beta_helix  13 iknntisnsggyGiylrgssn........vvienneian.nsgsGiyilgssnntisnntisdnn....gggialfg 76 
                                       ++n+ i++ g+ G+ l + s+          +++n+++  n   Gi++++ +  t  + +i++ +    g ++++f+
  gi|344210107|ref|YP_004786283.1| 336 LDNVLIDGGGWPGLDLPNRSTlqlnevaiKNVDKNNVERgNDRGGIRTEKLDFGTSGRISIHNVGtdnsGPALKIFE 412
                                       56666666677777777777744444333333323333356666666666644444444443333332144444444 PP

                                       -S- CS
                        Beta_helix  77 asn 79 
                                       +s+
  gi|344210107|ref|YP_004786283.1| 413 GSG 415
                                       444 PP

>> ChlamPMP_M  Chlamydia polymorphic membrane protein middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       0.2   1.2e+03      44      73 ..      14      55 ..      10      79 .. 0.69
   2 ?    9.9   0.0   0.00011      0.64      17      73 ..     139     242 ..     126     281 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.2
                        ChlamPMP_M 44 altinnlsidLssvlkngaaegeifvpPe..............a 73
                                      al i++ +i L  + ++  + ge +++P                
  gi|344210107|ref|YP_004786283.1| 14 ALGISGTGIGLYAIDSS--SRGENRNQPSdgddnsptpspspsT 55
                                      67899999999999999..9999999999555544444443330 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00011
                        ChlamPMP_M  17 eqtegsklvlgaGavLsiv.....kgataangaltinnlsidLssvlkngaaegeifvpPe................ 72 
                                       eq+ +++lv+++G     +         +++  + +++l+idL+s +++g+ +  i+++ +                
  gi|344210107|ref|YP_004786283.1| 139 EQE-TARLVMAPGQDGVHYglhitPRTGSEDDEIRLEHLTIDLNSDKQSGVGT-AIRTNGAdgqlamrdcvvtstrn 213
                                       566.9********864444444438888999***************9997655.45555554666666666666666 PP

                        ChlamPMP_M  73 ............................a 73 
                                                                   a
  gi|344210107|ref|YP_004786283.1| 214 sgvkmvggmdadiryctfkdngdesyahA 242
                                       66666666666666666666666555542 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3108.45
//
Query:       gi|344210108|ref|YP_004786284.1|  [L=323]
Description: glycosyltransferase [Haloarcula hispanica ATCC 33960]
Scores for 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-28   97.9   1.0    7.9e-28   97.4   0.5    1.5  2  Glycos_transf_2  Glycosyl transferase family 2
    7.8e-17   61.9   0.2    1.3e-16   61.3   0.2    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.1e-09   38.2   0.0    1.5e-09   37.8   0.0    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.071   13.3   0.9       0.18   12.0   0.9    1.7  1  TPR_2            Tetratricopeptide repeat
       0.17   11.2   0.0       0.24   10.7   0.0    1.2  1  Glyco_transf_64  Glycosyl transferase family 64 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 !   97.4   0.5   2.2e-31   7.9e-28       1     131 [.      14     141 ..      14     177 .. 0.86
   2 ?   -2.7   0.0       1.3   4.6e+03      88     103 ..     222     237 ..     201     276 .. 0.61

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 2.2e-31
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       +vvi+ty +++ l+++++ + aq  y+ +e+ivvDD S+  + ++l +    ++r+ + r+ en+G  +a+n+g++ 
  gi|344210108|ref|YP_004786284.1|  14 TVVITTYDRPEFLQKAVDTVTAQ-RYDPIELIVVDDHSPTPADDVLNDRDPDFERFEIHRHAENQGANAARNTGIEV 89 
                                       69*********************.**************9999******999************************** PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-S CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkr 131
                                       a+g+yi+flD+Dd +dp+++   v+a+++ g+   +g ++  ++  d     +r
  gi|344210108|ref|YP_004786284.1|  90 ASGEYIAFLDDDDRWDPEKIATQVNAFQDSGP--EVGVVYTGRKVVDDDGGVTR 141
                                       ******************************99..77777766666666666655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                                       SSEEE-TTHHHHHHHH CS
                   Glycos_transf_2  88 aDdepdpdwleklvea 103
                                       +D e+ ++  e ++e+
  gi|344210108|ref|YP_004786284.1| 222 DDYEVLEESYELFIEK 237
                                       2333333333333333 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 !   61.3   0.2   3.5e-20   1.3e-16       4     174 ..      13     177 ..      10     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 3.5e-20
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       ++v+++t+++++ l + ++ + aq y+++e++vv+d s + + +v+     ++++ +++  + a+n    g+  a n
  gi|344210108|ref|YP_004786284.1|  13 VTVVITTYDRPEFLQKAVDTVTAQRYDPIELIVVDDHSPTPADDVLNDRDPDFERFEIH--RHAENQ---GANAARN 84 
                                       89********************************************9977777777666..455554...5566678 PP

                   Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqff..ltpkvgavgtpv.fllnrstlvsalgalefaerhlrflaarra 154
                                        +++ +++++++++DdD++++P+ ++ ++++f    p+vg+v+t +  ++ +  +++++  ++++ + ++ l+ r+ 
  gi|344210108|ref|YP_004786284.1|  85 TGIEVASGEYIAFLDDDDRWDPEKIATQVNAFqdSGPEVGVVYTGRkVVDDDGGVTRVWAPDQPDGDMTKALLCRNV 161
                                       ********************************77777******6662667899999999988988888888888888 PP

                   Glyco_tranf_2_3 155 lgvltlnGsgslirrevlke 174
                                       +g+     s +++r ++ ke
  gi|344210108|ref|YP_004786284.1| 162 VGTQ----SSVMVRSDIAKE 177
                                       8765....345556665555 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 !   37.8   0.0     4e-13   1.5e-09       2     220 ..      15     217 ..      13     246 .. 0.72

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 4e-13
                   Glyco_tranf_2_2   2 vviplraseerhyieervlqkaky.ydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGa 77 
                                       vvi  +     ++++  v   + + yd+ ielivvdd S+ + ++ v +  d   + +  +   +  +  aarN G+
  gi|344210108|ref|YP_004786284.1|  15 VVITTYDR--PEFLQKAVDTVTAQrYDP-IELIVVDDHSPTP-ADDVLNDRDPDFERFEIHRHAENQGANAARNTGI 87 
                                       45554443..346888885544441565.9************.77777777777766656666678899******** PP

                   Glyco_tranf_2_2  78 skaesdlvlFlDaDcfissDkfekilklitikklr.enidaavvlpvvdlnkedsevlkdvedltassrvledllaa 153
                                       + a ++++ FlD D+ + ++k++ +++     +++   ++  vv++  + +++d  v +       ++++ + ll  
  gi|344210108|ref|YP_004786284.1|  88 EVASGEYIAFLDDDDRWDPEKIATQVN-----AFQdSGPEVGVVYTGRKVVDDDGGVTRVWAPDQPDGDMTKALLC- 158
                                       *********************999998.....44414578888888888888888877777777777777755555. PP

                   Glyco_tranf_2_2 154 kstlvkffapssssilinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellykarak 220
                                            + ++   ss++++   + +   +DE +  +   D + ++    ++++ ++  + + y+ ra+
  gi|344210108|ref|YP_004786284.1| 159 -----RNVVGTQSSVMVR-SDIAKETPFDETI--PRWADLEWYVAASTKCEFAAVDEPLVIYDRRAH 217
                                       .....4555555555554.4445555677777..777777777777777777777777777766665 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.9   4.9e-05      0.18       5      32 ..     259     286 ..     255     287 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.9e-05
                             TPR_2   5 ynlGlayyklgdyeeAleafekAleldP 32 
                                       y+ G+a +++  y+ A+++f +Al+l+P
  gi|344210108|ref|YP_004786284.1| 259 YRVGNASLNARYYDMARRYFFRALALYP 286
                                       999************************9 PP

>> Glyco_transf_64  Glycosyl transferase family 64 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   6.6e-05      0.24       2     118 ..      14     135 ..      13     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.6e-05
                   Glyco_transf_64   2 tvviltsekrkelllklvkrvaksps..lkkilvlWnnekpppek..kkwpsts.vpvtvirqkkkslnnRflpyke 73 
                                       tvvi+t ++r e+l+k v +v++ ++  ++ i+v   ++ p ++    + p+ +  +++ + +++    +R   ++ 
  gi|344210108|ref|YP_004786284.1|  14 TVVITT-YDRPEFLQKAVDTVTAQRYdpIELIVVDDHSPTPADDVlnDRDPDFErFEIHRHAENQGANAARNTGIEV 89 
                                       99***9.**************766551155555544445555444755555555566666666666777899999** PP

                   Glyco_transf_64  74 ieTdavlslDddillstdeldfAFsvwr.efpdrivGfvarshvwd 118
                                        + + +  lDdd   + +++    + ++ + p+  v + +r+ v d
  gi|344210108|ref|YP_004786284.1|  90 ASGEYIAFLDDDDRWDPEKIATQVNAFQdSGPEVGVVYTGRKVVDD 135
                                       *******************999999999667887788888886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2453.69
//
Query:       gi|344210109|ref|YP_004786285.1|  [L=382]
Description: UDP-N-acetylglucosamine 2-epimerase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-102  342.8   0.0     2e-102  342.6   0.0    1.0  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
  ------ inclusion threshold ------
      0.073   13.1   0.0       0.17   11.9   0.0    1.7  2  Glyco_transf_4   Glycosyltransferase Family 4
       0.11   12.9   0.0       0.38   11.2   0.0    1.9  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
       0.22   11.6   0.0       0.44   10.6   0.0    1.5  1  MGDG_synth       Monogalactosyldiacylglycerol (MGDG) synthase


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 !  342.6   0.0  4.5e-106    2e-102       3     346 ..      26     358 ..      24     359 .. 0.95

  Alignments for each domain:
  == domain 1  score: 342.6 bits;  conditional E-value: 4.5e-106
                                       HTTS-..EEEEEEE-S--SGGGTHHHHHHTT----SEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEEESSSHH CS
                       Epimerase_2   3 lkaeselelqlvvtGqHldremgdtvfeeleiekpdydlnsdsqslakstgrvligleevleeekpDlvlvlGDtne 79 
                                       ++++ ++++++++tGqH++++++ ++f++l+++ p ++l+++s+s++++tg+++ig+e+ l++ +pD+++v+GDtn+
  gi|344210109|ref|YP_004786285.1|  26 CDRR-DVSTIVIHTGQHYSKSLDTVFFRQLDLAPPAVNLDVGSGSHGEQTGEMVIGIEQHLKDADPDVLFVQGDTNS 101
                                       5555.899********************************************************************* PP

                                       HHHHHHHHHHTT-EEEEET-----S-TT..SHHHHHHHHHHHT-SEEEESSHHHHHHHHHTT--GGGEEE---HHHH CS
                       Epimerase_2  80 tlagalaAfklripvaHveAGlRsfdltegmpeEinRhlidklsdlhfapteearenLlkegeeeerifvvGntviD 156
                                       tlagala++kl+i+vaH+eAGlRs+d++  mpeE nR++id+  d +  pt e ++ L++eg++++ri+v+Gnt++D
  gi|344210109|ref|YP_004786285.1| 102 TLAGALAGSKLDIEVAHIEAGLRSYDRD--MPEERNRIIIDHAVDHLYPPTGETANLLREEGISDNRITVTGNTIVD 176
                                       ****************************..*********************************************** PP

                                       HHHHHHHHHH...T-HHHHHH..--SS-EEEEE---HHHHTSHHHHHHHHHHHHHHHHHH--EEEEE--..HHHHHH CS
                       Epimerase_2 157 alllskeeieeklkaseilke..lkekkyvlvtlHrrenedeperlkeilealkalakekdvevvvpvhnnprtrkr 231
                                       a++ + ++ +   + s il++  l+  ++ l+t+Hr+en+d+ +r+++il  ++a a +++  v++pvh  pr ++r
  gi|344210109|ref|YP_004786285.1| 177 AVMAYDDTSS---SVSSILADldLSPGEFDLLTAHRAENVDDRDRFANILFGVAAAATRRENDVIYPVH--PRAKDR 248
                                       **99999887...34699999999***********************************9999******..****** PP

                                       HHHHHHH-.TTEEEE----HHHHHHHHHC-SEEEES-HHHHHHHHHCT--EEESSSS-S-THHHHTTSEEE-TT-HH CS
                       Epimerase_2 232 lleeleel.envtlieplgyldflsllknaklvltdSgGiqeEapslgvpvvnlReeteRpegveagtnvlvgtdke 307
                                       l+e   ++ + ++ +epl++ dfl+l ++a lv tdSgG+qeE+++lg+p+v+lR+ teRpe+v ag+n++vg++++
  gi|344210109|ref|YP_004786285.1| 249 LEEFDLSVpDCIRTVEPLDFFDFLRLESTASLVFTDSGGVQEETCVLGTPCVTLRNGTERPETVFAGANCIVGHRPD 325
                                       *764445547******************************************************************* PP

                                       HHHHHHHHHCT-..--......--TT-SS-HHHHHHHHH CS
                       Epimerase_2 308 eIvaaleklledkkelekmanaknpYgdGkaseriveil 346
                                       +Iva +++++ +      + +++ p+gdG+ase i++ l
  gi|344210109|ref|YP_004786285.1| 326 DIVAGARQMRPK------VGDWELPFGDGNASEYILDDL 358
                                       **********55......778888***********9865 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.7e-05      0.17      62     166 ..      79     174 ..      24     177 .. 0.77
   2 ?   -3.5   0.0       2.1   9.3e+03     129     150 ..     230     251 ..     206     262 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.7e-05
                    Glyco_transf_4  62 rrlrrllkrekpDvvHahspaal.gaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrv 137
                                         + ++lk  +pDv+ +++     +a++la   +l+i + +   gl       + + + + ++r +     +++d++
  gi|344210109|ref|YP_004786285.1|  79 IGIEQHLKDADPDVLFVQGDTNStLAGALAGS-KLDIEVAHIEAGLR-----SYDRDMPEERNRIII---DHAVDHL 146
                                       56789999*******99975555055555555.59988877777777.....233333334444444...4569*** PP

                    Glyco_transf_4 138 iavSeatadelrerygvppekitVipnGv 166
                                         ++ +ta+ lre  g++ ++itV  n +
  gi|344210109|ref|YP_004786285.1| 147 YPPTGETANLLRE-EGISDNRITVTGNTI 174
                                       *************.**********98865 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.1
                    Glyco_transf_4 129 rllrradrviavSeatadelre 150
                                        + r  d +  v + ++d+l+e
  gi|344210109|ref|YP_004786285.1| 230 ATRRENDVIYPVHPRAKDRLEE 251
                                       3344444444445555555555 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 ?   11.2   0.0   8.5e-05      0.38      45     159 ..      63     172 ..      27     173 .. 0.77
   2 ?   -2.6   0.1       1.5   6.5e+03     118     148 ..     223     253 ..     204     264 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.5e-05
                   Glyco_trans_4_4  45 lpvprrpspladlaalralrrllrqrrerpdvvhahs.ptaglaarlarrrrgiplvvtlhglllrrgsgavrrlyr 120
                                       l+v+ ++++  + +++ + ++ l  ++  pdv+ +++   + la++la  + +i + +   gl   ++  ++ r + 
  gi|344210109|ref|YP_004786285.1|  63 LDVGSGSHGEQTGEMVIGIEQHL--KDADPDVLFVQGdTNSTLAGALAGSKLDIEVAHIEAGLRSYDRDMPEERNR- 136
                                       55555555555556666778889..99*********9788********9788999998888876555544444433. PP

                   Glyco_trans_4_4 121 alerrllrr.adavlvvseaeaeelralgvpadrvvvvpn 159
                                            ++ + +d++  ++ + a +lr+ g+ ++r++v +n
  gi|344210109|ref|YP_004786285.1| 137 ----IIIDHaVDHLYPPTGETANLLREEGISDNRITVTGN 172
                                       ....2333338**************************998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                   Glyco_trans_4_4 118 lyralerrllrradavlvvseaeaeelralg 148
                                       l+  +  ++ r  d++  v++   ++l+++ 
  gi|344210109|ref|YP_004786285.1| 223 LFGVAAAATRRENDVIYPVHPRAKDRLEEFD 253
                                       4444555556666677777777777777654 PP

>> MGDG_synth  Monogalactosyldiacylglycerol (MGDG) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   9.8e-05      0.44     135     166 ..     140     171 ..     135     174 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.8e-05
                                       -TT-SEEEESSHHHHHHHHHCT--GGGEEE-- CS
                        MGDG_synth 135 rkeidryyvaskevkkealekGidksnikvtG 166
                                          +d++y ++ e+++ ++e+Gi++++i vtG
  gi|344210109|ref|YP_004786285.1| 140 DHAVDHLYPPTGETANLLREEGISDNRITVTG 171
                                       5689***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 3171.41
//
Query:       gi|344210110|ref|YP_004786286.1|  [L=399]
Description: glycosyltransferase [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-29  101.5   0.0    5.3e-29  100.9   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    2.3e-23   83.1   0.0    5.1e-23   82.0   0.0    1.6  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.5e-12   47.9   0.1    3.5e-12   46.7   0.0    1.6  2  Glyco_transf_4   Glycosyltransferase Family 4
    3.7e-11   43.7   0.5    8.8e-10   39.2   0.0    2.7  3  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      1e-06   29.0   0.0    2.9e-06   27.6   0.0    1.7  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 !  100.9   0.0   1.5e-32   5.3e-29       4     171 ..     205     369 ..     202     370 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 1.5e-32
                                       HHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES..STTHHHHHHHHHHHCTTCGGGEEE CS
                   Glycos_transf_1   4 kkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG.ngeeekelkklaeelelsdnviflg 79 
                                       + r++lg++ +  ++l+vg + ++Kg+  + +++++l   + p++ +v++G +g+++ el++  +e   s ++ ++g
  gi|344210110|ref|YP_004786286.1| 205 QLRRELGIDADATVALFVGEFCERKGIPEVTTVLPEL---SLPDTEFVFIGhGGAQRSELQAALAESDFSGRHVYTG 278
                                       6789999****************************99...59*********99************************ PP

                                       CCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHH CS
                   Glycos_transf_1  80 evsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkll 156
                                         s  +l  +l+ ad++vlps+ Eg ++v++EAmaa ++v+ +++gg++e+v+dgetG+l++p +a ala+a+++l 
  gi|344210110|ref|YP_004786286.1| 279 ITS-LALRRWLTVADLLVLPSRAEGRPTVIYEAMAAETAVLGTDIGGVSEQVVDGETGVLIQPRDATALADALESLT 354
                                       999.88*********************************************************************** PP

                                       HSHHHHHHHHHHHHH CS
                   Glycos_transf_1 157 edeelrerlgenark 171
                                       +d+++ ++lg n+ +
  gi|344210110|ref|YP_004786286.1| 355 TDSDRLAELGSNGHQ 369
                                       **********99976 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 !   82.0   0.0   1.4e-26   5.1e-23       3     134 .]     218     356 ..     216     356 .. 0.90

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 1.4e-26
                                       EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHT..T-T.TEEEE---.THHHHHHHH-SE CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaa..gleerveftGfv.edlaellaaadv 75 
                                       v lfvG +  ++kg+  +   +p+l   d ++v++G g  +++el++ +a  +++ r ++tG     l+++l  ad+
  gi|344210110|ref|YP_004786286.1| 218 VALFVGEF-CERKGIPEVTTVLPELSLPDTEFVFIGHGGaQRSELQAALAesDFSGRHVYTGITsLALRRWLTVADL 293
                                       679*****.567**************889*******998866899976655888889999**88556********** PP

                                       EEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  76 fvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                       +v+Ps  eg + +++Eamaa+++v  td+gg++e v  ge+g+l++p+d+ ala+a++ L +d
  gi|344210110|ref|YP_004786286.1| 294 LVLPSraEGRPTVIYEAMAAETAVLGTDIGGVSEQVvdGETGVLIQPRDATALADALESLTTD 356
                                       *****999***********************988667*********************99876 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   9.6e-16   3.5e-12       7     170 .]      23     197 ..      20     197 .. 0.80
   2 ?   -2.8   0.0       1.6   5.6e+03     125     144 ..     282     301 ..     267     305 .. 0.76

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 9.6e-16
                    Glyco_transf_4   7 hvleLaraLarrGheVtvvtpgddgpleeev..............elvvrvprvplpllkrllr..slaflrrlrrl 67 
                                       + ++++r L++ G  V+ v+p++  p+                  ++v+ ++ ++l++++ ++     +f++r+ + 
  gi|344210110|ref|YP_004786286.1|  23 FNHRIIRSLQDSGLSVDAVAPRPFAPPVGPKseynmlpsveewdgYDVHHPRFWYLLPKRLFYGlsGDSFAKRVSEY 99 
                                       568999*************77765555555556777******88777777777776666665541135677888888 PP

                    Glyco_transf_4  68 lkre..kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSe 142
                                       +++   +pD+v a + +  g++ll  +r +++pl +  Hg++     +++  +++ ++ ++ + +l ++ +v++vS+
  gi|344210110|ref|YP_004786286.1| 100 VDETfeEPDLVQACHIYLDGYGLLPYCRNHDVPLFVVSHGHF----MNNYEDLARGVRSRVDE-TLTACSKVLCVSD 171
                                       888899*****999999999**9999999*************....55666666666666554.47*********** PP

                    Glyco_transf_4 143 atadelrerygvppekitVipnGvDler 170
                                       a+ad  r+  +v++ek++++p G  +er
  gi|344210110|ref|YP_004786286.1| 172 ALADTARS--HVSSEKVETVPIGATPER 197
                                       ********..999********9987765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.6
                    Glyco_transf_4 125 alerrllrradrviavSeat 144
                                         +rr+l  ad ++ +S+a+
  gi|344210110|ref|YP_004786286.1| 282 LALRRWLTVADLLVLPSRAE 301
                                       45677778899999999886 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 !   39.2   0.0   2.5e-13   8.8e-10       8     160 .]      25     192 ..      20     192 .. 0.82
   2 ?    1.6   0.1     0.096   3.4e+02      94     142 ..     228     303 ..     205     321 .. 0.54
   3 ?   -1.2   0.0      0.67   2.4e+03     105     126 ..     375     396 ..     338     398 .. 0.74

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 2.5e-13
                   Glyco_trans_4_4   8 aelaraLaarGheVtvltpapapg..........ape..leedgvrvh..rlp..vprrp.spladlaalralrrll 67 
                                       ++++r+L++ G +V+ ++p+p ++            +  +e+dg  vh  r++  +p r   +l   +++ ++ +++
  gi|344210110|ref|YP_004786286.1|  25 HRIIRSLQDSGLSVDAVAPRPFAPpvgpkseynmL-PsvEEWDGYDVHhpRFWylLPKRLfYGLSGDSFAKRVSEYV 100
                                       689***************99877767776655552.1457899****955555644444355677778********* PP

                   Glyco_trans_4_4  68 rqrrerpdvvhahsptaglaarlar.rrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaee 143
                                           e pd+v+a ++++ ++++l   r +++pl+v  hg+  + +   +r ++ ++ + +l+ +  vl+vs+a+a++
  gi|344210110|ref|YP_004786286.1| 101 DETFEEPDLVQACHIYLDGYGLLPYcRNHDVPLFVVSHGHFMNNYEDLARGVRSRV-DETLTACSKVLCVSDALADT 176
                                       8899**********999999999963578***********9999988888888776.78999*************** PP

                   Glyco_trans_4_4 144 lralgvpadrvvvvpng 160
                                       +r + v  ++v++vp g
  gi|344210110|ref|YP_004786286.1| 177 ARSH-VSSEKVETVPIG 192
                                       9988.566999999976 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.096
                   Glyco_trans_4_4  94 rrgiplvvtlh.......................glllrrgsgavrrlyralerrllrr....adavlvvseaeae 142
                                       r+gip v t+                        +++l++     r++y+ + +++lrr    ad+++ +s+ae +
  gi|344210110|ref|YP_004786286.1| 228 RKGIPEVTTVLpelslpdtefvfighggaqrselQAALAESDFSGRHVYTGITSLALRRwltvADLLVLPSRAEGR 303
                                       5566666666333333333333332233222222222333333344455444444444444448888888887765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.67
                   Glyco_trans_4_4 105 glllrrgsgavrrlyralerrl 126
                                       g+++++++++vr ly+++e   
  gi|344210110|ref|YP_004786286.1| 375 GWTWDGYATRVRELYAEFEGKG 396
                                       4555666777777777777655 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 !   27.6   0.0     8e-10   2.9e-06       4      87 ..     296     382 ..     293     388 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 8e-10
                   Glyco_trans_1_2   4 npsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarerv. 77 
                                        psr+e+  ++++Ea+a+ + +l +d+ g+ e + +g++++l++  d   la++++ l ++ ++ ++++ ++++r  
  gi|344210110|ref|YP_004786286.1| 296 LPSRAEGRPTVIYEAMAAETAVLGTDIGGVSEQVVDGETGVLIQprDATALADALESLTTDSDRLAELGSNGHQRLv 372
                                       5899999999****************************************************************975 PP

                   Glyco_trans_1_2  78 laehtydhra 87 
                                        +  t+d  a
  gi|344210110|ref|YP_004786286.1| 373 NQGWTWDGYA 382
                                       7788887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2870.46
//
Query:       gi|344210111|ref|YP_004786287.1|  [L=652]
Description: hypothetical protein HAH_5170 [Haloarcula hispanica ATCC 33960]
Scores for 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-36  124.2   2.1    1.4e-35  123.0   2.1    1.6  1  Hepar_II_III    Heparinase II/III-like protein
    1.6e-19   70.4   0.0    2.3e-19   69.9   0.0    1.1  1  Hepar_II_III_N  Heparinase II/III N-terminus


Domain annotation for each model (and alignments):
>> Hepar_II_III  Heparinase II/III-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.0   2.1   1.6e-39   1.4e-35      10     212 ..     387     595 ..     378     629 .. 0.81

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 1.6e-39
                                       TTTTEEEEEST-EEEEEEEECTCTTB.CTTS-S-TTEEEEEETTEESS---C-SSTTTHHHHHHHTSGGGSSSEEET CS
                      Hepar_II_III  10 pdsGyavlragatvlvvdagppgpgdlsghaHaDtLsfelssggqrlivdcGtytyggpewrnaarstaaHNTlvvd 86 
                                        +sGy++l  g+ +l+vd g++gp +l++h+H+D  +++ +++gqr+++d+G++ y   ++r++ rs +aHNT++ d
  gi|344210111|ref|YP_004786287.1| 387 TASGYYWLGTGRSRLLVDGGAIGPPHLPAHSHNDHFAVLWWADGQRILTDTGVFEYLPTTERQYSRSVEAHNTVQYD 463
                                       589************************************************************************** PP

                                       TBS--HCCCHHSCCEEEEEEEEEE.SSSEEEEEEEEEEE..T.TTTEEEEEEEEEETTTEEEEEEEEECSEEEEEEE CS
                      Hepar_II_III  87 gksssrfagkfrlgrraevereee.eggvellaaehdgy..aapfgvvhrRtllsldgeslrveDslegsgehepfa 160
                                       +++  + +g+++ grr+e+e+ +e  +g ++  + h       +++ +hrR+++  +++ ++v D+++++++++ + 
  gi|344210111|ref|YP_004786287.1| 464 DVEPIQTGGSYLFGRRIEPEVAYEhRDGLTCFDG-HYRTesSSQPQYSHRRHIY-GSDTWWLVWDTVSAEKSAP-IR 537
                                       **********************665777777777.444447899999*******.889***************9.** PP

                                       EEEEESTTECEEEETTTTEEEEESTTE.......EEEEEEECECEEEEEEECEEEEETC CS
                      Hepar_II_III 161 lrfhlhpdvevslgadgagvllalpsg.......eawvfraeggetlaleesvylpgyg 212
                                        r+hl p+v+v++   +++++l+ +s         a  +  +++ ++  +   y p++g
  gi|344210111|ref|YP_004786287.1| 538 SRLHLDPAVTVRSTPSDGQQHLVVSSLeggsetgIAHIYPLDTD-RIIRDQRPYYPEFG 595
                                       *********88888666666444443311222211134555555.55555555566666 PP

>> Hepar_II_III_N  Heparinase II/III N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.0   2.6e-23   2.3e-19      80     314 ..     122     353 ..      94     363 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 2.6e-23
                                       EETTCC-TT--STT..-CHHHHHHTTTTCHHHHHHHHHHH--CHHHHHHHHH.HHHHHHHS-HHHHSSS..CCCT-H CS
                    Hepar_II_III_N  80 skgkdidWeynptk.adnElrwQlhRhkwweplakaYratgdekyakewveq.ykdwikknPkeneaekkeksaWrt 154
                                       ++   +dW    +   +  +  Q h  +++      Y++  d + ++e  eq ++dw ++  +   +    + +W +
  gi|344210111|ref|YP_004786287.1| 122 ESASGVDWVGAGVPePSTLWGLQFHGFAFLMWPVLGYQSPTDCTAVEETLEQwLRDWDRSGSNRIGQPAYLRRSWTP 198
                                       455667776655542355566677777777777778999999988888887745899999998888899999***** PP

                                       HHHHHHHHHHHHHHHHHTTSTTS-HHHHHHHHHHHHHHHHHHHCC..STTSCCCHHHHHHHHHHHHHH-TTBTTHHH CS
                    Hepar_II_III_N 155 levseRlqdqveafelflnsksftpefLstflvsyaehaeyllkn..YseegNillfeaqalvtaGvlfPEfkeaek 229
                                         vs R+ + v+ +    ++  + p     + + ++++a +l+++  +   gN+l+ +  alv+aG +fPE    ++
  gi|344210111|ref|YP_004786287.1| 199 HAVSLRILNLVRFYAWAEDV--LEPPHSARLRKLVYKNAAFLSNHveHDIGGNHLIENGAALVMAGLFFPE--SGQQ 271
                                       *******8888777665555..6777777777888999*****99656669*******************9..789* PP

                                       HHHHHHHHHHHHHHHCB-TTS-BTT--HHHHHHHHHHHHHHHHHHHCTT-GGGS-CCCCCCHHHHHHHHHHTS-CCC CS
                    Hepar_II_III_N 230 WresgisilneeikkqvleDGvqyeldlgYHiaaidnflkllrlakanglenelpasyvetlekaievvlnllyPdy 306
                                       W ++g+++l  e+ +q+ +DG ++e ++ YH ++++  l +++l+k++g+  e+p +  +     +++  ++  Pd 
  gi|344210111|ref|YP_004786287.1| 272 WVKQGLDVLV-ETAEQFRADGGHFERSPMYHAVTVTRYLTVIDLLKRVGR--EIPPEVQRVATAGVRFLRDMEPPDG 345
                                       ********97.5789**********************************9..9************************ PP

                                       -S---SS- CS
                    Hepar_II_III_N 307 tlpafnDs 314
                                        lp +nDs
  gi|344210111|ref|YP_004786287.1| 346 RLPLLNDS 353
                                       *******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (652 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); 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: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 4430.32
//
Query:       gi|344210112|ref|YP_004786288.1|  [L=438]
Description: glycosyltransferase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-19   70.9   0.0    2.4e-19   70.1   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.1e-16   60.8   0.8    3.4e-16   60.1   0.8    1.3  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    2.7e-15   56.3   0.0    3.9e-15   55.8   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    5.3e-11   42.8   0.1    1.7e-10   41.2   0.1    1.8  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.2e-05   25.6   0.0    2.7e-05   24.5   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 !   70.1   0.0   6.7e-23   2.4e-19       2     133 ..     229     370 ..     228     371 .. 0.86

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 6.7e-23
                                       EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH- CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaa 73 
                                       p i++vG++  + +++d  ++a+ +l  +d++l+++G+g+  p +l+e +   g+e+ veftG +  e ++++l++a
  gi|344210112|ref|YP_004786288.1| 229 PAIVYVGNI-GHAQALDECIRAMGRLN-NDAELYLIGSGDaVP-HLREVVTegGVEDAVEFTGPIphEAVPAALDDA 302
                                       789******.4459*************.55*********9765.9998885599***********9777******** PP

                                       SEEEE--....-...--SHHHHHHHHTT-EEEE-TGGGTTT--TTSS..EE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  74 dvfvaPs....e...gfglkllEamaaglpvVatdvggiaevvgeng..llvppgdpealaeailrLle 133
                                        + +aP+    e    ++ k++E+m aglpvV+t  g ++++++++g  +     dp  +a a   Ll+
  gi|344210112|ref|YP_004786288.1| 303 AIGIAPLlddsEldyAMPTKVYEYMGAGLPVVTTGQGELERFIEQSGggIHTT-PDPGGIATAFDSLLA 370
                                       ********98747779*******************988999995544335553.4999***99999986 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 !   60.1   0.8   9.4e-20   3.4e-16       1     160 []      20     208 ..      20     208 .. 0.75

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 9.4e-20
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvlt..........papapgapeleedgvrvhrlp....vprrpspladla..alr 61 
                                       +G + +++++a +L  rG++V+v++          +++ +++ e+++  v+v+rl+    + ++p+ + +la   ++
  gi|344210112|ref|YP_004786288.1|  20 SGHASRIQNMATNLDSRGWDVEVVApppcfphgsfDRDWYRSKEIRQQDVTVRRLWawqpTEPNPGIVSRLAyyVTF 96 
                                       6999*********************55555444443333336679999*******8532233445666666633458 PP

                   Glyco_trans_4_4  62 alrrll..rqrrerpdvvhahspt.aglaarlarrrrgiplvvtlhglllrrg....sgavrrly....ralerrll 127
                                       al ++l     r+r+dvv + +p+ + ++a +  + ++  +vv++++l+ +        ++  ++    r ++r +l
  gi|344210112|ref|YP_004786288.1|  97 ALHAFLwlLITRRRYDVVMTTTPPiSTGLAGFVTVLTNSLWVVDVRDLWIDASvslgFIPEDGIIehgsRYFQRQVL 173
                                       88888876779***********76555555566669**********99966443323333445555566889***** PP

                   Glyco_trans_4_4 128 rradavlvvseaeaeelra.lg.vpadrvvvvpng 160
                                       +  da+ v++e + ++l++ +g +  +++ +vpng
  gi|344210112|ref|YP_004786288.1| 174 HTSDAIAVTTETLGDHLCEqYGaALSEKLLLVPNG 208
                                       *******************7886567899999998 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 !   55.8   0.0   1.1e-18   3.9e-15       6     169 ..     219     382 ..     215     385 .. 0.93

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 1.1e-18
                                       HHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCH CS
                   Glycos_transf_1   6 rkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevs 82 
                                       + +++ +++++ i++vg++ + + +d  i+a+ +l    n+++ l ++G+g+    l++ + e +++d v+f+g ++
  gi|344210112|ref|YP_004786288.1| 219 SGDSVVDSDDPAIVYVGNIGHAQALDECIRAMGRL----NNDAELYLIGSGDAVPHLREVVTEGGVEDAVEFTGPIP 291
                                       55677899*************************99....99************************************ PP

                                       SSSHHHHHHCESEEEEEESS.....BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHH CS
                   Glycos_transf_1  83 redleellknadifvlpsis.....EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairk 154
                                       +e++++ l  a i ++p         ++++ ++E+m aglpv+++  g +   +++   G++  p  +  +a a+++
  gi|344210112|ref|YP_004786288.1| 292 HEAVPAALDDAAIGIAPLLDdseldYAMPTKVYEYMGAGLPVVTTGQGELERFIEQSGGGIHTTPD-PGGIATAFDS 367
                                       *****************999999999****************************999988887776.********** PP

                                       HHHSHHHHHHHHHHH CS
                   Glycos_transf_1 155 lledeelrerlgena 169
                                       ll +e +r++ g+ +
  gi|344210112|ref|YP_004786288.1| 368 LLASEAKRRERGQSG 382
                                       *****9988877766 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.1   4.7e-14   1.7e-10       3     170 .]      21     213 ..      19     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 4.7e-14
                    Glyco_transf_4   3 GverhvleLaraLarrGheVtvvtpgddgpleeev....................elvvrvprvplpllkrllrsla 59 
                                       G +  + ++a +L  rG++V+vv+p +  p++  +                     +    p + ++++  ++ ++a
  gi|344210112|ref|YP_004786288.1|  21 GHASRIQNMATNLDSRGWDVEVVAPPPCFPHGSFDrdwyrskeirqqdvtvrrlwAWQPTEPNPGIVSRLAYYVTFA 97 
                                       7788899****************888776666666778889999999999999887777777777888999999999 PP

                    Glyco_transf_4  60 flrrlrrllkrekpDvvHahsp.aalgaallalrrrlgiplVltvHglye....krllkarlkplsrllralerrll 131
                                        +  l+ l+ r ++Dvv + +p ++ g+a++   + ++   V+ v +l+     +    +  +  +   r++ r++l
  gi|344210112|ref|YP_004786288.1|  98 LHAFLWLLITRRRYDVVMTTTPpISTGLAGFVTVL-TNSLWVVDVRDLWIdasvSLGFIPEDGIIEHGSRYFQRQVL 173
                                       999**************777741445555555554.67677777777777999955555677888889999999*** PP

                    Glyco_transf_4 132 rradrviavSeatadelrerygvpp.ekitVipnGvDler 170
                                       + +d++ +++e++ d+l+e yg +  ek+  +pnGvD +r
  gi|344210112|ref|YP_004786288.1| 174 HTSDAIAVTTETLGDHLCEQYGAALsEKLLLVPNGVDMDR 213
                                       **********************54459**********997 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 !   24.5   0.0   7.4e-09   2.7e-05      11      85 ..     319     394 ..     304     401 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 7.4e-09
                   Glyco_trans_1_2  11 pnlrlfEaaacGafaltddaegleelftpgkevilfe.dleelaekiryllanpeerraiaeaarervlaehtydh 85 
                                       + ++++E++++G +++t+   +le++++    +i    d+  +a +++ lla++++rr++++ ++  v   ++  h
  gi|344210112|ref|YP_004786288.1| 319 MPTKVYEYMGAGLPVVTTGQGELERFIEQSGGGIHTTpDPGGIATAFDSLLASEAKRRERGQSGQDYVSPTYDRSH 394
                                       4579**************99*******98877777778**************************987766655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 3333.96
//
Query:       gi|344210113|ref|YP_004786289.1|  [L=253]
Description: hypothetical protein HAH_5172 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-09   35.7   0.0    2.3e-08   34.1   0.0    1.9  1  Glycos_transf_2  Glycosyl transferase family 2
    1.1e-07   31.6   0.0     0.0073   15.8   0.0    2.2  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
    5.5e-06   26.4   0.0       0.03   14.2   0.0    2.3  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00048   19.6   0.0      0.024   14.1   0.0    2.2  1  Glyco_transf_21  Glycosyl transferase family 21
    0.00049   19.7   0.0    0.00079   19.0   0.0    1.3  1  Glyco_transf_7C  N-terminal domain of galactosyltransferase
    0.00079   19.4   0.0     0.0026   17.7   0.0    1.8  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 !   34.1   0.0   7.6e-12   2.3e-08      67     169 ..      40     129 ..      31     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 7.6e-12
                                       HHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCC CS
                   Glycos_transf_2  67 kagalnaglraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfker 143
                                        a+a+n+g+r+a+g+ ++flD+D++p+ +++ ++ e l++ +a   + +r +  g+++++             ++  
  gi|344210113|ref|YP_004786289.1|  40 AAAARNKGIREANGEKLVFLDDDSVPKGEYFDRVSELLDEYPA---VTGRIHDTGSPYTRGL----------SGQYD 103
                                       589*************************************777...5555555555555554..........47788 PP

                                       HCCCCCCSTTCSTCCCEEEEHHHHHC CS
                   Glycos_transf_2 144 krslkgnlsfeigsaallrrealeel 169
                                       ++  ++ +  ++g+++++rr++le++
  gi|344210113|ref|YP_004786289.1| 104 QGDNGHVTDTVVGCNMAIRRDVLEDV 129
                                       888888999999999999***99987 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 !   13.5   0.0   1.2e-05     0.036      68     102 ..      39      73 ..      34      80 .. 0.85
   2 !   15.8   0.0   2.4e-06    0.0073     166     206 ..     117     156 ..     110     174 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                   Glyco_tranf_2_2  68 slaaarNrGaskaesdlvlFlDaDcfissDkfeki 102
                                       s aaarN+G+ +a+++ ++FlD D     + f+++
  gi|344210113|ref|YP_004786289.1|  39 SAAAARNKGIREANGEKLVFLDDDSVPKGEYFDRV 73 
                                       789*********************98777666665 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.4e-06
                   Glyco_tranf_2_2 166 ssilinrraflevGGyDErfrGhgaEDfdlllRlakaiksl 206
                                        ++ i+r  +  vGG+DEr+   g E+ +l+ R+   +   
  gi|344210113|ref|YP_004786289.1| 117 CNMAIRRDVLEDVGGFDERL-PYGHEEVELIDRVFESYTVW 156
                                       6889****************.99**********99887655 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 !   14.2   0.0   9.9e-06      0.03      73     121 ..      38      84 ..      21      91 .. 0.83
   2 !    9.9   0.0   0.00021      0.64     158     221 ..     112     175 ..      99     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.9e-06
                   Glyco_tranf_2_3  73 tgksralnealravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavg 121
                                       ++++ a n ++r ++++ ++++DdD+v   ++++r+  ++ ++    av+
  gi|344210113|ref|YP_004786289.1|  38 GSAAAARNKGIREANGEKLVFLDDDSVPKGEYFDRVSELLdEY---PAVT 84 
                                       5788889******************************999444...4444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00021
                   Glyco_tranf_2_3 158 ltlnGsgslirrevlkelegldp.lflltdDyelglrlrragfrtayvpgaavrevfpsslkayi 221
                                       +t+ G  ++irr+vl++ +g+d+ l +  + +el  r+ +  + + y p+++v++ f +s+ +y 
  gi|344210113|ref|YP_004786289.1| 112 DTVVGCNMAIRRDVLEDVGGFDErLPYGHEEVELIDRVFE-SYTVWYSPDLLVEHPFAESIPDYL 175
                                       788899*****************55555588888777664.677778888888888887766655 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 !   14.1   0.0     8e-06     0.024      96     121 ..     109     134 ..      41     138 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8e-06
                   Glyco_transf_21  96 sglgfavGksmalrreaLeaiGGfea 121
                                         ++++vG  ma+rr++Le++GGf +
  gi|344210113|ref|YP_004786289.1| 109 HVTDTVVGCNMAIRRDVLEDVGGFDE 134
                                       34579*******************75 PP

>> Glyco_transf_7C  N-terminal domain of galactosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.6e-07   0.00079      16      58 ..     111     152 ..      96     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.6e-07
                   Glyco_transf_7C  16 yekyfgGvlalrkedfekiNGfsntfwgWGgEDdelyaRlakk 58 
                                        ++++g+++a+r++  e+++Gf++++  +G E  el++R++++
  gi|344210113|ref|YP_004786289.1| 111 TDTVVGCNMAIRRDVLEDVGGFDERL-PYGHEEVELIDRVFES 152
                                       5899*******************986.7************987 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 !   17.7   0.0   8.7e-07    0.0026       3     162 ..      57     236 ..      55     249 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.7e-07
                   Glyco_trans_2_3   3 lllDaDtvlppdclreiaaelaspevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsgafl 79 
                                       ++lD+D+v+  +++ ++ ++l  +e+ +v+g +  ++ +++++ l    +++  g  ++v+       ++vG ++++
  gi|344210113|ref|YP_004786289.1|  57 VFLDDDSVPKGEYFDRVSELL--DEYPAVTGRIHDTG-SPYTRGLSG-QYDQ--GDNGHVT------DTVVGCNMAI 121
                                       789999999999999998888..46999999999994.455555554.5653..3333443......3468****** PP

                   Glyco_trans_2_3  80 rrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGcel.eklil.... 151
                                       rr++l++vgg+d +     E  ++  r ++  y+v + p+ lv   +  ++ ++l   +R+     + +++i+    
  gi|344210113|ref|YP_004786289.1| 122 RRDVLEDVGGFDERLPYGHEEVELIDRVFES-YTVWYSPDLLVEHPFAESIPDYLEKQYRHGKES-IpYYKIRgenv 196
                                       ************7777889999999999887.9******9999999999***********99885.34444444544 PP

                   Glyco_trans_2_3 152 .............................lvrllgylgsl 162
                                                                     v+++g+l+ +
  gi|344210113|ref|YP_004786289.1| 197 prrimrfiliptyyldstvsksiistvgqVVSNIGMLHGY 236
                                       4444445555555555555555555555444555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.32s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1501.31
//
Query:       gi|344210114|ref|YP_004786290.1|  [L=144]
Description: phosphotransferase system IIB component [Haloarcula hispanica ATCC 33960]
Scores for 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-17   62.2   1.6    8.1e-17   61.7   1.6    1.2  1  PTS_IIB   PTS system, Lactose/Cellobiose specific IIB subunit


Domain annotation for each model (and alignments):
>> 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 !   61.7   1.6   4.5e-21   8.1e-17       2      87 ..       5      92 ..       4      95 .. 0.94

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 4.5e-21
                                      EEEEESSSHHHHHHHHHHHHHHHHHCT....EEEEETTEE..GGGHHHHHHT-SEEEEEESSGGCTHHHHTTSEEEEEC CS
                           PTS_IIB  2 illaCgaGmatSlmaaeklekaakelg....ieaegeagv..eleaeeiaddaDlvllapqvrvkdlarfagkpvavin 74
                                      +++ C++G+a+S+maae+le+ a+elg    +e++g++g+  el+ ++i++ aD+ ++a ++ v + +rf ++p+++ +
  gi|344210114|ref|YP_004786290.1|  5 AVTSCPTGIAHSQMAAENLEQTAEELGheikVEVQGAMGAenELSEADIES-ADAAIIASDTSV-SQDRFSNIPLIKGT 81
                                      89***************************************9999999999.***********9.*********99999 PP

                                      TTHHHCCHCHHHH CS
                           PTS_IIB 75 ikdalgimdgekv 87
                                      +kda+  +d+e +
  gi|344210114|ref|YP_004786290.1| 82 VKDAV--NDAEGM 92
                                      99988..777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1010.79
//
Query:       gi|344210115|ref|YP_004786291.1|  [L=561]
Description: phosphoenolpyruvate-protein phosphotransferase [Haloarcula hispanica ATCC 33960]
Scores for 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-106  353.6   0.0   9.8e-106  353.1   0.0    1.1  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
      3e-24   85.4   0.2      3e-24   85.4   0.2    2.9  4  PEP-utilisers_N  PEP-utilising enzyme, N-terminal
    4.3e-22   77.6   0.4    8.5e-22   76.7   0.4    1.5  1  PEP-utilizers    PEP-utilising enzyme, mobile domain


Domain annotation for each model (and alignments):
>> 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 !  353.1   0.0  1.6e-109  9.8e-106       8     292 ..     249     534 ..     243     536 .. 0.97

  Alignments for each domain:
  == domain 1  score: 353.1 bits;  conditional E-value: 1.6e-109
                                       CCCCCCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCCHHHHHHHHHHHHHHHHHTTTSEEEEEX CS
                   PEP-utilizers_C   8 ktllavtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmareelpteeeqaeaykkvleamngrpvvvRt 84 
                                       ++    t+dgk+i+v+aNi++p + + a++ ga+G+GL+RtEflf++re++p+e+eq+ea ++vl+++ +  vvvRt
  gi|344210115|ref|YP_004786291.1| 249 VDESVETTDGKHIEVAANIGQPAELDPAAQRGADGVGLYRTEFLFLDRETPPSEDEQYEAVREVLDTFPDGRVVVRT 325
                                       5667789********************************************************************** PP

                                       XXSSCCGGSGGCHHHH.XSXGGGSSXTHHHHCCS.HHHHHHHHHHHHHHCC..CCEEEEEESSXXSHHHHHHHHHHH CS
                   PEP-utilizers_C  85 lDiggdkelpelkeepeevNPmlGfRgirlglse.pelfetqlrAllrasa..agkleimlPmvasveeleeakkii 158
                                       lDiggdk +p+l ++p+e+NP+lG Rgir++l+   +lf tqlrAllra+a  ag l im+P+va+veel+ a   +
  gi|344210115|ref|YP_004786291.1| 326 LDIGGDKRIPYL-DLPAEENPFLGERGIRRSLDPdSDLFATQLRALLRAAAdgAGDLAIMFPLVATVEELDGALDAL 401
                                       ************.********************989***************7777********************** PP

                                       HHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTTSSEEEEXHHHHHHHHHTXXCCCHCHHHHSXTTTCHHCC CS
                   PEP-utilizers_C 159 eevkeelekegvkkkkkvkvGiMiEvpsaalladklakevdFfSiGtNDLtQytlavdRdneevaklydplepavlr 235
                                         ++++le +  ++  + +vG+MiE+psa+++a++la +vdF+SiGtNDLtQy++a+dR+ne+v  l+dp++p vlr
  gi|344210115|ref|YP_004786291.1| 402 DAAAADLEGR-ETEVADPEVGVMIETPSAVFMAEELAARVDFLSIGTNDLTQYVMAADRENERVGDLHDPTHPGVLR 477
                                       ********99.7777899*********************************************************** PP

                                       CHHHHHHHHHHCCXEEEEESCCCCSCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCT CS
                   PEP-utilizers_C 236 likevikaaeekglkvgiCGelagdpsavellvglGldelSmsaasvpaaraalaqv 292
                                       +i++++k a+ ++++vg+CGe+agdp  +ellvglGldelSmsa  +p +++a++++
  gi|344210115|ref|YP_004786291.1| 478 AIRQTVKSAHDEDAWVGMCGEMAGDPDLTELLVGLGLDELSMSAVTIPEVKTAVSET 534
                                       ****************************************************99876 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 !   85.4   0.2     5e-28     3e-24       1     116 []       7     127 ..       7     127 .. 0.93
   2 ?    0.1   0.1      0.14   8.6e+02      31      55 ..     392     420 ..     385     439 .. 0.65
   3 ?   -3.5   0.0       1.9   1.2e+04      58      76 ..     488     506 ..     475     508 .. 0.56
   4 ?   -2.5   0.4      0.95   5.7e+03      20      45 ..     532     557 ..     520     560 .. 0.48

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 5e-28
                                       E-EEEE-SEEEEEEE....---.-----G.GGHHHHHHHHHHHHHHHHHHHHHHHHHH...T-HHHHHHHHHHHHHH CS
                   PEP-utilisers_N   1 kGiaaspGiaiGkav....eveveeeeveaedveaelerleeAlekvreelealaeka...lgeeeaaifeahlmll 70 
                                       +G++a p  ++G +v    ++++   +  + d+e e er+ +A++++r+ele+ +e +   +ge+eaa+f+ah+++l
  gi|344210115|ref|YP_004786291.1|   7 HGTGATPRSGVGSVVwygrDISLLDPDGVEVDPEMEGERFADAVDTARTELESEREATaerVGEQEAAVFDAHIQFL 83 
                                       69****************96666667778899*********************8877789999************** PP

                                       T-HHHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHTT-HHHHHH CS
                   PEP-utilisers_N  71 eDpelleeveerIregglnaeaAveevveefaaqfealddeylreR 116
                                       eDp++ ++ve++I  +gl+a +Av++++ e+++qfe++d   ++eR
  gi|344210115|ref|YP_004786291.1|  84 EDPTIEDAVETMIG-EGLPAPNAVDAAFGEHIEQFEGMDG-RMAER 127
                                       **************.788********************99.9**99 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHHHHH....T CS
                   PEP-utilisers_N  31 aelerleeAlekvreelealaeka....l 55 
                                       +el+   +Al++++++le ++ ++    +
  gi|344210115|ref|YP_004786291.1| 392 EELDGALDALDAAAADLEGRETEVadpeV 420
                                       56666778999999999887766644331 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHT-HHHH CS
                   PEP-utilisers_N  58 eeaaifeahlmlleDpell 76 
                                       +e a + +  +++ Dp+l+
  gi|344210115|ref|YP_004786291.1| 488 DEDAWVGMCGEMAGDPDLT 506
                                       3455566666788888876 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 0.95
                                       -----G.GGHHHHHHHHHHHHHHHHH CS
                   PEP-utilisers_N  20 eeeeveaedveaelerleeAlekvre 45 
                                       +e+e +a++  a ++rl + + +v++
  gi|344210115|ref|YP_004786291.1| 532 SETEHSAASERADRARLAATRSEVHD 557
                                       23333333334455555555555555 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 !   76.7   0.4   1.4e-25   8.5e-22       2      73 .]     153     226 ..     152     226 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 1.4e-25
                                       --S-EEEEES---HHHHTTS-..GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--T.EEEEEETTTT CS
                     PEP-utilizers   2 leegvILvaeetspsdiagld..kaaGivterGGmtSHaAivArelgiPaVvgvgeatielkeg.dlitvDgstG 73 
                                       l+eg+++ ae ++psd+a+ld  ++aG+ t +GG+tSHaAi Ar+l +PaVvg+ge + e +eg ++++vDg+ G
  gi|344210115|ref|YP_004786291.1| 153 LPEGSVVLAERLTPSDTAQLDpeRVAGFATVTGGRTSHAAIFARSLALPAVVGIGETL-ESVEGgTEVVVDGDDG 226
                                       789*******************************************************.555555*******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3921.59
//
Query:       gi|344210116|ref|YP_004786292.1|  [L=95]
Description: phosphocarrier protein Hpr [Haloarcula hispanica ATCC 33960]
Scores for 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-23   81.1   0.1    5.7e-23   81.0   0.1    1.0  1  PTS-HPr   PTS HPr component phosphorylation site


Domain annotation for each model (and alignments):
>> PTS-HPr  PTS HPr component phosphorylation site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.1   3.2e-27   5.7e-23       1      81 [.       3      84 ..       3      85 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 3.2e-27
                                      EEEEEEEESTCCCSHHHHHHHHHHHTTSSSEEEEEE.....EETTSHHHHHHCTCSTT-EEEEEEESTTHHHHHHHHHH CS
                           PTS-HPr  1 vekkvtiknekGlhaRpAamlvqaasefksevtlekkd.kpvnaksilglmsLgvkkGeevtvsaeGedeeealealae 78
                                      ve++vti  e GlhaRpA+ +vqa+++ ++ev+  + d + v+a s++++ sLgv +++ +++ a+G+d+e++l++l++
  gi|344210116|ref|YP_004786292.1|  3 VERTVTIVPEAGLHARPASAFVQAVNDHEAEVSAGRPDgDLVQAASMIAVTSLGVGQDDDIKLVADGPDAEAVLDELER 81
                                      589************************99****9997779*************************************** PP

                                      HHC CS
                           PTS-HPr 79 lle 81
                                      +l+
  gi|344210116|ref|YP_004786292.1| 82 ILT 84
                                      986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 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:                        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 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 697.18
//
Query:       gi|344210117|ref|YP_004786293.1|  [L=158]
Description: sugar phosphotransferase system IIA component [Haloarcula hispanica ATCC 33960]
Scores for 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-35  119.8   0.0    9.6e-35  119.6   0.0    1.0  1  PTS_EIIA_2  Phosphoenolpyruvate-dependent sugar phosphotransf


Domain annotation for each model (and alignments):
>> PTS_EIIA_2  Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.6   0.0   5.4e-39   9.6e-35       3     143 ..      14     155 ..      12     156 .. 0.96

  Alignments for each domain:
  == domain 1  score: 119.6 bits;  conditional E-value: 5.4e-39
                                       HHCCGEEEEC--SSHHHHHHHHHHHHHHTTSB-CH..HHHHHHHHHHHH-STTETCEE----SCCCBSS-EEEEEEE CS
                        PTS_EIIA_2   3 ltkelifldleakskeeaieqlaqklaeagavkpaeeyleallerekksstgigngvAiPHarleavkkpaiavlkl 79 
                                       +   +i l +  + ke +ie+l ++l++ g v++ ++ l+allere + +tg+g g+ iPHa+++av++p +a++  
  gi|344210117|ref|YP_004786293.1|  14 IPASHISLSEPPAEKEACIEFLLDLLVDGGKVEDRDRALDALLERESETTTGVGMGIGIPHAKTDAVNRPSLAFAHS 90 
                                       55678888888889*************************************************************** PP

                                       EEEEE-T-GCC-CEEEEEEEE-SSCHH..HHHHHHHHHHHHCSCCHHHHHHC--SHHHHHHHHCH CS
                        PTS_EIIA_2  80 kepvdfeasdgkpvklifllalpekdae.hlkilaqLaellkdeefvekLrkakseeeilellee 143
                                       +e+vdf++ dg+p++lif++++pe++ e hl+il++L++ l+ ++++++L +a++e+ +++ l+e
  gi|344210117|ref|YP_004786293.1|  91 EEGVDFGSMDGEPATLIFMILVPEAGGEeHLNILSSLSRALMHDDVRDRLHEAEDETTVQDALRE 155
                                       *************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1086.03
//
Query:       gi|344210118|ref|YP_004786294.1|  [L=379]
Description: sugar phosphotransferase system IIC component [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-21   75.5  37.7    3.7e-21   75.5  37.7    1.9  2  PTS_EIIC  Phosphotransferase system, EIIC


Domain annotation for each model (and alignments):
>> PTS_EIIC  Phosphotransferase system, EIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5  37.7   2.1e-25   3.7e-21       2     324 .]      24     305 ..      23     305 .. 0.81
   2 !    1.2   0.1    0.0084   1.5e+02      97     142 ..     313     358 ..     306     366 .. 0.66

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 2.1e-25
                          PTS_EIIC   2 dgfmlpiplliagGillglgnlpnssdlkglsslgvqtilsslaeilkqagnavfanLpllfaigiayglakggkgv 78 
                                        g++++ip++ +gGi+l+++++   +d++ +      +  +s  ++l+q+g a +++++++++ +iay++   +++ 
  gi|344210118|ref|YP_004786294.1|  24 TGVSFMIPFVTIGGIFLAVAYAI--GDTQTVF-----ENTGSAGWFLAQVGTAGLTIMVPILGGYIAYAI--ADRPG 91 
                                       6899*****************33..3333332.....23344558*************************..78888 PP

                          PTS_EIIC  79 aglagligllafnllaaisvlllaagalasakasilgiktlstgvfgaiivgllaaylynkfeknitikLPeslpff 155
                                       +++++l++++        +v+++aa+      ++i+  +  + g++gai++glla+y+ ++f++     +Pe++++ 
  gi|344210118|ref|YP_004786294.1|  92 LAPGFLLAYILQQG----NVVAEAATV-----IGIS-GGEAGAGYLGAIVAGLLAGYVARFFKN---LDVPEFIQPM 155
                                       88999999999554....444444333.....3444.456778*********************...9********* PP

                          PTS_EIIC 156 vgkrfvpiittlvvllvvglvllli.wpaiqgglnalglllggsgsllgvlifgflerllipfGlHhafiapfwfts 231
                                           ++p  t+  vl++++l++l + + + + +l++   +l++++ +  ++++g++ + ++ f++++++++++++++
  gi|344210118|ref|YP_004786294.1| 156 MPVLLIPVATMA-VLTPIMLFVLGVpVALANEALTS---FLQSMQ-GGQAIVVGLILGGMMAFDMGGPVNKVAYVFA 227
                                       *******99999.77776665555505555555555...466666.67899************************99 PP

                          PTS_EIIC 232 aggslaianqqlygagkeaahiltgefvsvmfGgpgatlalyiaaflekkskqkkllgsaaltpflfGItepleFgf 308
                                        g + ++    +y            ++ +vm+Gg+ ++++l++  f++  +  + +  ++    +++G++++ e ++
  gi|344210118|ref|YP_004786294.1| 228 TGLITEE----IYA-----------PMAAVMIGGMVPPIGLALSNFIAPHKYAAEMYENGKSG-VVLGLSFITEGAI 288
                                       8666666....444...........4667********************99999999999996.8************ PP

                          PTS_EIIC 309 pfvlnll.lfipallag 324
                                       p+ +  +  +ipa++ag
  gi|344210118|ref|YP_004786294.1| 289 PYAAADPlRVIPAIVAG 305
                                       **9988879*****998 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.0084
                          PTS_EIIC  97 svlllaagalasakasilgiktlstgvfgaiivgllaaylynkfek 142
                                       s++l ++ +++++++ + ++ +    ++g+i+ g l++ +++ + k
  gi|344210118|ref|YP_004786294.1| 313 SMALGVTMPAPHGGIFVVLLSNQPLAFLGSILLGSLVTAVVATVIK 358
                                       3333333343466677777777777888889888888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); 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:                         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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2451.75
//
Query:       gi|344210119|ref|YP_004786295.1|  [L=643]
Description: Kinetochore-Ndc80 subunit Spc25 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   28.4  44.9     0.0012   19.1  11.1    6.0  6  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
    3.7e-06   26.1  29.9    0.00013   21.0   6.1    2.3  2  DUF812           Protein of unknown function (DUF812)
    7.5e-06   25.0  49.1    0.00011   21.2  13.3    4.3  3  Spc7             Spc7 kinetochore protein
    8.7e-06   26.0  35.9       0.29   11.6   0.2    7.0  6  FlaC_arch        Flagella accessory protein C (FlaC)
    1.3e-05   25.3  43.8     0.0062   16.6  12.5    4.8  4  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
    2.4e-05   24.0  33.5     0.0028   17.2  14.7    2.5  2  HMMR_N           Hyaluronan mediated motility receptor N-term
    0.00013   20.3  34.5     0.0011   17.2  15.0    2.7  2  EzrA             Septation ring formation regulator, EzrA
    0.00035   19.8  35.1     0.0015   17.7   2.4    3.7  4  Atg14            Vacuolar sorting 38 and autophagy-related su
     0.0004   19.1  23.3      0.016   13.9   3.4    3.8  3  FapA             Flagellar Assembly Protein A
    0.00058   19.3  36.7      0.044   13.1  11.7    3.9  4  GAS              Growth-arrest specific micro-tubule binding
     0.0012   19.0  28.0        1.1    9.4   4.4    4.4  4  Fib_alpha        Fibrinogen alpha/beta chain family
     0.0024   18.3  33.3        2.1    8.9   2.7    7.1  6  NPV_P10          Nucleopolyhedrovirus P10 protein
     0.0044   16.5  51.1      0.091   12.2  14.8    4.1  4  Golgin_A5        Golgin subfamily A member 5
     0.0071   16.8  42.7        1.3    9.4  18.3    3.6  3  Fez1             Fez1
     0.0082   16.4  32.6        3.5    8.0   0.5    6.7  7  BLOC1_2          Biogenesis of lysosome-related organelles co
  ------ inclusion threshold ------
      0.015   14.0  31.7      0.047   12.3  14.3    2.3  2  AAA_13           AAA domain
      0.052   13.6  27.7       0.14   12.2   2.3    5.4  6  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
       0.07   12.9  57.6       0.05   13.4   1.5    8.1  7  DivIC            Septum formation initiator
       0.11   12.6  66.7      0.022   14.8  12.8    5.6  4  DHR10            Designed helical repeat protein 10 domain
       0.11   12.8  35.6      0.036   14.4   2.8    5.7  6  kleA_kleC        Uncharacterized KorC regulated protein A
       0.14   12.4  52.3       0.32   11.2   6.9    4.8  4  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
       0.16   11.3  27.1      0.092   12.0   1.7    4.1  3  HemX             HemX, putative uroporphyrinogen-III C-methyl
       0.16   10.5  38.0       0.47    8.9  15.4    2.6  3  FUSC             Fusaric acid resistance protein family
       0.17   10.9  31.5      0.028   13.4   5.6    3.9  4  IFT57            Intra-flagellar transport protein 57
       0.25   11.4  32.6        1.2    9.2   3.4    5.4  5  DUF1664          Protein of unknown function (DUF1664)
       0.28   11.3  29.3        2.4    8.3   0.5    5.4  5  COG2             COG (conserved oligomeric Golgi) complex com
       0.29   11.6  37.1    1.8e+04   -6.1  37.1    4.1  0  AAA_23           AAA domain
        0.3   10.4  29.9        1.1    8.5   0.4    4.7  5  DUF4763          Domain of unknown function (DUF4763)
        0.3   11.0   9.5       0.57   10.1   0.2    4.2  3  Shugoshin_N      Shugoshin N-terminal coiled-coil region
       0.31   10.9  28.1        1.5    8.6   4.9    3.5  3  STAT_alpha       STAT protein, all-alpha domain
       0.36   10.1  40.5        1.8    7.8  13.7    3.2  3  DUF4407          Domain of unknown function (DUF4407)
       0.37   11.3  64.4       0.98    9.9   7.0    5.3  5  APG6_N           Apg6 coiled-coil region
       0.39   10.7  53.1        1.9    8.5  13.5    5.6  4  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.43   10.4  51.8       0.11   12.3  15.3    3.5  3  ERM              Ezrin/radixin/moesin family
       0.43   10.8  62.0       0.06   13.6  17.5    4.3  4  ATG16            Autophagy protein 16 (ATG16)
       0.46   10.8   0.1       0.46   10.8   0.1    3.9  4  Retrotrans_gag   Retrotransposon gag protein
       0.48   10.9  37.4       0.43   11.1   3.6    5.8  5  Spectrin         Spectrin repeat
       0.63   10.0  34.8       0.88    9.5   0.4    7.4  8  Prefoldin        Prefoldin subunit
       0.75    9.5   9.8       0.58    9.9   0.8    3.1  3  DUF745           Protein of unknown function (DUF745)
       0.77    9.6  43.0        2.6    7.8  20.7    3.6  3  KASH_CCD         Coiled-coil region of CCDC155 or KASH
       0.82    9.7  36.3        6.1    6.9   2.0    6.0  6  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
       0.85   10.4  19.2        2.4    8.9   0.4    5.3  6  Occludin_ELL     Occludin homology domain
        1.1    7.5  45.2        0.6    8.4  17.4    2.7  2  MAD              Mitotic checkpoint protein
        1.1    8.7  53.1        2.8    7.4   7.4    3.9  3  Filament         Intermediate filament protein
        1.1    7.7  22.5       0.02   13.5   4.6    3.3  3  Zw10             Centromere/kinetochore Zw10
        1.2    8.8  39.2       0.62    9.8   5.7    4.3  3  DUF4201          Domain of unknown function (DUF4201)
        1.3    9.8   9.7         55    4.5   1.5    4.8  3  FliD_N           Flagellar hook-associated protein 2 N-termin
        2.6    7.8  32.5       0.78    9.5   7.0    4.0  4  DUF724           Protein of unknown function (DUF724)
        2.8    5.4  47.6       0.72    7.3  20.5    2.3  2  DUF3584          Protein of unknown function (DUF3584)
        3.3    7.7  30.4       0.14   12.2   5.4    3.9  3  Laminin_II       Laminin Domain II
        3.6    8.3  32.5        3.4    8.4   1.7    5.2  5  YabA             Initiation control protein YabA
        4.5    8.0  32.9       0.27   12.0   2.0    4.8  5  DUF2203          Uncharacterized conserved protein (DUF2203)
        4.8    6.8  25.7        0.5   10.0   2.1    4.7  3  LXG              LXG domain of WXG superfamily
        5.1    7.4  51.8        9.4    6.6   0.1    7.6  8  ABC_tran_CTD     ABC transporter C-terminal domain
        5.1    7.0  24.4        4.8    7.0   3.7    4.9  4  Sec34            Sec34-like family
        5.2    7.2  36.5          3    7.9   6.8    4.5  4  Mod_r            Modifier of rudimentary (Mod(r)) protein
        5.5    6.5  28.1        6.3    6.3  11.9    2.7  2  Exonuc_VII_L     Exonuclease VII, large subunit
        5.7    6.4  24.3       0.68    9.4   5.4    3.8  3  TBK1_CCD1        TANK-binding kinase 1 coiled-coil domain 1
        7.3    6.6  23.2       0.57   10.2   0.5    4.6  3  FlxA             FlxA-like protein
        7.5    6.1   9.2        0.3   10.6   1.3    2.2  2  DUF3153          Protein of unknown function (DUF3153)
        8.5    4.4  49.7      0.096   10.8  23.8    2.5  3  HOOK             HOOK protein
        8.6    6.1  11.8        2.3    7.9   1.3    3.1  2  Baculo_p24       Baculovirus P24 capsid protein
        8.6    6.1  18.9        1.4    8.7   4.6    4.1  5  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
        9.1    7.0  11.8        6.4    7.5   0.2    4.3  2  AKNA             AT-hook-containing transcription factor
         10    6.6  46.1        0.8   10.1   6.2    5.8  4  DUF4200          Domain of unknown function (DUF4200)


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 !   11.5   1.5   0.00094      0.26      55      99 ..     130     174 ..     104     181 .. 0.94
   2 ?    2.8   8.4      0.48   1.3e+02       8      82 ..     176     244 ..     168     284 .. 0.42
   3 ?    2.7   0.2      0.52   1.4e+02      35      98 ..     253     317 ..     250     321 .. 0.79
   4 ?    2.8   0.3      0.49   1.4e+02      72     100 ..     343     371 ..     332     376 .. 0.53
   5 !    9.8   2.6    0.0032      0.87      19      63 ..     373     417 ..     367     422 .. 0.89
   6 !   19.1  11.1   4.3e-06    0.0012       8      99 ..     406     499 ..     400     503 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00094
                                       HHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  55 lskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelek 99 
                                       + ++I  a ++ke++++ ++++++lk +l +le ++++l++e+++
  gi|344210119|ref|YP_004786295.1| 130 IHRQIRAAEQRKEEIDAELDRIASLKRDLPDLERQQATLRDEITE 174
                                       6789*************************************9986 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.48
                                       HH-HHHHHHHHCCCT.CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHH CS
                      Seryl_tRNA_N   8 renpeavkeklkkRg.edkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkee 82 
                                       r+ ++ v++++ +R  +       +   +e+r el+++l+elqa r el +    +  ++e +++l++e  +l  e
  gi|344210119|ref|YP_004786295.1| 176 RDKLQRVEDRIDERDvD-------FQTTQENRDELETALDELQATRSELKRVRNDIQSEQESIAALRDERGSLAVE 244
                                       33444445555555432.......3344444444444444444444444443333333334444444443333332 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.52
                                       HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  35 dekrrelqveleelqaerNelskeIgkakkkk.edaeeliaevkelkeelkaleaelkeleaele 98 
                                       de+ ++l+++++ l++++ els+   ++ +    + e l  e +e+ + ++a+ + + +++++l 
  gi|344210119|ref|YP_004786295.1| 253 DERLEALESDIDRLRERKRELSEYTTRLQNVVgFNEELLSGEHREITDAIDAKPESVGDITDQLY 317
                                       77888899999999999999999888887766566677788888888888888888888888875 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.49
                                       CCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  72 liaevkelkeelkaleaelkeleaelekl 100
                                       +++  +e  +e++++++el+el+++ +++
  gi|344210119|ref|YP_004786295.1| 343 MRDHLQETVTEIDDIDDELDELTDRRDEI 371
                                       34444455555555555555555554444 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.0032
                                       CCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC CS
                      Seryl_tRNA_N  19 kkRgedkadvdelleldekrrelqveleelqaerNelskeIgkak 63 
                                       ++R ++ ++ +++ e+d++ ++ q+++ +l+++rN+ls+ ++++ 
  gi|344210119|ref|YP_004786295.1| 373 ETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSARVEELE 417
                                       5677789999*****************************999876 PP

  == domain 6  score: 19.1 bits;  conditional E-value: 4.3e-06
                                       HH-HHHHHHHHCCCT..CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHH CS
                      Seryl_tRNA_N   8 renpeavkeklkkRg..edkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkee 82 
                                       r+n+ a  e l++R     ++++de+lel +k  el+ el+ l +er e+ +eI+ +  +    +el a+ +++ +e
  gi|344210119|ref|YP_004786295.1| 406 RNNLSARVEELEERVtsLRTEEFDEVLELHTKANELELELDRLESERDEVREEIADIESDIRRNDELAAQREDVVDE 482
                                       8899999999999986667899*************************************99**************** PP

                                       HHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  83 lkaleaelkeleaelek 99 
                                       l +l  + + leae ++
  gi|344210119|ref|YP_004786295.1| 483 LIDLRSRIDRLEAEATD 499
                                       ************99876 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   6.1   4.7e-07   0.00013     317     466 ..     136     281 ..      38     293 .. 0.85
   2 !   10.8  15.8   0.00058      0.16     335     480 ..     336     481 ..     330     494 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.7e-07
                            DUF812 317 kaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpd 393
                                       +ae+ +e   ++ + +++l++ + +le++ ++l++ei + ++++++ve+ ++e++   ++++++ +  + +l+ l+ 
  gi|344210119|ref|YP_004786295.1| 136 AAEQRKEEIDAELDRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQENRDELETALDELQA 212
                                       333444444455557899*********************************************************** PP

                            DUF812 394 aeeniekLqalveasaqrlvelakqWekhRvplieeyrelkesksekekeaerkleeikklrekmkevaeelr 466
                                       + + +++  +++++ ++++  l ++    R  l  e   l es +e+ +  e+ ++++++ ++++ e +  l+
  gi|344210119|ref|YP_004786295.1| 213 TRSELKRVRNDIQSEQESIAALRDE----RGSLAVERSGLPESPDERLEALESDIDRLRERKRELSEYTTRLQ 281
                                       *********************9975....99999999999999999999999999999999999888887776 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00058
                            DUF812 335 lqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLqalveasaqr 411
                                       +++ +++++  ++e   ei+++++++ ++++  +e  e++++  + +++ + + + ++  ++ +  L +  ++ ++r
  gi|344210119|ref|YP_004786295.1| 336 IESTLQSMRDHLQETVTEIDDIDDELDELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSAR 412
                                       33444444444444444444444444444444444444444444444444444455555555555666666667777 PP

                            DUF812 412 lvelakqWekhRvplieeyrelkesksekekeaerkleeikklrekmkevaeelrqkeellkqLvaele 480
                                       + el+++  + R+   +e  el ++++e e e  r  +e  ++re++ ++++++r+ +el  q ++ ++
  gi|344210119|ref|YP_004786295.1| 413 VEELEERVTSLRTEEFDEVLELHTKANELELELDRLESERDEVREEIADIESDIRRNDELAAQREDVVD 481
                                       777778888888899999999999999999999999999999999999999999999999988654444 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3  17.6    0.0017      0.48     147     265 ..     150     275 ..     137     299 .. 0.57
   2 !   21.2  13.3     4e-07   0.00011     176     281 ..     337     444 ..     331     446 .. 0.95
   3 ?    5.4   6.2     0.026       7.1     214     282 ..     430     497 ..     426     511 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0017
                              Spc7 147 nlegleedkelLekqeeeldellpeleeekaeleeeleklqe.......aaeelesidkeeLeelreelaelkaeie 216
                                       ++++l++d   Le+q++ l +   e++ + +++e+++++           ++ele    +eL+++r+el+++ ++i+
  gi|344210119|ref|YP_004786295.1| 150 RIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVdfqttqeNRDELE-TALDELQATRSELKRVRNDIQ 225
                                       3455666666666666666555555555555555555443322111111333332.356777777777777777777 PP

                              Spc7 217 ekkkelaelqeqleeleekieelkeqkseleeeiaea.ervleeckgwse 265
                                       + ++ +a l++++ +l+ + + l e+ +e  e++++  +r++e++++ se
  gi|344210119|ref|YP_004786295.1| 226 SEQESIAALRDERGSLAVERSGLPESPDERLEALESDiDRLRERKRELSE 275
                                       77777777777777777777777666666666665541344444444433 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 4e-07
                              Spc7 176 kaeleeeleklqeaaeelesid..keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeei 250
                                       +++l++  ++lqe ++e+++id   +eL   r+e+ae  +  +e+ + ++e+ +++e+ ++++ +l+e++++l +++
  gi|344210119|ref|YP_004786295.1| 337 ESTLQSMRDHLQETVTEIDDIDdeLDELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSARV 413
                                       67899999************997779*************************************************** PP

                              Spc7 251 aeaervleeckgwsesevsrlkeevkaleel 281
                                       +e e+ +   +  + +ev +l+++ ++le +
  gi|344210119|ref|YP_004786295.1| 414 EELEERVTSLRTEEFDEVLELHTKANELELE 444
                                       **************************99965 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.026
                              Spc7 214 eieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleelt 282
                                       e+ e+ ++ +el+ +l++le++ +e++e+++++e++i++  + l ++++   +e+  l+++ ++le + 
  gi|344210119|ref|YP_004786295.1| 430 EVLELHTKANELELELDRLESERDEVREEIADIESDIRRN-DELAAQREDVVDELIDLRSRIDRLEAEA 497
                                       5556677777888888888888888888888888888744.4455567777778888888888887654 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 !   11.6   0.2     0.001      0.29       1      38 [.     150     187 ..     150     191 .. 0.93
   2 ?    2.5   0.9      0.72     2e+02       3      31 ..     201     232 ..     198     237 .. 0.60
   3 ?    2.1   0.1      0.97   2.7e+02       7      37 ..     254     284 ..     252     292 .. 0.77
   4 !    9.0   0.2    0.0064       1.8      10      40 ..     334     364 ..     332     366 .. 0.91
   5 !   10.6   2.3    0.0021      0.58       2      40 ..     385     423 ..     384     435 .. 0.89
   6 !   10.3   2.5    0.0026      0.72       4      38 ..     433     467 ..     430     493 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.001
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVk 38 
                                       ri +l  +l++l+ + +t+++e+ e +++++++++++ 
  gi|344210119|ref|YP_004786295.1| 150 RIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRID 187
                                       789999*****************************994 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.72
                         FlaC_arch   3 delEnklsklst...eletvkkeneelsksve 31 
                                       delE+ l++l+    el+ v++++++ ++s+ 
  gi|344210119|ref|YP_004786295.1| 201 DELETALDELQAtrsELKRVRNDIQSEQESIA 232
                                       67777666666544466666666666555555 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.97
                         FlaC_arch   7 nklsklsteletvkkeneelsksveelkenV 37 
                                       ++l+ l++ ++ +++   els+  ++l+  V
  gi|344210119|ref|YP_004786295.1| 254 ERLEALESDIDRLRERKRELSEYTTRLQNVV 284
                                       5789999999999999999999888887666 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0064
                         FlaC_arch  10 sklsteletvkkeneelsksveelkenVkdl 40 
                                       ++++++l+++++ ++e  +++++++++  +l
  gi|344210119|ref|YP_004786295.1| 334 DRIESTLQSMRDHLQETVTEIDDIDDELDEL 364
                                       5899*********************998876 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.0021
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                       i+e++ ++++ +t++  +++  ++ls  veel+e+V  l
  gi|344210119|ref|YP_004786295.1| 385 IEEVDAEIERRQTTVVDLRERRNNLSARVEELEERVTSL 423
                                       89**********************************544 PP

  == domain 6  score: 10.3 bits;  conditional E-value: 0.0026
                         FlaC_arch   4 elEnklsklsteletvkkeneelsksveelkenVk 38 
                                       el +k ++l+ el+ +++e +e+++++ +++ +++
  gi|344210119|ref|YP_004786295.1| 433 ELHTKANELELELDRLESERDEVREEIADIESDIR 467
                                       77788889999999999999999999999998886 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 ?    6.9   9.0     0.022       6.1      32     116 ..     131     218 ..     127     219 .. 0.81
   2 !   16.6  12.5   2.2e-05    0.0062       6     119 ..     161     277 ..     160     282 .. 0.81
   3 !   11.3   7.9   0.00096      0.27      54     116 ..     359     424 ..     334     428 .. 0.81
   4 ?    6.5   5.0     0.029       8.1      58     117 ..     437     495 ..     422     498 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.022
                        TPR_MLP1_2  32 ekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleese...esweeqkeelekel 105
                                         q + a++ ++    el   a+  ++l +l  + ++l++ei+e ++++++++  ++e     +  +e ++ele+ l
  gi|344210119|ref|YP_004786295.1| 131 HRQIRAAEQRKEEIDAELDRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDvdfQTTQENRDELETAL 207
                                       56778888888888889999999999999999999999999999999999999999888722245677888999999 PP

                        TPR_MLP1_2 106 selekriedln 116
                                       +el++ + +l+
  gi|344210119|ref|YP_004786295.1| 208 DELQATRSELK 218
                                       99999998886 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.2e-05
                        TPR_MLP1_2   6 leeeikslkeekeeaeaklqklqedlekqaeiakeaqqk...Yerelvkhaedvkelqalreelnelkaeiaelkae 79 
                                       le ++++l++e++e ++klq +++ + +     ++ q++    e+ l +  ++  el+++r+++++ ++ ia l++e
  gi|344210119|ref|YP_004786295.1| 161 LERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQENrdeLETALDELQATRSELKRVRNDIQSEQESIAALRDE 237
                                       566667777777777777777777776665444444433222788999999************************** PP

                        TPR_MLP1_2  80 aesakaeleeseesweeqkeelekelselekriedlneqN 119
                                       + s+  e +   es +e+ e+le++++ l++r  +l+e  
  gi|344210119|ref|YP_004786295.1| 238 RGSLAVERSGLPESPDERLEALESDIDRLRERKRELSEYT 277
                                       ************************************9865 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00096
                        TPR_MLP1_2  54 edvkelqalreelnelkaeiaelkaeaesakaeleesees...weeqkeelekelselekriedln 116
                                       ++++el++ r+e++e++++++el+a  e++ ae+e+ +     + e++++l  +++ele+r++ l 
  gi|344210119|ref|YP_004786295.1| 359 DELDELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTvvdLRERRNNLSARVEELEERVTSLR 424
                                       6778899999999999999999999999999999888764222799***************99986 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.029
                        TPR_MLP1_2  58 elqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedlne 117
                                       + ++l  el++l++e+ e+++e  + ++++ ++  +++ q+e   +el +l++ri+ l++
  gi|344210119|ref|YP_004786295.1| 437 KANELELELDRLESERDEVREEIADIESDIRRN-DELAAQREDVVDELIDLRSRIDRLEA 495
                                       334444444555555555555555555555444.35677888888899999999988765 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 !   12.3  10.7   0.00032     0.088     193     316 ..     160     282 ..     126     299 .. 0.80
   2 !   17.2  14.7     1e-05    0.0028     183     302 ..     332     458 ..     328     504 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00032
                            HMMR_N 193 vtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLks 269
                                        ++++  + + ++++ ++kl+ +e+   e   + +   e  +el+ + ++l+  + +++ +++ ++++++ i  L+ 
  gi|344210119|ref|YP_004786295.1| 160 DLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQENRDELETALDELQATRSELKRVRNDIQSEQESIAALRD 236
                                       44444445588888999999999998888888889999999999999999999999999999999999999999999 PP

                            HMMR_N 270 sLeekeqelskqvkdlnekckllekekeelvreeeekeqtlsaElee 316
                                       +    ++e s   ++ +e+++ le++ +  +re +   +++++ l++
  gi|344210119|ref|YP_004786295.1| 237 ERGSLAVERSGLPESPDERLEALESDID-RLRERKRELSEYTTRLQN 282
                                       9888888899999999999999999999.555555555666666666 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1e-05
                            HMMR_N 183 kQedmeaklqvtqknLeeskakvaqLkeklvslekek...ieekseteklleyieelsnvseqlekykldiaqleel 256
                                       k   +e+ lq++  +L+e+ +++  + + l +l + +   +e+++  ++l++ iee+ +++e+ +    d+++ +++
  gi|344210119|ref|YP_004786295.1| 332 KPDRIESTLQSMRDHLQETVTEIDDIDDELDELTDRRdeiAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNN 408
                                       56678999******************999887765444449999999**************9999999999999999 PP

                            HMMR_N 257 lkekndeiesLkssLeeke....qelskqvkdlnekckllekekeelvre 302
                                       l+++ +e+e+  +sL+ +e     el++++++l+ +++ le+e++e+ +e
  gi|344210119|ref|YP_004786295.1| 409 LSARVEELEERVTSLRTEEfdevLELHTKANELELELDRLESERDEVREE 458
                                       99988888766666654441111556777777777777777766643332 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8  11.1    0.0029      0.81     106     460 ..     140     273 ..     123     283 .. 0.48
   2 !   17.2  15.0   4.1e-06    0.0011      56     233 ..     334     510 ..     329     513 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHH...HHHHHHHHHH------ CS
                              EzrA 106 leeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygeal...eelekqleniekefse 179
                                        +ee+d    +i++++ +l +l  ++   r+ei++ ++k +++++++ ++  ++++++   +ele+ l++++   se
  gi|344210119|ref|YP_004786295.1| 140 RKEEIDAELDRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQenrDELETALDELQATRSE 216
                                       33334444444555555666666666666666666666666666666666666655542223455555555555555 PP

                                       ----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTSHHHHHHHHHHHHHSTTS--SGGGSSSSSHHHH CS
                              EzrA 180 feeltengdyveakeilkkleeeideleevieeiPelleelkkelpkqleelkegykemkeegYaleelniekeiee 256
                                       ++ +   +d +  +e + +l++e  +l                                                  
  gi|344210119|ref|YP_004786295.1| 217 LKRVR--NDIQSEQESIAALRDERGSLA------------------------------------------------- 242
                                       55443..334444444444444444444................................................. PP

                                       HHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS CS
                              EzrA 257 lekkieeilerlkeleledveeelktieeeidsLyddlekEveAkkeveknlkelkeklehlekqnkelkeeldrlk 333
                                                                                                                    
  gi|344210119|ref|YP_004786295.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       -GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 334 qsYeLseeeleklrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEk 410
                                                                                                                    
  gi|344210119|ref|YP_004786295.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       HHHHHHHHHHHHHHHHHHHSSS-SS-S-TTTHHHHSTTTSTTTHHHHHHH CS
                              EzrA 411 rAreqldeikkelkeikrkieksnLPgiPesyleelkeasdeieelakeL 460
                                                          +e+s LP  P++ le+l+   d+++e ++eL
  gi|344210119|ref|YP_004786295.1| 243 -------------------VERSGLPESPDERLEALESDIDRLRERKREL 273
                                       ...................4444444444444444444444444444444 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 4.1e-06
                                       TTTHHHHHHHHHHHHHHHHHHTHHHHHT-GGGT--S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTT CS
                              EzrA  56 geseekfeewkkkwdeiktkklpeieellfeaeelldkykfkkakkklaeleeeldeveekikkileelkeltesee 132
                                       + +e+++++++   +e +t ++++i+++l e+ +  d  ++ +++++ +el+++++ev+++i++ ++ + +l+e  +
  gi|344210119|ref|YP_004786295.1| 334 DRIESTLQSMRDHLQETVT-EIDDIDDELDELTDRRD--EIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRN 407
                                       5688999999999999999.99999999999998655..68999********************************* PP

                                       TTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH------------..----HHHHHHHHHHHHHHHHHH CS
                              EzrA 133 knreeieklkekYrelrkkllanrfsygealeelekqleniekefsefeelte..ngdyveakeilkkleeeidele 207
                                       + ++++e+l+e+  +lr++  ++  ++ + ++ele++l+ +e+e +e  e     ++d    +e+  + e+ +del 
  gi|344210119|ref|YP_004786295.1| 408 NLSARVEELEERVTSLRTEEFDEVLELHTKANELELELDRLESERDEVREEIAdiESDIRRNDELAAQREDVVDELI 484
                                       ************************************************887762368999999999999******** PP

                                       HHHHHHHHHHTTTTTTSHHHHHHHHH CS
                              EzrA 208 evieeiPelleelkkelpkqleelke 233
                                       ++  +i  l +e+++++ +++++l +
  gi|344210119|ref|YP_004786295.1| 485 DLRSRIDRLEAEATDQFNEKMDDLLD 510
                                       ***********************965 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 !   12.2  11.0   0.00026     0.071      53     158 ..     119     228 ..      94     248 .. 0.70
   2 ?    1.9   0.6      0.34        95      17      80 ..     220     277 ..     220     285 .. 0.59
   3 !   17.7   2.4   5.5e-06    0.0015      12     101 ..     323     424 ..     316     427 .. 0.87
   4 ?    3.7   2.5       0.1        28      25      79 ..     439     493 ..     425     510 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                             Atg14  53 e.........eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdles 120
                                       e         + +++ ++++++k+ ++    +ia+l++ l  l+ ++ +l++ei e++ kl++  d + +R  d   
  gi|344210119|ref|YP_004786295.1| 119 EiimrpvdvaSIHRQIRAAEQRKEEIDAELDRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVD--- 192
                                       45555555555566777889999999999999999999999999999999999999999999999999855555... PP

                             Atg14 121 lqneleerrkkqiaklqdaikrieqklsslssktlesr 158
                                         ++  ++ ++++++ +d+++ ++  l+ +++++++ +
  gi|344210119|ref|YP_004786295.1| 193 --FQTTQENRDELETALDELQATRSELKRVRNDIQSEQ 228
                                       ..666666666666666666666666666666655542 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.34
                             Atg14  17 lrngperlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlr 80 
                                       +rn   ++ +++e +a l+ e+ sl  + + + e+++   ++ ++++++ ++l+e k + ++  
  gi|344210119|ref|YP_004786295.1| 220 VRN---DIQSEQESIAALRDERGSLAVERSGLPESPD---ERLEALESDIDRLRERKRELSEYT 277
                                       577...8888888889999998888888888888888...333333333333333333333222 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 5.5e-06
                             Atg14  12 iCesC...lrng.........perlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksli 76 
                                       +C +C   ++ +         +++l e  +++ ++  e ++l  + +++ e++++a +l++ i+   a +e+ ++++
  gi|344210119|ref|YP_004786295.1| 323 TCWTCgsrVKPDriestlqsmRDHLQETVTEIDDIDDELDELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTV 399
                                       67777444333367777777799****************************************************** PP

                             Atg14  77 adlrerlqelkdklsqlkkeieekk 101
                                        dlrer ++l++++++l +++   +
  gi|344210119|ref|YP_004786295.1| 400 VDLRERRNNLSARVEELEERVTSLR 424
                                       ******************9998776 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.1
                             Atg14  25 yelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadl 79 
                                       +el  +l +l se+++++++i ++++  +++++l+++ +   + l +l+s+i +l
  gi|344210119|ref|YP_004786295.1| 439 NELELELDRLESERDEVREEIADIESDIRRNDELAAQREDVVDELIDLRSRIDRL 493
                                       3455555555555555555555555555544444444444444444444444443 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   3.4   5.7e-05     0.016     329     422 ..     155     246 ..     139     252 .. 0.86
   2 !    8.6   2.2    0.0023      0.63     324     410 ..     350     415 ..     278     440 .. 0.46
   3 ?    6.4   2.7      0.01       2.9     331     411 ..     437     508 ..     429     520 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.7e-05
                              FapA 329 gldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelk 405
                                         d p+l ++++ l++e+ e++++l++++++i++ +    + q ++e +++l+ +l ++++ ++el+ +++++++ +
  gi|344210119|ref|YP_004786295.1| 155 KRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDV---DFQTTQENRDELETALDELQATRSELKRVRNDIQSEQ 228
                                       5567899999999999999999999999999888887...778899******************************* PP

                              FapA 406 eeleskkeea.kikvnke 422
                                       e+++  ++e  +++v++ 
  gi|344210119|ref|YP_004786295.1| 229 ESIAALRDERgSLAVERS 246
                                       ***999666667777665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0023
                              FapA 324 teiev.gldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleelee 399
                                       t +e+  +d  el+e  ++ ++e+ e++ + ++l+++i+++++                    + e+ ++ + +l+e
  gi|344210119|ref|YP_004786295.1| 350 TVTEIdDID-DELDEL-TDRRDEIAETRTRARELTATIEEVDA--------------------EIERRQTTVVDLRE 404
                                       222222222.222111.22333333333333333333333333....................22333333333333 PP

                              FapA 400 elkelkeeles 410
                                       ++++l++++e+
  gi|344210119|ref|YP_004786295.1| 405 RRNNLSARVEE 415
                                       33333333333 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.01
                              FapA 331 depelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelk.elke 406
                                       + +el  +l++le e  e++ee+ +++++i+++++l+           q + +  +++ l++++  le+e   + +e
  gi|344210119|ref|YP_004786295.1| 437 KANELELELDRLESERDEVREEIADIESDIRRNDELA----------AQREDVVDELIDLRSRIDRLEAEATdQFNE 503
                                       4457777889999999999999999999999999855..........577788888888888888888887777777 PP

                              FapA 407 elesk 411
                                       ++++ 
  gi|344210119|ref|YP_004786295.1| 504 KMDDL 508
                                       77665 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 !   13.1  11.7   0.00016     0.044      24     162 ..     147     306 ..     141     316 .. 0.68
   2 !   10.2   4.1    0.0012      0.34      22      87 ..     358     423 ..     333     428 .. 0.66
   3 !   11.2  13.1   0.00063      0.17      22     120 ..     358     464 ..     354     483 .. 0.68
   4 ?    6.2   4.9     0.021       5.9      49     114 ..     431     496 ..     424     510 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00016
                               GAS  24 NLelIkslKeeieelkkkeernekelseisqenkrlkepL.......kkaeeeveeLrkqlknyekdkqslknlkar 93 
                                        L+ I slK ++ +l+++++  + e+ e+  + +r ++ +       ++ +e+++eL+ +l + +  +++lk++++ 
  gi|344210119|ref|YP_004786295.1| 147 ELDRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIderdvdfQTTQENRDELETALDELQATRSELKRVRND 223
                                       68888888888888888888888888887777777776552222222667888889999999999999999999999 PP

                               GAS  94 lkelekelkdlkwehevl...........eqrfekvekerdelykkfeaa...iqevqqktglknllLekklkalqe 156
                                       +++ ++ + +l+ e  +l            +r+e++e+++d+l+++ ++       +q  +g+++ lL     ++++
  gi|344210119|ref|YP_004786295.1| 224 IQSEQESIAALRDERGSLaversglpespDERLEALESDIDRLRERKRELseyTTRLQNVVGFNEELLSGEHREITD 300
                                       99988888888888765522222222222577777777777777777665444566677777777777666666666 PP

                               GAS 157 elEkke 162
                                       ++++k 
  gi|344210119|ref|YP_004786295.1| 301 AIDAKP 306
                                       666665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0012
                               GAS  22 rnNLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqsl 87 
                                       ++ L+  +  ++ei+e ++++++ +  ++e+ +e +r + ++  ++e +++L +++++ e+   sl
  gi|344210119|ref|YP_004786295.1| 358 DDELDELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSARVEELEERVTSL 423
                                       455666666667777777777777777777777777777777777777777777777666666665 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00063
                               GAS  22 rnNLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslk........nl 90 
                                       ++ L+  +  ++ei+e ++++++ +  ++e+ +e +r + ++  ++e +++L +++++ e+   sl+        +l
  gi|344210119|ref|YP_004786295.1| 358 DDELDELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSARVEELEERVTSLRteefdevlEL 434
                                       6788999999********************************************99999998888872111111133 PP

                               GAS  91 karlkelekelkdlkwehevleqrfekvek 120
                                       +++ +ele el +l+ e + ++++++ +e+
  gi|344210119|ref|YP_004786295.1| 435 HTKANELELELDRLESERDEVREEIADIES 464
                                       444444444444444444444444444444 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.021
                               GAS  49 lseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqr 114
                                       + e+ ++ ++l+ +L ++e e++e r+++++ e+d  + ++l a+ +++ +el dl+   + le +
  gi|344210119|ref|YP_004786295.1| 431 VLELHTKANELELELDRLESERDEVREEIADIESDIRRNDELAAQREDVVDELIDLRSRIDRLEAE 496
                                       557778888999999999999999999999999999999999999999999999998887777654 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 !    8.5   5.9    0.0077       2.1      35     123 ..     149     236 ..     132     242 .. 0.88
   2 ?    4.4   0.0      0.15        40      34      66 ..     253     285 ..     249     305 .. 0.86
   3 !    9.4   4.4    0.0042       1.1      39     129 ..     335     424 ..     330     426 .. 0.83
   4 ?    7.8   0.8     0.013       3.6      33     110 ..     434     511 ..     429     519 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0077
                                       HHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHH CS
                         Fib_alpha  35 kdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvl 111
                                       +++++l+++l ++++++ + ++ ++e++d+l++ +   ++ d  ++  +++ + e ++  ++++a+ s+++  +n +
  gi|344210119|ref|YP_004786295.1| 149 DRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQENRD-ELETALDELQATRSELKRVRNDI 224
                                       58999***************************999999988877777777777.8888888999999********** PP

                                       HHHHHHHHHHHH CS
                         Fib_alpha 112 esneqkiqkLeq 123
                                       +s +++i+ L+ 
  gi|344210119|ref|YP_004786295.1| 225 QSEQESIAALRD 236
                                       ******999975 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.15
                                       CHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  34 kkdlekleneleeisnstkeaeelvkeikdslr 66 
                                       +++le le+++++++++++e +e+++++++++ 
  gi|344210119|ref|YP_004786295.1| 253 DERLEALESDIDRLRERKRELSEYTTRLQNVVG 285
                                       789*************************99875 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0042
                                       CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHH CS
                         Fib_alpha  39 kleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesne 115
                                       ++e++l+++++  +e+ + + +i+d l e     + +   ++  ++el   i++++++i +  +++  L++  ++++
  gi|344210119|ref|YP_004786295.1| 335 RIESTLQSMRDHLQETVTEIDDIDDELDELTDRRD-EIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLS 410
                                       57888888888888888888888888887777766.46667777888888999999999999999999999999999 PP

                                       HHHHHHHHHHHHHH CS
                         Fib_alpha 116 qkiqkLeqdidqke 129
                                        ++++Le+ +++++
  gi|344210119|ref|YP_004786295.1| 411 ARVEELEERVTSLR 424
                                       99999999998775 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.013
                                       CCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH.HHHHHHH CS
                         Fib_alpha  33 vkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe.snirvLq 108
                                       ++++ ++le el++++++  e++e + +i++ +r++ + +++ + v+ ++  +l+++i rl+++ ++q+ +++  L 
  gi|344210119|ref|YP_004786295.1| 434 LHTKANELELELDRLESERDEVREEIADIESDIRRNDELAAQREDVVDELI-DLRSRIDRLEAEATDQFnEKMDDLL 509
                                       567788999999999999999999999999999999999998899998886.6888999999999999877777776 PP

                                       HH CS
                         Fib_alpha 109 nv 110
                                       ++
  gi|344210119|ref|YP_004786295.1| 510 DI 511
                                       65 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.1     0.052        14      12      65 ..     126     179 ..     122     184 .. 0.85
   2 ?    7.3   4.2     0.024       6.5       9      62 ..     168     225 ..     165     236 .. 0.68
   3 ?    3.0   0.0      0.53   1.5e+02      17      46 ..     253     282 ..     250     321 .. 0.68
   4 !    8.9   2.7    0.0077       2.1       5      60 ..     339     394 ..     336     404 .. 0.87
   5 !    8.5   1.0    0.0096       2.6      14      61 ..     407     462 ..     396     471 .. 0.67
   6 ?    3.5   0.9      0.35        97      21      66 ..     470     513 ..     453     529 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.052
                           NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65 
                                       d++ +  ++ a +q+ ++++++l  +  l+  L ++  q a+l +++++  d L
  gi|344210119|ref|YP_004786295.1| 126 DVASIHRQIRAAEQRKEEIDAELDRIASLKRDLPDLERQQATLRDEITETRDKL 179
                                       788899999999999999999999999999999999999999999888877766 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.024
                           NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvt....elnekLdaqsaqLaeletkvenIq 62 
                                        r++i+++ dk++ +++++d+ + ++++++    el++ Ld+++a+  el+   ++Iq
  gi|344210119|ref|YP_004786295.1| 168 LRDEITETRDKLQRVEDRIDERDVDFQTTQenrdELETALDELQATRSELKRVRNDIQ 225
                                       6999***************866666665551111566666666666555555555555 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.53
                           NPV_P10  17 ddkVdalqqqvddvqenlpdvtelnekLda 46 
                                       d++++al++ +d+++e  ++++e +++L++
  gi|344210119|ref|YP_004786295.1| 253 DERLEALESDIDRLRERKRELSEYTTRLQN 282
                                       567777777777777777777777777765 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0077
                           NPV_P10   5 iLlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                        L   r+  +++ + +d +++++d++++   ++ e  ++  +++a+++e+++++e 
  gi|344210119|ref|YP_004786295.1| 339 TLQSMRDHLQETVTEIDDIDDELDELTDRRDEIAETRTRARELTATIEEVDAEIER 394
                                       68889999999999999999999999999999999999999999999999998875 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0096
                           NPV_P10  14 kavddkVdalqqqvddvqe.nlpdvtelnekLdaqsaqLaelet.......kvenI 61 
                                       ++++ +V+ l+++v+++++ ++ +v el++k +++  +L+ le+       ++ +I
  gi|344210119|ref|YP_004786295.1| 407 NNLSARVEELEERVTSLRTeEFDEVLELHTKANELELELDRLESerdevreEIADI 462
                                       67788888888888888641567777888887777777777776333222244444 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.35
                           NPV_P10  21 dalqqqvddvqenlpdvtelnekLdaqsaq.LaeletkvenIqdiLn 66 
                                       d l +q +dv ++l d   l +++d++ a+  +++++k+++  diL 
  gi|344210119|ref|YP_004786295.1| 470 DELAAQREDVVDELID---LRSRIDRLEAEaTDQFNEKMDDLLDILG 513
                                       4566666666666666...5566666654414457777777777775 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 !   12.2  14.8   0.00033     0.091      57     140 ..     138     227 ..     126     237 .. 0.84
   2 !   11.4   6.7   0.00057      0.16      40     162 ..     201     323 ..     194     332 .. 0.88
   3 ?    4.8  12.0      0.06        17      57     152 ..     334     424 ..     326     437 .. 0.47
   4 ?    4.8   9.3      0.06        17      28     109 ..     421     504 ..     417     511 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00033
                         Golgin_A5  57 dllreelqklnqqieqlrtelqdleaqqq...aeaeslreqlqeleeqlee...erkakeeveaelerlkeelryle 127
                                       ++ +ee+ +   +i +l+ +l dle+qq     e+ ++r++lq++e++++e   + ++ +e ++ele   +el++++
  gi|344210119|ref|YP_004786295.1| 138 EQRKEEIDAELDRIASLKRDLPDLERQQAtlrDEITETRDKLQRVEDRIDErdvDFQTTQENRDELETALDELQATR 214
                                       677899*******************998522269999*********999862225688899999************* PP

                         Golgin_A5 128 eelvrskatlqsr 140
                                       +el+r+++++qs+
  gi|344210119|ref|YP_004786295.1| 215 SELKRVRNDIQSE 227
                                       ********99986 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00057
                         Golgin_A5  40 esstalsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveael 116
                                       +  +++ +el+++++e + +r+++q+ +++i  lr e   l  +++   es  e+l+ le+ ++  r++k+e+++  
  gi|344210119|ref|YP_004786295.1| 201 DELETALDELQATRSELKRVRNDIQSEQESIAALRDERGSLAVERSGLPESPDERLEALESDIDRLRERKRELSEYT 277
                                       444556778888899999999****************9988888888888899************************ PP

                         Golgin_A5 117 erlkeelryleeelvrskatlqsrikdrekeieklrnqlttkslss 162
                                        rl++ + ++ee l+ ++ ++   i  + + + +++ ql + s+++
  gi|344210119|ref|YP_004786295.1| 278 TRLQNVVGFNEELLSGEHREITDAIDAKPESVGDITDQLYKGSKTT 323
                                       **************************************99877765 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.06
                         Golgin_A5  57 dllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryleeelvrs 133
                                       d +++ lq+++ ++++  te++d++++   e    r++++e +++ +e +++ eev+ae+er +  +     +l++ 
  gi|344210119|ref|YP_004786295.1| 334 DRIESTLQSMRDHLQETVTEIDDIDDEL-DELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTV----VDLRER 405
                                       3444444444444444444444444443.34444444444444444444444444444444443322....234444 PP

                         Golgin_A5 134 katlqsrikdrekeieklr 152
                                       +++l +r+++ e+ + +lr
  gi|344210119|ref|YP_004786295.1| 406 RNNLSARVEELEERVTSLR 424
                                       4444555555554444444 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.06
                         Golgin_A5  28 asLkegsgeegles...stalsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeq 101
                                        sL+ ++ +e le+   +++l++eld l++erd +ree+++ ++ i++   el+   + +  e   lr ++ +le +
  gi|344210119|ref|YP_004786295.1| 421 TSLRTEEFDEVLELhtkANELELELDRLESERDEVREEIADIESDIRR-NDELAAQREDVVDELIDLRSRIDRLEAE 496
                                       566666655555541113446778888888888888888888888875.4677777777777777778888777777 PP

                         Golgin_A5 102 leeerkak 109
                                        + + ++k
  gi|344210119|ref|YP_004786295.1| 497 ATDQFNEK 504
                                       66665554 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2  15.3    0.0056       1.6      12     148 ..     151     274 ..     136     297 .. 0.49
   2 ?    3.1   3.0      0.41   1.1e+02      26     119 ..     276     377 ..     266     387 .. 0.55
   3 !    9.4  18.3    0.0048       1.3      25     145 ..     363     498 ..     358     516 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0056
                              Fez1  12 islLKqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrek 88 
                                       i+ LK  L d   ++++  +ei + + +l+ ++ +++e++   ++++e+     +ele+  +elq ++se + +r+ 
  gi|344210119|ref|YP_004786295.1| 151 IASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQEN----RDELETALDELQATRSELKRVRND 223
                                       4445555555555555544444444444444444444444444433332....244555555555555555555555 PP

                              Fez1  89 vekleeelkelreelselsleeeeaalesdeakaqrqe..........aeeleelkreverlraeLkeer 148
                                       +++ +e ++ lr+e  +l                   +           e+le+l+++++rlr++ +e  
  gi|344210119|ref|YP_004786295.1| 224 IQSEQESIAALRDERGSL-------------------AversglpespDERLEALESDIDRLRERKRELS 274
                                       555555555555544443...................033333443334556666666666665433322 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.41
                              Fez1  26 vtqklseiva.....lkaqlrelrakleekeeeikeleeslee.ktlelevcenelqrk..kseaellrekveklee 94 
                                        t++l+++v      l ++ re++ ++++k e++ ++ ++l +  ++   +c ++++    +s+ + +r++++++ +
  gi|344210119|ref|YP_004786295.1| 276 YTTRLQNVVGfneelLSGEHREITDAIDAKPESVGDITDQLYKgSKTTCWTCGSRVKPDriESTLQSMRDHLQETVT 352
                                       55566666642222245566777777777777777777665441334455666666543225555566777777777 PP

                              Fez1  95 elkelreelselsleeeeaalesde 119
                                       e+ ++ +el el+ +++e a++ ++
  gi|344210119|ref|YP_004786295.1| 353 EIDDIDDELDELTDRRDEIAETRTR 377
                                       7777777777665555444333333 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0048
                              Fez1  25 evtqklseivalkaqlrelrakleekeeeikelees...leektlelevcenelqrk...............kseae 83 
                                       e+t + +ei + +++ rel+a++ee ++ei++ +++   l+e+ ++l    +el+++               +++a+
  gi|344210119|ref|YP_004786295.1| 363 ELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTvvdLRERRNNLSARVEELEERvtslrteefdevlelHTKAN 439
                                       66667777777777777766666666666665554411134444444444444444344445555433333333333 PP

                              Fez1  84 llrekvekleeelkelreelselsleeeeaalesdeakaqrqe.aeeleelkreverlraeLk 145
                                        l+ ++++le+e  e+ree+++ +    + + + de  aqr++  +el +l+++++rl+ae +
  gi|344210119|ref|YP_004786295.1| 440 ELELELDRLESERDEVREEIADIE----SDIRRNDELAAQREDvVDELIDLRSRIDRLEAEAT 498
                                       333333444444444444333322....22344555555555545666677777777766544 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 ?    7.5   0.3     0.018         5      43      80 ..     127     164 ..     124     175 .. 0.89
   2 ?    3.4   2.4      0.34        93      14      77 ..     171     234 ..     164     242 .. 0.61
   3 ?    4.6   0.0      0.14        39      67      93 ..     256     282 ..     250     285 .. 0.58
   4 ?    8.0   0.5     0.013       3.5      52      79 ..     339     366 ..     334     377 .. 0.84
   5 ?    5.3   0.6     0.091        25      37      91 ..     372     423 ..     366     426 .. 0.72
   6 ?    3.3   1.7      0.36        99      35      76 ..     430     468 ..     425     483 .. 0.70
   7 ?    4.9   0.4      0.11        32      37      81 ..     453     497 ..     450     508 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.018
                           BLOC1_2  43 aaslekkleklnekyeelqpylqqidqiekqvteLeea 80 
                                       +as+++++ + ++++ee++  l++i  +++++ +Le  
  gi|344210119|ref|YP_004786295.1| 127 VASIHRQIRAAEQRKEEIDAELDRIASLKRDLPDLERQ 164
                                       6899*****************************99975 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.34
                           BLOC1_2  14 eleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteL 77 
                                       e++ t+++++ +e    +    ++  +++ ++le+ l++l+++  el+   + i+  +++++ L
  gi|344210119|ref|YP_004786295.1| 171 EITETRDKLQRVEDRIDERDVDFQTTQENRDELETALDELQATRSELKRVRNDIQSEQESIAAL 234
                                       5555555555555555555555666666666666666666666666666666666666666655 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.14
                           BLOC1_2  67 idqiekqvteLeeavseLDeyskeLEa 93 
                                       ++++e ++++L e   eL ey+++L++
  gi|344210119|ref|YP_004786295.1| 256 LEALESDIDRLRERKRELSEYTTRLQN 282
                                       455555555555555556666555554 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.013
                           BLOC1_2  52 klnekyeelqpylqqidqiekqvteLee 79 
                                        l+++ ++lq+ +++id+i+++++eL++
  gi|344210119|ref|YP_004786295.1| 339 TLQSMRDHLQETVTEIDDIDDELDELTD 366
                                       5777788******************986 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.091
                           BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeL 91 
                                       ++ +++a +l++++e++++   e++   + + ++ ++ + L + v+eL+e +++L
  gi|344210119|ref|YP_004786295.1| 372 AETRTRARELTATIEEVDA---EIERRQTTVVDLRERRNNLSARVEELEERVTSL 423
                                       4555666666666666666...888888888888888888888888888888777 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.36
                           BLOC1_2  35 kykklkdvaaslekkleklnekyeelqpylqqidqiekqvte 76 
                                       ++ +l ++a++le +l++l+++    ++  ++i +ie ++++
  gi|344210119|ref|YP_004786295.1| 430 EVLELHTKANELELELDRLESER---DEVREEIADIESDIRR 468
                                       56788999999999999999955...5555566677766665 PP

  == domain 7  score: 4.9 bits;  conditional E-value: 0.11
                           BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeav 81 
                                       +++++++a++e+++ + +e+ ++ +  ++++ ++  ++++Le+ +
  gi|344210119|ref|YP_004786295.1| 453 DEVREEIADIESDIRRNDELAAQREDVVDELIDLRSRIDRLEAEA 497
                                       5789999***********************************865 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  10.5    0.0073         2     285     467 ..     127     316 ..     110     324 .. 0.64
   2 ?   12.3  14.3   0.00017     0.047     319     463 ..     336     483 ..     286     503 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0073
                            AAA_13 285 qerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksve....l 357
                                       ++++ + i   e++k+e+ ++l+ ++  ++  +  e+++++l++e+ +++++L+ ++++++++  +  ++ e    l
  gi|344210119|ref|YP_004786295.1| 127 VASIHRQIRAAEQRKEEIDAELDRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQEnrdeL 203
                                       57788888888888888888899988888888999999999999999999999999999999987777654421124 PP

                            AAA_13 358 esvkakiesikklvaeineliakhNekvanleeekeeakkklelhlv........eeleseldeykkkykklekaie 426
                                       e + +++++  ++++++ + i++  e +a l +e+ +++++  ++ +        e les++d++ + +++l++  +
  gi|344210119|ref|YP_004786295.1| 204 ETALDELQATRSELKRVRNDIQSEQESIAALRDERGSLAVE--RSGLpespderlEALESDIDRLRERKRELSEYTT 278
                                       55555557777778888888888888888887777776544..3333223333335555555555555555554444 PP

                            AAA_13 427 klekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeL 467
                                        l+   +    + + l +e +e+   +  + +++ +i+++L
  gi|344210119|ref|YP_004786295.1| 279 RLQ---NVVGFNEELLSGEHREITDAIDAKPESVGDITDQL 316
                                       443...33333344455556666666666666666655555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00017
                            AAA_13 319 feedkeelkaeaealeeqLkg...lqraleaKrkepfksve.lesvkakiesikklvaeineliakhNekvanleee 391
                                        e+  + ++++++++ ++++      ++l+++r+e++++ +   +++a ie++  ++++ ++++ +  e+ +nl ++
  gi|344210119|ref|YP_004786295.1| 336 IESTLQSMRDHLQETVTEIDDiddELDELTDRRDEIAETRTrARELTATIEEVDAEIERRQTTVVDLRERRNNLSAR 412
                                       44556666666666666655511155677889999999766469999999999999999999999999999999999 PP

                            AAA_13 392 keeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeei 463
                                       +ee+++ +   + ee+++ l e+++k ++le ++  le e +e  +e++ +e +i+   +   + +  ++e+
  gi|344210119|ref|YP_004786295.1| 413 VEELEERVTSLRTEEFDEVL-ELHTKANELELELDRLESERDEVREEIADIESDIRRNDELAAQREDVVDEL 483
                                       99999999999999996655.577777777777777777777777777777777776666666666655555 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 ?    5.1   0.1     0.078        22      30      83 ..     132     186 ..     114     193 .. 0.69
   2 ?    6.0   4.1      0.04        11      28     102 ..     154     232 ..     141     244 .. 0.54
   3 ?    0.3   0.0       2.4   6.7e+02      44      76 ..     253     284 ..     246     316 .. 0.78
   4 ?    3.8   0.7       0.2        55      43      90 ..     336     374 ..     330     395 .. 0.39
   5 ?   12.2   2.3   0.00051      0.14      24      94 ..     391     466 ..     380     469 .. 0.86
   6 ?    4.0   0.2      0.17        47      35      76 ..     471     512 ..     467     546 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.078
                      Baculo_PEP_C  30 vqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtl 83 
                                        qi  + ++ +++i+ +L+ +++ lk+ l++l+++ +tl +++t++  +lq   d +
  gi|344210119|ref|YP_004786295.1| 132 RQI-RAAEQRKEEIDAELDRIAS-LKRDLPDLERQQATLRDEITETRDKLQrveDRI 186
                                       455.4557778888888888665.888888888877777777776666665333444 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.04
                      Baculo_PEP_C  28 qnvqilaqlatlldaietqLnalsedlksllaeldt......rldtlltnLtdalnalqdtlrneLtnlnsiltnLl 98 
                                       ++  +  +l+++ +++  ++++  ++l+++   +d+        +++ ++L++al +lq + r+eL+ + +++ + +
  gi|344210119|ref|YP_004786295.1| 154 LKRDL-PDLERQQATLRDEITETRDKLQRVEDRIDErdvdfqTTQENRDELETALDELQ-ATRSELKRVRNDIQSEQ 228
                                       44444.45555555555555555555555555555565633334445556777777776.44555555555544444 PP

                      Baculo_PEP_C  99 ssvt 102
                                        s++
  gi|344210119|ref|YP_004786295.1| 229 ESIA 232
                                       4433 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 2.4
                      Baculo_PEP_C  44 etqLnalsedlksllaeldtrldtlltnLtdal 76 
                                       +++L+al++d+ + l e +++l++ +t+L++ +
  gi|344210119|ref|YP_004786295.1| 253 DERLEALESDIDR-LRERKRELSEYTTRLQNVV 284
                                       5678888888888.6667788888888887755 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.2
                      Baculo_PEP_C  43 ietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnl 90 
                                       ie++L+++ ++l++ ++e+d+ +d+ l++Ltd   +++         +
  gi|344210119|ref|YP_004786295.1| 336 IESTLQSMRDHLQETVTEIDD-IDDELDELTDRRDEIA--------ET 374
                                       444444444444444444432.3333333333333332........22 PP

  == domain 5  score: 12.2 bits;  conditional E-value: 0.00051
                      Baculo_PEP_C  24 airlqnvqilaqlatlldaietqLnalsedlksllae.ldt..rldtlltnLtdalnalq...dtlrneLtnlnsil 94 
                                        i   ++++  +l +  +++  ++++l+e+++sl +e +d+  +l+t +++L+  l +l+   d++r+e+  ++s++
  gi|344210119|ref|YP_004786295.1| 391 EIERRQTTV-VDLRERRNNLSARVEELEERVTSLRTEeFDEvlELHTKANELELELDRLEserDEVREEIADIESDI 466
                                       566667777.899********************9764166699999****************************997 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.17
                      Baculo_PEP_C  35 qlatlldaietqLnalsedlksllaeldtrldtlltnLtdal 76 
                                       +la++ +++  +L +l +++ +l ae ++++++ ++ L d l
  gi|344210119|ref|YP_004786295.1| 471 ELAAQREDVVDELIDLRSRIDRLEAEATDQFNEKMDDLLDIL 512
                                       588899999999**********************99998876 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   5.3      0.99   2.7e+02      23      52 ..     141     170 ..     120     192 .. 0.56
   2 ?    7.6   4.2     0.012       3.3      18      58 ..     192     232 ..     190     239 .. 0.92
   3 ?    4.2   0.5      0.14        37      24      51 ..     254     281 ..     250     291 .. 0.84
   4 ?    5.6   1.6      0.05        14      23      59 ..     337     373 ..     329     382 .. 0.82
   5 ?   13.4   1.5   0.00018      0.05      18      51 ..     384     417 ..     380     428 .. 0.90
   6 ?    4.7   2.8     0.095        26      21      53 ..     433     465 ..     429     473 .. 0.68
   7 ?    7.0   1.0     0.018         5      13      49 ..     463     499 ..     460     505 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.99
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                             DivIC  23 kqeiaalqaelaklkaeneeLeaevkdLks 52 
                                       k+ei+a  + +a+lk +  +Le++ + L++
  gi|344210119|ref|YP_004786295.1| 141 KEEIDAELDRIASLKRDLPDLERQQATLRD 170
                                       555555555555555555555554444431 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXX CS
                             DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyie 58 
                                       +++ +++++++l+  l++l+a++ eL++  +d +s+++ i+
  gi|344210119|ref|YP_004786295.1| 192 DFQTTQENRDELETALDELQATRSELKRVRNDIQSEQESIA 232
                                       6788999**************************99999997 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                             DivIC  24 qeiaalqaelaklkaeneeLeaevkdLk 51 
                                       + ++al+ ++++l+++++eL +   +L+
  gi|344210119|ref|YP_004786295.1| 254 ERLEALESDIDRLRERKRELSEYTTRLQ 281
                                       5678999************999888885 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXX CS
                             DivIC  23 kqeiaalqaelaklkaeneeLeaevkdLksdedyiee 59 
                                       ++ ++   ++l++   e+++ ++e+++L++ +d i+e
  gi|344210119|ref|YP_004786295.1| 337 ESTLQSMRDHLQETVTEIDDIDDELDELTDRRDEIAE 373
                                       6667788899999999999999999999998888877 PP

  == domain 5  score: 13.4 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                             DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevkdLk 51 
                                       ++ ++++ei++ q +++ l++++++L a+v++L+
  gi|344210119|ref|YP_004786295.1| 384 TIEEVDAEIERRQTTVVDLRERRNNLSARVEELE 417
                                       7899****************************94 PP

  == domain 6  score: 4.7 bits;  conditional E-value: 0.095
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
                             DivIC  21 qlkqeiaalqaelaklkaeneeLeaevkdLksd 53 
                                       +l+ + ++l+ el++l  e++e  +e++d +sd
  gi|344210119|ref|YP_004786295.1| 433 ELHTKANELELELDRLESERDEVREEIADIESD 465
                                       566667777777777777777777777776554 PP

  == domain 7  score: 7.0 bits;  conditional E-value: 0.018
                                       XXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                             DivIC  13 kkgllaykqlkqeiaalqaelaklkaeneeLeaevkd 49 
                                       ++ +++  +l +++++  +el  l+ ++++Leae  d
  gi|344210119|ref|YP_004786295.1| 463 ESDIRRNDELAAQREDVVDELIDLRSRIDRLEAEATD 499
                                       5567777888888888888888888888888888765 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 ?   10.0   9.7    0.0025       0.7      44     111 ..     129     196 ..     127     199 .. 0.93
   2 ?    3.1   5.1      0.34        95      58      99 ..     195     236 ..     189     240 .. 0.79
   3 ?   14.8  12.8     8e-05     0.022      30     103 ..     335     408 ..     333     425 .. 0.82
   4 ?    1.2  16.5       1.3   3.6e+02       2     103 ..     397     499 ..     396     507 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0025
                             DHR10  44 eieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakar 111
                                        i++++++ e+ k+++++  d++++++++l +ler+++ l+  +   ++kl+r++ + +e++ + +++
  gi|344210119|ref|YP_004786295.1| 129 SIHRQIRAAEQRKEEIDAELDRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTT 196
                                       58899999**************************************************9998877766 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.34
                             DHR10  58 klkelrdaleekeielrelerkeerlqrqlenaeeklerlre 99 
                                       + +e+rd+le+   el+   ++ +r++  +++ +e ++ lr 
  gi|344210119|ref|YP_004786295.1| 195 TTQENRDELETALDELQATRSELKRVRNDIQSEQESIAALRD 236
                                       567888888888888888888888888888888888888876 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 8e-05
                             DHR10  30 vvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaee 103
                                       ++e  l+s  + l+e  +e+   +++ ++l++ rd+++e ++++rel++++e +   +e+ +     lre++++
  gi|344210119|ref|YP_004786295.1| 335 RIESTLQSMRDHLQETVTEIDDIDDELDELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNN 408
                                       789999999999*****************************************999999999999999876543 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 1.3
                             DHR10   2 eslaeekeelaelErkarelqakidalqvve.kdlrsciklleeieaelakleeakkklkelrdaleekeielrele 77 
                                       +++ + +e  ++l ++  el++++ +l   e  ++ ++ + ++e+e el +le++++++ e  + +e+  ++  el 
  gi|344210119|ref|YP_004786295.1| 397 TTVVDLRERRNNLSARVEELEERVTSLRTEEfDEVLELHTKANELELELDRLESERDEVREEIADIESDIRRNDELA 473
                                       5677778899999999999****99999888467999**************************************** PP

                             DHR10  78 rkeerlqrqlenaeeklerlreqaee 103
                                       +++e +   l   + +++rl+ +a +
  gi|344210119|ref|YP_004786295.1| 474 AQREDVVDELIDLRSRIDRLEAEATD 499
                                       ********************998865 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 ?   10.4   2.2    0.0023      0.64      16      54 ..     141     179 ..     134     194 .. 0.85
   2 ?    2.7   0.6      0.59   1.6e+02      10      43 ..     208     234 ..     200     263 .. 0.59
   3 ?   14.4   2.8   0.00013     0.036       9      52 ..     354     397 ..     348     403 .. 0.87
   4 ?    5.0   0.7      0.11        31      18      52 ..     401     432 ..     396     440 .. 0.77
   5 ?    1.4   4.4       1.5   4.1e+02       7      60 ..     411     468 ..     406     474 .. 0.79
   6 ?   -0.1   1.0       4.3   1.2e+03      10      42 ..     446     478 ..     444     504 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0023
                         kleA_kleC  16 atdlvarRdkiAaklaeAeeLvrqaeeLRakvyeesaaL 54 
                                       ++++ a+ d+iA + ++  +L+rq + LR ++ e +  L
  gi|344210119|ref|YP_004786295.1| 141 KEEIDAELDRIASLKRDLPDLERQQATLRDEITETRDKL 179
                                       58999**************************99988776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.59
                         kleA_kleC  10 DeLpevatdlvarRdkiAaklaeAeeLvrqaeeL 43 
                                       DeL+    +l+  R++i   +++ +       +L
  gi|344210119|ref|YP_004786295.1| 208 DELQATRSELKRVRNDIQSEQESIA-------AL 234
                                       3444333444444444443333333.......33 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 0.00013
                         kleA_kleC   9 iDeLpevatdlvarRdkiAaklaeAeeLvrqaeeLRakvyeesa 52 
                                       iD +++  ++l+ rRd+iA+   +A eL+  +ee  a++ + ++
  gi|344210119|ref|YP_004786295.1| 354 IDDIDDELDELTDRRDEIAETRTRARELTATIEEVDAEIERRQT 397
                                       788888889*************************9999877665 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.11
                         kleA_kleC  18 dlvarRdkiAaklaeAeeLvrqaeeLRakvyeesa 52 
                                       dl+ rR+++ a   + eeL+ ++  LR++ + e  
  gi|344210119|ref|YP_004786295.1| 401 DLRERRNNLSA---RVEELEERVTSLRTEEFDEVL 432
                                       78999999887...5689999******98776655 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 1.5
                         kleA_kleC   7 pWiDeLpevatdlvar.RdkiAaklaeAeeLvrqaeeL...RakvyeesaaLedrakk 60 
                                       + ++eL+e  t l+ +  d++ ++  +A+eL+ + ++L   R +v+ee a +e ++++
  gi|344210119|ref|YP_004786295.1| 411 ARVEELEERVTSLRTEeFDEVLELHTKANELELELDRLeseRDEVREEIADIESDIRR 468
                                       5578999988888865269999999999999988877766688999999999888865 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 4.3
                         kleA_kleC  10 DeLpevatdlvarRdkiAaklaeAeeLvrqaee 42 
                                       D L+   ++++ +  +i   +++ +eL  q e+
  gi|344210119|ref|YP_004786295.1| 446 DRLESERDEVREEIADIESDIRRNDELAAQRED 478
                                       555555555555555555666666666666554 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 ?    4.5   9.0      0.14        38      27     102 ..     150     225 ..     118     226 .. 0.72
   2 ?    2.3   7.3      0.69   1.9e+02      17      86 ..     213     283 ..     195     300 .. 0.75
   3 ?    8.6  11.9    0.0074         2      24     107 ..     336     419 ..     328     429 .. 0.62
   4 ?   11.2   6.9    0.0012      0.32      25      83 ..     435     493 ..     429     513 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.14
                       TMF_TATA_bd  27 ElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEeveELraDva 102
                                        +aslk++l  le+++ ++r+ei +   + +++++  +e +   +  +e ++++et+L  l+    e +  r+D++
  gi|344210119|ref|YP_004786295.1| 150 RIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQENRDELETALDELQATRSELKRVRNDIQ 225
                                       4688899999999999999999888887777777777777766777777777777777777777777777777775 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.69
                       TMF_TATA_bd  17 lsseirrlEgElaslkeelerleaerdeareeivklmke.neelkelkkeleelekeleelqeryetlLel 86 
                                         se++r  ++++s +e+++ l  er +++ e   l ++  e+l++l+++++ l+++ +el+e    l  +
  gi|344210119|ref|YP_004786295.1| 213 TRSELKRVRNDIQSEQESIAALRDERGSLAVERSGLPESpDERLEALESDIDRLRERKRELSEYTTRLQNV 283
                                       46889999999999999999999999999999999986525667788888888877666666555444444 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0074
                       TMF_TATA_bd  24 lEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEeveELraD 100
                                        E+ l+s+++ l++  +e d++ +e+ +l+ + +e +e+ ++ +el++ +ee++ + e   +      E+ + L a 
  gi|344210119|ref|YP_004786295.1| 336 IESTLQSMRDHLQETVTEIDDIDDELDELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSAR 412
                                       56667777777777777777777777777777777777777777777766666655555555555555555555555 PP

                       TMF_TATA_bd 101 vaDlKem 107
                                       v++l e 
  gi|344210119|ref|YP_004786295.1| 413 VEELEER 419
                                       5555443 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.0012
                       TMF_TATA_bd  25 EgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetl 83 
                                        +  ++l+ el rle+erde+reei+++ ++  +++el+++ e++  el +l++r + l
  gi|344210119|ref|YP_004786295.1| 435 HTKANELELELDRLESERDEVREEIADIESDIRRNDELAAQREDVVDELIDLRSRIDRL 493
                                       55667788899999999999999999999999999999999999999999988887754 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 ?    2.3  11.8      0.31        86      26      98 ..     162     233 ..     128     289 .. 0.73
   2 ?   12.0   1.7   0.00033     0.092      31     102 ..     348     419 ..     338     427 .. 0.88
   3 ?    3.3   0.4      0.15        42      32      85 ..     447     500 ..     427     513 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.31
                              HemX  26 gqqqvqeltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlsk 98 
                                       + qq ++l+ e++e +++l+ +e+  ++ + + ++ qe  ++l+++ ++l+a+++el+   +++++ q+ +++
  gi|344210119|ref|YP_004786295.1| 162 ERQQ-ATLRDEITETRDKLQRVEDRIDERDVDFQTTQENRDELETALDELQATRSELKRVRNDIQSEQESIAA 233
                                       3344.46666667777777777777777555555555555555555555555555555555555555555554 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00033
                              HemX  31 qeltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsga 102
                                       qe+ +e+++++++l +l +  +++++ +++  el++++++ + ++e++++++ +l ++ ++l++++++++ +
  gi|344210119|ref|YP_004786295.1| 348 QETVTEIDDIDDELDELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSARVEELEER 419
                                       35667789***********************************************************99865 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.15
                              HemX  32 eltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleql 85 
                                       +l++e +e+++++a +e+   + +++++q +++ ++l +l +++++le+e +++
  gi|344210119|ref|YP_004786295.1| 447 RLESERDEVREEIADIESDIRRNDELAAQREDVVDELIDLRSRIDRLEAEATDQ 500
                                       344555677777777777777777777777777777777777777776655443 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  12.6    0.0024      0.67     214     339 ..     107     233 ..      95     248 .. 0.65
   2 ?    6.6   1.5    0.0088       2.4     231     330 ..     206     299 ..     201     331 .. 0.76
   3 ?    8.9  15.4    0.0017      0.47     158     332 ..     336     500 ..     325     515 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0024
                              FUSC 214 irararalrrllsrmlallallsslarllarlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlralr 290
                                        r+++++   l+  +++ + +    a+ +++ ra+e++  +e++a l+++a+l  +++  +le + a+lr++++++r
  gi|344210119|ref|YP_004786295.1| 107 ARRAVERGEDLREIIMRPVDV----ASIHRQIRAAEQRK-EEIDAELDRIASL--KRDLPDLERQQATLRDEITETR 176
                                       444444444444444444443....33333344433333.3478888888884..4566666677777777777777 PP

                              FUSC 291 rale..........adadtaalllarlaellaelaqllaslraleaaiaaarraerlar 339
                                         l+           d++t ++   +l + l+el++++ +l++ +++i++  ++e +a 
  gi|344210119|ref|YP_004786295.1| 177 DKLQrvedriderdVDFQTTQENRDELETALDELQATRSELKRVRNDIQS--EQESIAA 233
                                       777677777779999********************************998..3333333 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0088
                              FUSC 231 llallsslarllarlraeeaaavpelaallaelaal..eaaaaaealeaalaalrarlralrraleadadtaallla 305
                                       +l  l++++++l+r+r   + +++++aal +e  +l  e++ ++e ++++l+al+ ++++lr++           l+
  gi|344210119|ref|YP_004786295.1| 206 ALDELQATRSELKRVRNDIQSEQESIAALRDERGSLavERSGLPESPDERLEALESDIDRLRERKR--------ELS 274
                                       6777899999******999999888999999999999988999***************99999988........456 PP

                              FUSC 306 rlaellaelaqllaslraleaaiaa 330
                                       +  ++l++++  +++l + e++  +
  gi|344210119|ref|YP_004786295.1| 275 EYTTRLQNVVGFNEELLSGEHREIT 299
                                       6666666666666666666666555 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0017
                              FUSC 158 lrarlrallrdalalaaaalageegaeareaararlaadilalealrsqaayesprirararalrrllsrmlallal 234
                                       + ++l+++ +++ ++++++ + +++ ++  ++r ++a++ ++  +l +  +  +++i +r   +  l+ r  +l+a+
  gi|344210119|ref|YP_004786295.1| 336 IESTLQSMRDHLQETVTEIDDIDDELDELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSAR 412
                                       455666666666666666777777777777788888888888888888888888888889999999999******** PP

                              FUSC 235 lsslarllarlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlralrraleadadtaalllarlaell 311
                                       + +l+++   lr+ee ++v el++   el+        ++le +++++r+++++++++      ++++l+a+  +++
  gi|344210119|ref|YP_004786295.1| 413 VEELEERVTSLRTEEFDEVLELHTKANELEL-----ELDRLESERDEVREEIADIESDIR----RNDELAAQREDVV 480
                                       ******************9999999999999.....589999999**********99999....************* PP

                              FUSC 312 aelaqllaslraleaaiaaar 332
                                       +el++l+  +++lea++++ +
  gi|344210119|ref|YP_004786295.1| 481 DELIDLRSRIDRLEAEATD-Q 500
                                       ***************9987.4 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   5.6    0.0001     0.028     235     327 ..     153     241 ..     129     251 .. 0.85
   2 ?    2.2   0.1      0.26        73     271     316 ..     258     304 ..     256     314 .. 0.85
   3 ?    6.5   5.7     0.013       3.6     224     311 ..     338     424 ..     330     433 .. 0.67
   4 ?    1.5  10.6      0.43   1.2e+02     228     347 ..     380     496 ..     365     506 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                             IFT57 235 sieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeis 311
                                       s++ +lp+++ q + l ++i++t +k++  E ++++       +++++qe+ +e++  +++l+++ sel+r  ++i+
  gi|344210119|ref|YP_004786295.1| 153 SLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDE----RDVDFQTTQENRDELETALDELQATRSELKRVRNDIQ 225
                                       788999*********************999998875....4568999999999999999999999999999999999 PP

                             IFT57 312 eelekvkqemeergss 327
                                        e e++    +ergs 
  gi|344210119|ref|YP_004786295.1| 226 SEQESIAALRDERGSL 241
                                       9999999999999886 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.26
                             IFT57 271 qleellqeyreaqeelsevkekykqlsegvsel.trelaeiseelek 316
                                        le+ ++ +re ++else + +++++ + ++el + e +ei++ +++
  gi|344210119|ref|YP_004786295.1| 258 ALESDIDRLRERKRELSEYTTRLQNVVGFNEELlSGEHREITDAIDA 304
                                       58999*********************999888537788888888765 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.013
                             IFT57 224 ahleqmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegv 300
                                       ++l++m++h ++  +++ ++  +l++l +  ++   +  +r + l+  +ee  +e +  q+++ +++e+ ++ls++v
  gi|344210119|ref|YP_004786295.1| 338 STLQSMRDHLQETVTEIDDIDDELDELTDRRDEIA-ETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSARV 413
                                       44566666666666666666666666655554443.34677777778888888888888888888888888888888 PP

                             IFT57 301 seltrelaeis 311
                                       +el++  +++ 
  gi|344210119|ref|YP_004786295.1| 414 EELEERVTSLR 424
                                       87777777664 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.43
                             IFT57 228 qmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvselt 304
                                       ++    +++++++++ ++ + +l e  ++   ++e+ E++++s   e+ +e  e++++ +e++ +++ l+++  e +
  gi|344210119|ref|YP_004786295.1| 380 ELTATIEEVDAEIERRQTTVVDLRERRNNLSARVEELEERVTSLRTEEFDEVLELHTKANELELELDRLESERDEVR 456
                                       44444556777777778888888888888888888888888888888888888888888888888888888888888 PP

                             IFT57 305 relaeiseelekvkqemeergssmtDgsplvkikkaltklkkE 347
                                       +e a+i+ ++++  +   +r++ +   + l+ ++  +++l+ E
  gi|344210119|ref|YP_004786295.1| 457 EEIADIESDIRRNDELAAQREDVV---DELIDLRSRIDRLEAE 496
                                       888888888888777777776655...3466677777776666 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   3.1     0.066        18      66     105 ..     149     188 ..     125     211 .. 0.62
   2 ?    7.3   4.5     0.017       4.7      47     120 ..     162     234 ..     152     244 .. 0.61
   3 ?    1.0   0.0       1.5   4.2e+02      49      89 ..     258     298 ..     241     322 .. 0.61
   4 ?    9.2   3.4    0.0044       1.2      51     114 ..     334     396 ..     321     405 .. 0.57
   5 ?    4.8   4.9       0.1        28      43     110 ..     406     473 ..     398     508 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.066
                           DUF1664  66 sridrvdkkldeqkeiskeikeevtevredlseigedves 105
                                       +ri+++ + l + ++ ++ +++e+te r++l+++++ +++
  gi|344210119|ref|YP_004786295.1| 149 DRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDE 188
                                       4666777777777777777777777777777777766554 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.017
                           DUF1664  47 skqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                        +q  ++ +++++t+++L++  dr+d++ d   ++++e ++e++++ ++l++++++++ v++ +++ +++++ +
  gi|344210119|ref|YP_004786295.1| 162 ERQQATLRDEITETRDKLQRVEDRIDER-DVDFQTTQENRDELETALDELQATRSELKRVRNDIQSEQESIAAL 234
                                       4555566777888888776544444433.333445555566666666666666677777666666666655554 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.5
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeev 89 
                                        le+  + l++ kr+Ls+   r+++ +  ++e+ +  ++e+
  gi|344210119|ref|YP_004786295.1| 258 ALESDIDRLRERKRELSEYTTRLQNVVGFNEELLSGEHREI 298
                                       45555566777777776655555555555555444444444 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0044
                           DUF1664  51 eqvseslaatkrhLss...ridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       +++ ++l++ ++hL++   +id +d++lde ++      +e++e r   +e+   +e+v++ +e  +
  gi|344210119|ref|YP_004786295.1| 334 DRIESTLQSMRDHLQEtvtEIDDIDDELDELTDRR----DEIAETRTRARELTATIEEVDAEIERRQ 396
                                       56778899999999872224555555555555544....4444444444444444444444444333 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.1
                           DUF1664  43 vesvskqleqvseslaatkr.......hLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav 110
                                        +++s ++e++ e +++ +        +L  + ++++ +ld  +    e++ee++++++d+++ +e       + 
  gi|344210119|ref|YP_004786295.1| 406 RNNLSARVEELEERVTSLRTeefdevlELHTKANELELELDRLESERDEVREEIADIESDIRRNDE-------LA 473
                                       445555555555555555540000000455555555555555555555555555555555543333.......22 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 ?    8.3   0.5    0.0085       2.4      66     113 ..     153     200 ..     149     208 .. 0.77
   2 ?    4.9   1.2     0.091        25      75     116 ..     200     241 ..     191     261 .. 0.69
   3 ?    6.5   0.8     0.031       8.6      74     119 ..     336     381 ..     328     395 .. 0.52
   4 ?    3.8   3.6      0.21        57      63     113 ..     363     413 ..     359     440 .. 0.80
   5 ?    4.1   7.8      0.17        47      24      97 ..     398     471 ..     387     497 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0085
                              COG2  66 glqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr 113
                                       +l+++l  +e + a++r++++++r+kl++ e +++++  + +  +e+r
  gi|344210119|ref|YP_004786295.1| 153 SLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQENR 200
                                       6778899999999999*********99999999987655555555555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.091
                              COG2  75 esplaaarkkvesvreklsereeeveskleeakeleekrell 116
                                       + +l++a ++++++r++l++ +++++s+ e  ++l+++r +l
  gi|344210119|ref|YP_004786295.1| 200 RDELETALDELQATRSELKRVRNDIQSEQESIAALRDERGSL 241
                                       455666667777777777777777777666666666666444 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.031
                              COG2  74 vesplaaarkkvesvreklsereeeveskleeakeleekrellkll 119
                                       +es l+++r+++++++ ++++   e+++  + + e++e+r   + l
  gi|344210119|ref|YP_004786295.1| 336 IESTLQSMRDHLQETVTEIDDIDDELDELTDRRDEIAETRTRAREL 381
                                       4555555555555555555555555555555555555555333333 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.21
                              COG2  63 hLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr 113
                                       +L++ ++e+ e ++   +++  +e+v +++++r+++v +  e +++l +  
  gi|344210119|ref|YP_004786295.1| 363 ELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSARV 413
                                       689999999999999999999999999999999999987766666665544 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.17
                              COG2  24 hgvpLeslrrdLeaylkllekellelvnedyadFvslSghLvglqeeleevesplaaarkkvesvreklseree 97 
                                       + v+L++ r++L a +++le+++ +l  e++ + ++l ++   l+ el+++es+  ++r+++ ++++ + ++ e
  gi|344210119|ref|YP_004786295.1| 398 TVVDLRERRNNLSARVEELEERVTSLRTEEFDEVLELHTKANELELELDRLESERDEVREEIADIESDIRRNDE 471
                                       56889999999999999999999999999999999999999999999999999999999999999988876544 PP

>> AAA_23  AAA domain
   [No individual domains that satisfy reporting thresholds (although complete target did)]

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   5.3     0.064        18      83     155 ..     139     211 ..     105     212 .. 0.85
   2 ?    7.3   1.2    0.0096       2.6     113     150 ..     200     237 ..     194     242 .. 0.86
   3 ?   -1.0   0.0       3.1   8.5e+02     127     155 ..     253     281 ..     249     284 .. 0.80
   4 ?    6.7   3.3     0.014         4      62     154 ..     337     423 ..     330     426 .. 0.71
   5 ?    8.5   0.4    0.0039       1.1      95     146 ..     424     475 ..     420     492 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.064
                           DUF4763  83 decvdedlelelltseqpeileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrlneld 155
                                       +  ++ d el+++ s + ++ +L r+++ Lr +++e   +l++ ++ + e + + +  +++ ++l++ l+el+
  gi|344210119|ref|YP_004786295.1| 139 QRKEEIDAELDRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQENRDELETALDELQ 211
                                       5667788888889999999999999999999999999999999999999999999999999999999999886 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0096
                           DUF4763 113 rqqlaelqqhlkasrkslkelreslcqekkrlrklqkr 150
                                       r +l+ +   l+a+r++lk++r+++++e++ +++l+ +
  gi|344210119|ref|YP_004786295.1| 200 RDELETALDELQATRSELKRVRNDIQSEQESIAALRDE 237
                                       6688888999**********************999876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 3.1
                           DUF4763 127 rkslkelreslcqekkrlrklqkrlneld 155
                                       ++ l++l++++ ++++r r+l++ +++l+
  gi|344210119|ref|YP_004786295.1| 253 DERLEALESDIDRLRERKRELSEYTTRLQ 281
                                       67889999999999999999998887776 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.014
                           DUF4763  62 KqrvlelrskLalnvpecPeidecvdedlelelltseqpeileLqrnnhkLrqqlaelqqhlkasrkslkelreslc 138
                                       +  ++ +r  L  +v       e +d d el++lt+  +ei e + +   L   ++e+    ++ ++++ +lre++ 
  gi|344210119|ref|YP_004786295.1| 337 ESTLQSMRDHLQETV------TEIDDIDDELDELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRN 407
                                       555555555555554......56677777777777778888888888888888888888888888888888888888 PP

                           DUF4763 139 qekkrlrklqkrlnel 154
                                       ++  r+++l++r + l
  gi|344210119|ref|YP_004786295.1| 408 NLSARVEELEERVTSL 423
                                       8888888888777654 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0039
                           DUF4763  95 ltseqpeileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrk 146
                                        t+e +e+leL+ +   L  +l++l++ + + r+++ +++++++++ + +++
  gi|344210119|ref|YP_004786295.1| 424 RTEEFDEVLELHTKANELELELDRLESERDEVREEIADIESDIRRNDELAAQ 475
                                       566778***************************************9998876 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 ?   -1.7   0.0       9.7   2.7e+03      22      44 ..     150     172 ..     150     172 .. 0.80
   2 ?   10.1   0.2    0.0021      0.57      18      38 ..     408     428 ..     405     430 .. 0.90
   3 ?    3.4   1.3      0.26        72      21      44 ..     436     459 ..     432     460 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 9.7
                       Shugoshin_N  22 kirelekevseLlsENlnLReli 44 
                                       +i +l   + +L +++ +LR +i
  gi|344210119|ref|YP_004786295.1| 150 RIASLKRDLPDLERQQATLRDEI 172
                                       5677777788999*******875 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0021
                       Shugoshin_N  18 alslkirelekevseLlsENl 38 
                                        ls+++ ele +v++L++E  
  gi|344210119|ref|YP_004786295.1| 408 NLSARVEELEERVTSLRTEEF 428
                                       69****************975 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.26
                       Shugoshin_N  21 lkirelekevseLlsENlnLReli 44 
                                       +k +ele e+ +L sE ++ Re+i
  gi|344210119|ref|YP_004786295.1| 436 TKANELELELDRLESERDEVREEI 459
                                       6889***************99987 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 ?    8.0   6.8    0.0087       2.4       3      75 ..     160     241 ..     159     271 .. 0.79
   2 ?    8.6   4.9    0.0056       1.5       3      94 ..     335     428 ..     334     433 .. 0.74
   3 ?    8.1   4.4    0.0082       2.3       3      94 ..     401     498 ..     399     503 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0087
                        STAT_alpha   3 eieqrleelrskvqeteqdirkLedeqeeFdfqyqelqkl.........eqeraesekkelkkqkellqqmlnaLdq 70 
                                       ++e++ ++lr++++et  +++++ed  +e d+++q+ q++         e + ++se k++++  ++ q+++ aL +
  gi|344210119|ref|YP_004786295.1| 160 DLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQENrdeletaldELQATRSELKRVRNDIQSEQESIAALRD 236
                                       57889999******************************996666666664445555555566666666666666776 PP

                        STAT_alpha  71 kRkel 75 
                                       +R +l
  gi|344210119|ref|YP_004786295.1| 237 ERGSL 241
                                       66665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0056
                        STAT_alpha   3 eieqrleelrskvqeteqdirkLedeqeeFdfqyqelqkl..eqeraesekkelkkqkellqqmlnaLdqkRkelvd 77 
                                       +ie++l+ +r++ qet+ +i ++ de +e+  +  e+ +    + + + + +e+  + e  q ++  L ++R++l  
  gi|344210119|ref|YP_004786295.1| 335 RIESTLQSMRDHLQETVTEIDDIDDELDELTDRRDEIAETrtRARELTATIEEVDAEIERRQTTVVDLRERRNNLSA 411
                                       699****************************999999988222222222223344444444445555******9999 PP

                        STAT_alpha  78 klkellnlleslqekll 94 
                                       +++el ++++sl ++  
  gi|344210119|ref|YP_004786295.1| 412 RVEELEERVTSLRTEEF 428
                                       99999999999887655 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0082
                        STAT_alpha   3 eieqrleelrskvqeteqdirkLedeqeeFdfqyqelqkl.....eqeraesekkelkkqkellqqmlna...Ldqk 71 
                                       ++++r ++l+++v+e+e+ + +L    eeFd   + ++k      e +r ese+ e++++ + +++ +++   L  +
  gi|344210119|ref|YP_004786295.1| 401 DLRERRNNLSARVEELEERVTSLR--TEEFDEVLELHTKAnelelELDRLESERDEVREEIADIESDIRRndeLAAQ 475
                                       567788899**************9..5666633333333344668889999999999******9999998999**** PP

                        STAT_alpha  72 Rkelvdklkellnlleslqekll 94 
                                       R+++vd+l +l ++++ l ++ +
  gi|344210119|ref|YP_004786295.1| 476 REDVVDELIDLRSRIDRLEAEAT 498
                                       ***********999999987766 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  17.0     0.013       3.6     129     227 ..     136     246 ..     123     290 .. 0.53
   2 ?    4.9   4.3      0.05        14     134     235 ..     255     377 ..     244     395 .. 0.33
   3 ?    7.8  13.7    0.0065       1.8     106     235 ..     355     499 ..     354     513 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.013
                           DUF4407 129 aa..ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelk 203
                                       aa   ++e++++ ++ia+l++ +  +e++ ++lr+e ++  d   +  + ++  +   +++ +++ d+++++l+el+
  gi|344210119|ref|YP_004786295.1| 136 AAeqRKEEIDAELDRIASLKRDLPDLERQQATLRDEITETRDK-LQRVEDRIDERDVDFQTTQENRDELETALDELQ 211
                                       2222445555555555555555555555555555555533332.333333355556666666666666666666666 PP

                           DUF4407 204 akld...........atarlaalraelaeleaera 227
                                       a+++           +++ +aalr+e+ +l+ er+
  gi|344210119|ref|YP_004786295.1| 212 ATRSelkrvrndiqsEQESIAALRDERGSLAVERS 246
                                       66666666555555755555555555555544443 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.05
                           DUF4407 134 elaeleaqiaalqaeidaaearldalraeaqkeldgtk....................gtgttgvaGkgpaake... 187
                                       +l++le++i++l++  +++++  ++l++ +  + +  +                    +             ++   
  gi|344210119|ref|YP_004786295.1| 255 RLEALESDIDRLRERKRELSEYTTRLQNVVGFNEELLSgehreitdaidakpesvgdiT-------------DQlyk 318
                                       44555555554444444444444444444432222211122222211111114433331.............11333 PP

                           DUF4407 188 ..........kkaqldaaqaelaelkakld.atarlaalraelaeleaerakeraasqa 235
                                                  + + d+++ +l+++++ l+   +++++ ++el+el+++r++++++ ++
  gi|344210119|ref|YP_004786295.1| 319 gskttcwtcgSRVKPDRIESTLQSMRDHLQeTVTEIDDIDDELDELTDRRDEIAETRTR 377
                                       33333344553333333333333333332221122222222222222222222222111 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0065
                           DUF4407 106 keIdaelaeeqqeeakelkeqlaaa.ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk....gtgttg 177
                                       ++Id el+e   ++ + ++++++a  lta+++e +a+i++ q+++  +++r+++l a ++ el+       +++   
  gi|344210119|ref|YP_004786295.1| 355 DDIDDELDELTDRRDEIAETRTRAReLTATIEEVDAEIERRQTTVVDLRERRNNLSARVE-ELEERVtslrTEEFDE 430
                                       579999999999888888888877788888888888888666666666666666665555.3333332233222223 PP

                           DUF4407 178 vaGkgpaakekkaqldaaqaelaelkakld...........atarlaalraelaeleaerakeraasqa 235
                                       v    + a e + +ld+++ e +e+++++             +a++++  +el +l++++++ +a+ ++
  gi|344210119|ref|YP_004786295.1| 431 VLELHTKANELELELDRLESERDEVREEIAdiesdirrndeLAAQREDVVDELIDLRSRIDRLEAEATD 499
                                       333333344444444444444444444433555544465554444455555555555555554444333 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   6.4      0.46   1.3e+02      50      95 ..     138     183 ..     105     191 .. 0.58
   2 ?    8.1  11.2     0.013       3.7      12     107 ..     187     278 ..     185     297 .. 0.69
   3 ?    8.3  16.1     0.012       3.2       9     111 ..     338     440 ..     336     442 .. 0.93
   4 ?    9.9   7.0    0.0036      0.98      55      97 ..     430     472 ..     428     476 .. 0.90
   5 ?    2.1   1.1      0.93   2.6e+02      71     104 ..     470     503 ..     463     511 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.46
                            APG6_N  50 eeleeeleklekeeeelleeLkelekereeleaelaaleeeleale 95 
                                       e+ +ee+++  +  ++l + L +le++++ l++e+ + + +l+++e
  gi|344210119|ref|YP_004786295.1| 138 EQRKEEIDAELDRIASLKRDLPDLERQQATLRDEITETRDKLQRVE 183
                                       3334444444444444444444444444444444444444444443 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.013
                            APG6_N  12 eeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaale 88 
                                       +e d  ++++++ rd++e+ l++l+++++e ++ ++++++ +e++++l++e+ +l  e   l +  +   + l+ale
  gi|344210119|ref|YP_004786295.1| 187 DERDVDFQTTQENRDELETALDELQATRSELKRVRNDIQSEQESIAALRDERGSLAVERSGLPESPD---ERLEALE 260
                                       5667789999999999999999999998888878999999999999999999999999988865443...3444444 PP

                            APG6_N  89 eelealeeeeerfwreyne 107
                                       +  ++l e  +r+++ey  
  gi|344210119|ref|YP_004786295.1| 261 SDIDRLRER-KRELSEYTT 278
                                       444444332.223333333 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.012
                            APG6_N   9 lLleeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaela 85 
                                       + l+ +  +l+++  e+d+  + l++l+++++e  ++++  +el   +e++++e e+ ++   +l + r +l a ++
  gi|344210119|ref|YP_004786295.1| 338 STLQSMRDHLQETVTEIDDIDDELDELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSARVE 414
                                       6899*************************9999988999999*********************************** PP

                            APG6_N  86 aleeelealeeeeerfwreynelqle 111
                                       +lee    l  ee  ++ e + ++ e
  gi|344210119|ref|YP_004786295.1| 415 ELEERVTSLRTEEFDEVLELHTKANE 440
                                       *************9999888877655 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0036
                            APG6_N  55 eleklekeeeelleeLkelekereeleaelaaleeelealeee 97 
                                       e+ +l+ + +el+ eL++le+er+e+++e+a++e+  ++ +e 
  gi|344210119|ref|YP_004786295.1| 430 EVLELHTKANELELELDRLESERDEVREEIADIESDIRRNDEL 472
                                       6789999****************************99988775 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.93
                            APG6_N  71 kelekereeleaelaaleeelealeeeeerfwre 104
                                       +el ++re++ +el +l++  ++le+e +  ++e
  gi|344210119|ref|YP_004786295.1| 470 DELAAQREDVVDELIDLRSRIDRLEAEATDQFNE 503
                                       5777888888888888888888888777665555 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 ?    8.5  13.5    0.0069       1.9      19     108 ..     144     226 ..     128     244 .. 0.74
   2 ?    3.2   0.2      0.29        81      66      92 ..     254     280 ..     249     296 .. 0.80
   3 ?    6.7  10.9     0.026       7.1      19     101 ..     340     425 ..     332     430 .. 0.72
   4 ?    4.5   8.1      0.12        33      25      98 ..     430     507 ..     428     511 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0069
                    CENP-F_leu_zip  19 adsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqer 95 
                                        d   d++ +L+r+l ++e++q  +  e  + + +++ +++ i+e         +d+++++++++eLe  l + q +
  gi|344210119|ref|YP_004786295.1| 144 IDAELDRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDE-------RDVDFQTTQENRDELETALDELQAT 213
                                       344459999999999999998887777777777777777766666.......6788888888888888888888888 PP

                    CENP-F_leu_zip  96 vseLeslnsslen 108
                                        seL++++ ++++
  gi|344210119|ref|YP_004786295.1| 214 RSELKRVRNDIQS 226
                                       8888888877754 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.29
                    CENP-F_leu_zip  66 eelreleldLvalrsekeeLekelqkk 92 
                                       e+l+ le+d++ lr+ k eL +     
  gi|344210119|ref|YP_004786295.1| 254 ERLEALESDIDRLRERKRELSEYTTRL 280
                                       678899999999999999997655555 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.026
                    CENP-F_leu_zip  19 adsLkdkvenLerelemseenqekvi...leaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkk 92 
                                         s++d+ ++   e+ +++ ++++++    e  + +  + +l + iee  +e ++ ++ +v+lr+ +++L   +++ 
  gi|344210119|ref|YP_004786295.1| 340 LQSMRDHLQETVTEIDDIDDELDELTdrrDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSARVEEL 416
                                       44555555555555555555555544111355567888899999999999999999999999999999999999999 PP

                    CENP-F_leu_zip  93 qervseLes 101
                                        erv +L +
  gi|344210119|ref|YP_004786295.1| 417 EERVTSLRT 425
                                       999999976 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.12
                    CENP-F_leu_zip  25 kvenLerelemseenqekvileaEtskaevetlkeei...eelaeelreleldLvalrsekeeLekelq.kkqervs 97 
                                        v++L    +++e ++++++ e ++ ++e+  +++ i   +ela+++++   +L +lrs  + Le e   + +e+++
  gi|344210119|ref|YP_004786295.1| 430 EVLELHTKANELELELDRLESERDEVREEIADIESDIrrnDELAAQREDVVDELIDLRSRIDRLEAEATdQFNEKMD 506
                                       55666666666666666666666666666666666662223677777777777777777777776654313455555 PP

                    CENP-F_leu_zip  98 e 98 
                                       +
  gi|344210119|ref|YP_004786295.1| 507 D 507
                                       5 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3  15.3    0.0004      0.11       9     126 ..     160     277 ..     152     315 .. 0.85
   2 ?    6.8  11.4     0.019       5.3       3      98 ..     336     427 ..     334     431 .. 0.89
   3 ?    4.1   8.5      0.13        36      33     101 ..     429     500 ..     425     511 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0004
                               ERM   9 eleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklr 85 
                                        le++   l++e+ +++++L++ e+++++ +   +  +e++++Le    e+++  ++lk+ +++ ++e+e++++  +
  gi|344210119|ref|YP_004786295.1| 160 DLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQENRDELETALDELQATRSELKRVRNDIQSEQESIAALRD 236
                                       678888899******************************************************************** PP

                               ERM  86 eaeleaarleeeserkeeeaerLkeeleeareaeeeakekl 126
                                       e  ++a +     e  +e  e L++++ + re+++e +e  
  gi|344210119|ref|YP_004786295.1| 237 ERGSLAVERSGLPESPDERLEALESDIDRLRERKRELSEYT 277
                                       *****999999999999999999999888888776555432 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.019
                               ERM   3 aerekreleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekek 79 
                                       +e + + +++ L++   e++   ++L e +++ ++ ae + ra+    +L++  +e+ +ei+r + +  +  e +++
  gi|344210119|ref|YP_004786295.1| 336 IESTLQSMRDHLQETVTEIDDIDDELDELTDRRDEIAETRTRAR----ELTATIEEVDAEIERRQTTVVDLRERRNN 408
                                       57777889999999999999999999999999999999988875....58899999********************* PP

                               ERM  80 lerklreaeleaarleees 98 
                                       l ++++e e++++ l+ e+
  gi|344210119|ref|YP_004786295.1| 409 LSARVEELEERVTSLRTEE 427
                                       *************999875 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.13
                               ERM  33 etaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeee...ekeklerklreaeleaarleeeserk 101
                                       +++ +L  ka ++e e ++Le ++ e++eei+ ++ + ++++e   ++e++ ++l +  +++ rle e + +
  gi|344210119|ref|YP_004786295.1| 429 DEVLELHTKANELELELDRLESERDEVREEIADIESDIRRNDElaaQREDVVDELIDLRSRIDRLEAEATDQ 500
                                       567788888888888888888888888888888887776665422266666777777777777777776655 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6  17.5   0.00022      0.06      68     162 ..     136     230 ..     102     237 .. 0.88
   2 ?    0.9   2.4       1.6   4.5e+02      77     131 ..     225     279 ..     222     304 .. 0.51
   3 ?    9.1  11.0    0.0052       1.4      71     149 ..     342     423 ..     313     429 .. 0.68
   4 ?    3.1  11.3      0.35        98     110     175 ..     430     498 ..     425     510 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00022
                             ATG16  68 snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdree 144
                                        +++++++i +  +++a+l+ +l +l +++++l + ++e+ ++lq+ e+++ e++   +  +++r +let+l+++++
  gi|344210119|ref|YP_004786295.1| 136 AAEQRKEEIDAELDRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQENRDELETALDELQA 212
                                       24457899999****************************************************************** PP

                             ATG16 145 elrekeklvqdlqDElsa 162
                                       +  e++++ +d+q E ++
  gi|344210119|ref|YP_004786295.1| 213 TRSELKRVRNDIQSEQES 230
                                       *************99765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.6
                             ATG16  77 qsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleae 131
                                       qs ++ +a+lr+e   l  +r+ l ++  e  e+l+ + ++l+e++++l e +++
  gi|344210119|ref|YP_004786295.1| 225 QSEQESIAALRDERGSLAVERSGLPESPDERLEALESDIDRLRERKRELSEYTTR 279
                                       4555555555555555555555554443333333444444444444443333333 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0052
                             ATG16  71 kqsakiqsleqklaqlreelaelyksrgela...qrllelneelqkleeklkedeerlaeleaeraaletklkdree 144
                                       + ++++q++ +++  + +el el  +r e a   +r +el++++++ +++++++++++ +l+++r++l+ +++++ee
  gi|344210119|ref|YP_004786295.1| 342 SMRDHLQETVTEIDDIDDELDELTDRRDEIAetrTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSARVEELEE 418
                                       45566666666666666777666666644332226777777777777777777777777777777777777777777 PP

                             ATG16 145 elrek 149
                                       ++  +
  gi|344210119|ref|YP_004786295.1| 419 RVTSL 423
                                       76544 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.35
                             ATG16 110 elqkleeklkedeerlaeleaeraaletklkdreeelrekeklvq...dlqDElsaLqlqlnqaEeklr 175
                                       e+ +l +k++e e +l++le+er +++++++d e  +r  ++l     d+ DEl+ L+ +   +E++  
  gi|344210119|ref|YP_004786295.1| 430 EVLELHTKANELELELDRLESERDEVREEIADIESDIRRNDELAAqreDVVDELIDLRSRIDRLEAEAT 498
                                       666888999999999*******************99998888775555999*******99999998865 PP

>> Retrotrans_gag  Retrotransposon gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       8.9   2.4e+03      50      84 ..     131     165 ..     124     183 .. 0.72
   2 ?   -0.6   0.8         6   1.7e+03      44      83 ..     184     223 ..     170     236 .. 0.70
   3 ?   10.8   0.1    0.0017      0.46      42      74 ..     252     284 ..     250     303 .. 0.84
   4 ?   -1.0   0.2       8.2   2.3e+03      41      78 ..     352     386 ..     326     408 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 8.9
                    Retrotrans_gag  50 eeelsslrQgtesvreYvtrfktladqldevltee 84 
                                       +++++   Q++e ++  ++r  +l ++l++ + ++
  gi|344210119|ref|YP_004786295.1| 131 HRQIRAAEQRKEEIDAELDRIASLKRDLPDLERQQ 165
                                       67788888888888888888888888888633333 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 6
                    Retrotrans_gag  44 erkdqleeelsslrQgtesvreYvtrfktladqldevlte 83 
                                       +r d+ + ++++ +++   ++ ++++++ ++++l++v+++
  gi|344210119|ref|YP_004786295.1| 184 DRIDERDVDFQTTQENRDELETALDELQATRSELKRVRND 223
                                       5777777788888888888888888888888888874443 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0017
                    Retrotrans_gag  42 pserkdqleeelsslrQgtesvreYvtrfktla 74 
                                       p+er ++le+++ +lr++++ ++eY+tr++ ++
  gi|344210119|ref|YP_004786295.1| 252 PDERLEALESDIDRLRERKRELSEYTTRLQNVV 284
                                       5678899**********************9887 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 8.2
                    Retrotrans_gag  41 lpserkdqleeelsslrQgtesvreYvtrfktladqld 78 
                                        +    d+ ++el +l+ +   ++e  tr ++l + ++
  gi|344210119|ref|YP_004786295.1| 352 TE---IDDIDDELDELTDRRDEIAETRTRARELTATIE 386
                                       22...555556666666666666666666666555555 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   2.2      0.61   1.7e+02      31      91 ..     125     181 ..     115     195 .. 0.63
   2 ?   11.1   3.6    0.0016      0.43      26      94 ..     200     268 ..     178     269 .. 0.84
   3 ?    7.2   0.1     0.025       6.9      31      91 ..     254     315 ..     247     322 .. 0.80
   4 ?    7.3   5.3     0.023       6.4      13     101 ..     336     418 ..     331     426 .. 0.64
   5 ?    1.6   3.2       1.4   3.7e+02      22      66 ..     457     499 ..     430     512 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.61
                                       SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHH CS
                          Spectrin  31 kdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWee 91 
                                        d++++ +++++ ++ ++e++a+ +r+ +l+    +l+  +    +ei+e     +++ + 
  gi|344210119|ref|YP_004786295.1| 125 VDVASIHRQIRAAEQRKEEIDAELDRIASLKRDLPDLERQQATLRDEITE----TRDKLQR 181
                                       57788888888888888888888888888886666664443333333333....3333333 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0016
                                       CSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  26 sedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLke 94 
                                        ++l+  l+e+qa   ++k+++++++++qe + al +   +l+ e    +e   erle+l++  + L+e
  gi|344210119|ref|YP_004786295.1| 200 RDELETALDELQATRSELKRVRNDIQSEQESIAALRDERGSLAVERSGLPESPDERLEALESDIDRLRE 268
                                       3555778888999999**************************9998999999999*****999999987 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.025
                                       SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTT.HHHHHHHHHHHHHHHHH CS
                          Spectrin  31 kdleevqallkkhkaleaelaaqqervkalnelaeklldeghsa.seeieerleelnerWee 91 
                                       + le++++ ++++++ ++el+++ +r++++  + e+ll+ +h + +++i ++ e + +  ++
  gi|344210119|ref|YP_004786295.1| 254 ERLEALESDIDRLRERKRELSEYTTRLQNVVGFNEELLSGEHREiTDAIDAKPESVGDITDQ 315
                                       57899999999**************************7766655157788887777665555 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHTTHTTHHHHHHHHHHHHHH CS
                          Spectrin  13 leeWieekeellssedlgkdleevqallkkhkaleaelaaqqervkalnelaekl.ldeghsaseeieerleelner 88 
                                       +e+ ++ ++ +l  ++   +++++ + l+++++ ++e+a+ ++r ++l+++ e++ ++      e+ ++++ +l+er
  gi|344210119|ref|YP_004786295.1| 336 IESTLQSMRDHL--QETVTEIDDIDDELDELTDRRDEIAETRTRARELTATIEEVdAEI-----ERRQTTVVDLRER 405
                                       666777777777..566668888888888888888888888888888887777774333.....4445555555555 PP

                                       HHHHHHHHHHHHH CS
                          Spectrin  89 WeeLkelaaerkq 101
                                         +L+++++e ++
  gi|344210119|ref|YP_004786295.1| 406 RNNLSARVEELEE 418
                                       5555555544433 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 1.4
                                       HHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  22 ellssedlgkdleevqallkkhkaleaelaaqqervkalnelaek 66 
                                       e++   d+++d+    +l  + +++ +el + + r+++l++ a++
  gi|344210119|ref|YP_004786295.1| 457 EEI--ADIESDIRRNDELAAQREDVVDELIDLRSRIDRLEAEATD 499
                                       222..3555566666666666666666666666666666655544 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.4    0.0032      0.88      79     116 ..     151     188 ..     149     192 .. 0.83
   2 ?    5.6   1.7     0.052        14       6      35 ..     194     227 ..     190     237 .. 0.78
   3 ?    4.6   0.1      0.11        30       3      34 ..     254     285 ..     253     302 .. 0.81
   4 ?    3.0   1.2      0.32        88      24      37 ..     356     370 ..     334     398 .. 0.49
   5 ?   -0.1   0.3       3.1   8.4e+02      83     103 ..     403     423 ..     386     440 .. 0.59
   6 ?    2.5   0.6      0.47   1.3e+02      85     114 ..     437     466 ..     426     471 .. 0.66
   7 ?    2.2   0.6      0.58   1.6e+02       2      33 ..     442     473 ..     441     479 .. 0.73
   8 ?    3.9   0.2      0.18        49      84     114 ..     467     497 ..     462     503 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0032
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  79 iellkkkleelekqlekleeeleklkdqittleanlaq 116
                                       i+ lk+ l +le+q+ +l +e+++ +d+++ +e+ +++
  gi|344210119|ref|YP_004786295.1| 151 IASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDE 188
                                       56789999999999999999999999999999888776 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.052
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTT..... CS
                         Prefoldin   6 eslqaelaqlkeaieelektletlktlkk....e 35 
                                       ++ q+++++l++a++el++t++ lk++++    e
  gi|344210119|ref|YP_004786295.1| 194 QTTQENRDELETALDELQATRSELKRVRNdiqsE 227
                                       5678999999999999999999999999975332 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                         Prefoldin   3 eeleslqaelaqlkeaieelektletlktlkk 34 
                                       e le+l++++++l+e+++el +   +l+++  
  gi|344210119|ref|YP_004786295.1| 254 ERLEALESDIDRLRERKRELSEYTTRLQNVVG 285
                                       568999999*****999999999999998776 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.32
                                       HHHHHHHHHTT..-T CS
                         Prefoldin  24 ktletlktlkk.ede 37 
                                       ++ + l++l + +de
  gi|344210119|ref|YP_004786295.1| 356 DIDDELDELTDrRDE 370
                                       333333333332222 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  83 kkkleelekqlekleeelekl 103
                                        ++ ++l++ +e+lee ++ l
  gi|344210119|ref|YP_004786295.1| 403 RERRNNLSARVEELEERVTSL 423
                                       333333334444444333333 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.47
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  85 kleelekqlekleeeleklkdqittleanl 114
                                       k +ele  l+ le e ++ +++i  +e  +
  gi|344210119|ref|YP_004786295.1| 437 KANELELELDRLESERDEVREEIADIESDI 466
                                       556666666666666666666666666554 PP

  == domain 7  score: 2.2 bits;  conditional E-value: 0.58
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                         Prefoldin   2 keeleslqaelaqlkeaieelektletlktlk 33 
                                       + el++l++e+++++e+i ++e+ + + ++l 
  gi|344210119|ref|YP_004786295.1| 442 ELELDRLESERDEVREEIADIESDIRRNDELA 473
                                       55788899999999999999988776666655 PP

  == domain 8  score: 3.9 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  84 kkleelekqlekleeeleklkdqittleanl 114
                                       ++ +el +q+e++ +el +l+++i+ lea++
  gi|344210119|ref|YP_004786295.1| 467 RRNDELAAQREDVVDELIDLRSRIDRLEAEA 497
                                       67899***********************987 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.8    0.0021      0.58      68     159 ..     176     267 ..     167     277 .. 0.88
   2 ?    3.8   0.3      0.15        41     107     166 ..     338     396 ..     306     400 .. 0.83
   3 ?    2.7   1.4      0.32        89     108     166 ..     339     396 ..     335     441 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0021
                            DUF745  68 eqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaA 144
                                        ++l+  e+ ++e     q++++n +  ++a ++ q+  + lk++ + ++++ e++ ++ ++  + + e++ l e+ 
  gi|344210119|ref|YP_004786295.1| 176 RDKLQRVEDRIDERDVDFQTTQENRDELETALDELQATRSELKRVRNDIQSEQESIAALRDERGSLAVERSGLPESP 252
                                       4566677888889999999********************************************************** PP

                            DUF745 145 kkRveeLkkqlkear 159
                                        +R+e L+++++  r
  gi|344210119|ref|YP_004786295.1| 253 DERLEALESDIDRLR 267
                                       *******99887766 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.15
                            DUF745 107 ealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlektk 166
                                       ++l+++ ++ +e++++++++ ++   el ++++ +++ ++R+ eL+  ++e+ ++ e+ +
  gi|344210119|ref|YP_004786295.1| 338 STLQSMRDHLQETVTEIDDIDDEL-DELTDRRDEIAETRTRARELTATIEEVDAEIERRQ 396
                                       688999999999999999999887.589999999999*************9999988765 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.32
                            DUF745 108 alkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlektk 166
                                       +l+++ ++ +e++++++++ ++   el ++++ +++ ++R+ eL+  ++e+ ++ e+ +
  gi|344210119|ref|YP_004786295.1| 339 TLQSMRDHLQETVTEIDDIDDEL-DELTDRRDEIAETRTRARELTATIEEVDAEIERRQ 396
                                       45555566666666666666554.35666666666666666666666666666655543 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 ?    2.8   9.6      0.33        90     114     179 ..     154     219 ..     111     234 .. 0.54
   2 ?    5.7  12.4     0.043        12      24     153 ..     151     298 ..     145     307 .. 0.61
   3 ?    7.8  20.7    0.0093       2.6      20     155 ..     340     482 ..     334     504 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.33
                          KASH_CCD 114 llaekdelkkklkeLlkekaeLkkqlheleellaekealleektkqieeLkltieEyssiieeLra 179
                                       l+ +   l+++ + L +e+ e + +l+ +e  + e++   +  +++ +eL+++++E++++  eL+ 
  gi|344210119|ref|YP_004786295.1| 154 LKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQENRDELETALDELQATRSELKR 219
                                       223333334444444444444444444455555555555555555555555555555555555543 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.043
                          KASH_CCD  24 nskLkkavetaeetnakLteeieeLkkklkst...........QqalqkaklleeEleelkalvkeleEkrarlkaq 89 
                                        ++Lk+ +   e + a L +ei+e + kl+ +           Q + ++   le  l+el+a+ +el+  r+ ++ +
  gi|344210119|ref|YP_004786295.1| 151 IASLKRDLPDLERQQATLRDEITETRDKLQRVedriderdvdfQTTQENRDELETALDELQATRSELKRVRNDIQSE 227
                                       45666666666666666666666666666644222222222223344444455555555555555555555555544 PP

                          KASH_CCD  90 nk...qlekenqsLiakiesL....qeenikllaekdelkkklkeLlkekaeLkkqlheleellaekeall 153
                                       ++    l  e+ sL ++   L    +e+++ l +++d l+++++eL++ +  L++ +   eell+   +++
  gi|344210119|ref|YP_004786295.1| 228 QEsiaALRDERGSLAVERSGLpespDERLEALESDIDRLRERKRELSEYTTRLQNVVGFNEELLSGEHREI 298
                                       43111567788888888776633335678889999999999999999999999999988888877666655 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0093
                          KASH_CCD  20 LaeenskLkkavetaeetnakLte......eieeLkkklkstQqalqkaklleeEleelkalvkeleEkrarlkaqn 90 
                                       L+     L+++v  +++ +  L e      ei e +++++    +    + ++ E+e  +++v +l E+r++l+a+ 
  gi|344210119|ref|YP_004786295.1| 340 LQSMRDHLQETVTEIDDIDDELDEltdrrdEIAETRTRARE---LTATIEEVDAEIERRQTTVVDLRERRNNLSARV 413
                                       45555566666666666666553211111155555555554...4455678999*********************** PP

                          KASH_CCD  91 kqlekenqsLia....kiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekeallee 155
                                       ++le    sL++    ++ +L  +   l  e d l++   e  +e+a++ +++   +el+a++e ++ e
  gi|344210119|ref|YP_004786295.1| 414 EELEERVTSLRTeefdEVLELHTKANELELELDRLESERDEVREEIADIESDIRRNDELAAQREDVVDE 482
                                       **********87333368999999999*************************************99877 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 ?    6.9   2.0     0.022       6.1      27      72 ..     143     188 ..     134     190 .. 0.87
   2 ?    5.1   2.6      0.08        22      14      72 ..     210     272 ..     198     274 .. 0.89
   3 ?    4.1   0.2      0.17        46      31      61 ..     336     366 ..     331     380 .. 0.79
   4 ?    4.9   6.4     0.093        26      12      72 ..     383     447 ..     375     449 .. 0.70
   5 ?    5.3   2.4     0.071        20      36      71 ..     432     467 ..     429     470 .. 0.88
   6 ?   -0.4   0.1       4.3   1.2e+03      39      69 ..     456     489 ..     452     503 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.022
                        TMF_DNA_bd  27 kelklnntikkLrkknkelekeikelkkkleklekeleeleerlke 72 
                                       + +++   i +L+ ++ +le ++++l +++ +   +l++ e+r +e
  gi|344210119|ref|YP_004786295.1| 143 EIDAELDRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDE 188
                                       5667778899*******************************99775 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.08
                        TMF_DNA_bd  14 IaqLmeEGekLskkelklnntikkLrkknkelekeikelk....kkleklekeleeleerlke 72 
                                       +++ ++E+++ +   + + ++i  Lr +   l  e + l     ++le le+++++l+er++e
  gi|344210119|ref|YP_004786295.1| 210 LQATRSELKRVRNDIQSEQESIAALRDERGSLAVERSGLPespdERLEALESDIDRLRERKRE 272
                                       567789999999999999***************99999955788***************9886 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.17
                        TMF_DNA_bd  31 lnntikkLrkknkelekeikelkkkleklek 61 
                                        + t+ ++r +++e+ +ei++ +++l++l+ 
  gi|344210119|ref|YP_004786295.1| 336 IESTLQSMRDHLQETVTEIDDIDDELDELTD 366
                                       5789999***************988888765 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.093
                        TMF_DNA_bd  12 eqIaqLmeEGekLskkelklnntikkLrkknkelekeikelk....kkleklekeleeleerlke 72 
                                       ++I+++ +E e+ + + ++l++   +L + ++ele+ +++l     +++ +l  + +ele +l++
  gi|344210119|ref|YP_004786295.1| 383 ATIEEVDAEIERRQTTVVDLRERRNNLSARVEELEERVTSLRteefDEVLELHTKANELELELDR 447
                                       57888888888888888888888888888888888888888766664444444455555555544 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.071
                        TMF_DNA_bd  36 kkLrkknkelekeikelkkkleklekeleeleerlk 71 
                                        +L  k++ele e+++l+++ +++ +e++ +e+  +
  gi|344210119|ref|YP_004786295.1| 432 LELHTKANELELELDRLESERDEVREEIADIESDIR 467
                                       57999***********************99998765 PP

  == domain 6  score: -0.4 bits;  conditional E-value: 4.3
                        TMF_DNA_bd  39 rkknkelekeikelk...kkleklekeleeleer 69 
                                       r+++++ e++i++ +    + e+++ el  l++r
  gi|344210119|ref|YP_004786295.1| 456 REEIADIESDIRRNDelaAQREDVVDELIDLRSR 489
                                       5666666666666552223334444444444444 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.6      0.24        67      29      91 ..     142     209 ..     128     213 .. 0.56
   2 ?    3.3   0.5      0.48   1.3e+02      31      68 ..     193     230 ..     188     239 .. 0.76
   3 ?   -0.3   0.0       6.4   1.8e+03      36      62 ..     254     280 ..     246     294 .. 0.68
   4 ?    8.9   0.4    0.0088       2.4      25      95 ..     348     419 ..     338     425 .. 0.56
   5 ?    3.6   0.4      0.39   1.1e+02      19      57 ..     426     464 ..     424     497 .. 0.64
   6 ?    0.1   0.0       4.9   1.4e+03      26      59 ..     471     505 ..     467     512 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.24
                      Occludin_ELL  29 aeleevskkfseLerelkelkegsk....eykkieeeilqeykklkk.dpeyqekkkrceyLkekLsh 91 
                                       +e+++  ++++ L+r+l +l++++     e++++ +++++   ++ + d ++q++++  ++L+  L+ 
  gi|344210119|ref|YP_004786295.1| 142 EEIDAELDRIASLKRDLPDLERQQAtlrdEITETRDKLQRVEDRIDErDVDFQTTQENRDELETALDE 209
                                       45555555666666666666555554434444444442222222222377788888877777777765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.48
                      Occludin_ELL  31 leevskkfseLerelkelkegskeykkieeeilqeykk 68 
                                       +++++++  eLe+ l+el+ +++e k++ ++i++e ++
  gi|344210119|ref|YP_004786295.1| 193 FQTTQENRDELETALDELQATRSELKRVRNDIQSEQES 230
                                       56677777888888888888888888888888877655 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 6.4
                      Occludin_ELL  36 kkfseLerelkelkegskeykkieeei 62 
                                       ++++ Le+++++l+e+++e ++ + ++
  gi|344210119|ref|YP_004786295.1| 254 ERLEALESDIDRLRERKRELSEYTTRL 280
                                       566777777777777777555544443 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0088
                      Occludin_ELL  25 kelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkk.dpeyqekkkrceyLkekLshiKkl 95 
                                       +e  +e++++ +++ eL ++ +e +e++++ +++++ i +  +++++ +++  + ++r + L+++ + + ++
  gi|344210119|ref|YP_004786295.1| 348 QETVTEIDDIDDELDELTDRRDEIAETRTRARELTATIEEVDAEIERrQTTVVDLRERRNNLSARVEELEER 419
                                       344455666666666666666666666665555555555555555554566666666666666666655555 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.39
                      Occludin_ELL  19 keYkeYkelhaeleevskkfseLerelkelkegskeykk 57 
                                       +e++e  elh++ +e++ ++ +Le+e +e +e+   +++
  gi|344210119|ref|YP_004786295.1| 426 EEFDEVLELHTKANELELELDRLESERDEVREEIADIES 464
                                       567777888888888888888888887777665543322 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 4.9
                      Occludin_ELL  26 elhaeleevskkfseLerelkelkegsk.eykkie 59 
                                       el a+ e+v +++ +L++++++l+ + + ++++ +
  gi|344210119|ref|YP_004786295.1| 471 ELAAQREDVVDELIDLRSRIDRLEAEATdQFNEKM 505
                                       68888999999******999999877665665555 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  17.4    0.0022       0.6      88     217 ..     130     274 ..     102     292 .. 0.64
   2 ?    4.0  19.8     0.047        13      45     240 ..     359     493 ..     333     507 .. 0.40

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0022
                               MAD  88 lnkkekekesklaear...evisalknelaelkrqiekqelelsekeseleelqerldllkkklseleqliqqlekk 161
                                       ++++ +  e++++e+    + i +lk +l +l+rq      e++e++ +l++++ r d+ +  ++ +++ + +le++
  gi|344210119|ref|YP_004786295.1| 130 IHRQIRAAEQRKEEIDaelDRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQENRDELETA 206
                                       44444444444443322135567788899999999999999999999999999999999999999999999999999 PP

                               MAD 162 qkelaeaeqrikeLefeiqsqeddslivknsksel.a...........ripelekelerlreenkkln 217
                                        +el++    +k     iqs +++ + +++ +  l +           r+  le++++rlre+ ++l+
  gi|344210119|ref|YP_004786295.1| 207 LDELQATRSELKRVRNDIQSEQESIAALRDERGSLaVersglpespdeRLEALESDIDRLRERKRELS 274
                                       99999999999999999999666666666555555321110000011144444444444444444444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.047
                               MAD  45 eesdrnqelqkrikllekreeekeealreqiElarlkkknlealnkkekekesklaearevisalknelaelkrqie 121
                                        e                                                  ++l++ r+ i + + + +el   ie
  gi|344210119|ref|YP_004786295.1| 359 DEL-------------------------------------------------DELTDRRDEIAETRTRARELTATIE 386
                                       222.................................................2233333333334444444444555 PP

                               MAD 122 kqelelsekeseleelqerldllkkklseleqliqqlekkq.kelaeaeqrikeLefeiqsqeddslivknsksela 197
                                       + + e++++++ + +l+er + l ++++ele+++ +l +++ +e  e   +  eLe e+   e++  +v++      
  gi|344210119|ref|YP_004786295.1| 387 EVDAEIERRQTTVVDLRERRNNLSARVEELEERVTSLRTEEfDEVLELHTKANELELELDRLESERDEVRE------ 457
                                       55555555555555555555555555555555554444332144444444444555444444444433332...... PP

                               MAD 198 ripelekelerlreenkklnelkenkelLkEevedlkkkLere 240
                                        i+++e++++r    n +l   +e+   +  e+ dl+++++r 
  gi|344210119|ref|YP_004786295.1| 458 EIADIESDIRR----NDELAAQRED---VVDELIDLRSRIDRL 493
                                       23333333332....1112222222...112223333333333 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.5     0.022         6     204     257 ..     130     183 ..     124     191 .. 0.82
   2 ?    7.4   7.4      0.01       2.8     198     286 ..     197     277 ..     183     292 .. 0.55
   3 ?    3.8  26.9      0.13        36      52     184 ..     336     476 ..     321     503 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.022
                                       XXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 204 aeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleael 257
                                       ++++  a+++ keei     +i sl+ +l +l+ q+a+l+++++e+ ++l++  
  gi|344210119|ref|YP_004786295.1| 130 IHRQIRAAEQRKEEIDAELDRIASLKRDLPDLERQQATLRDEITETRDKLQRVE 183
                                       567778889999999999999999999999999999999999999998887654 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.01
                                       XXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 198 eelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaei 274
                                       +e +++ e+  ++l+++++e++ +r  iqs +  +++l+ ++ sl  + + l e          e l++le+++ ++
  gi|344210119|ref|YP_004786295.1| 197 QENRDELETALDELQATRSELKRVRNDIQSEQESIAALRDERGSLAVERSGLPES-------PDERLEALESDIDRL 266
                                       3334455555555566666666666666666666666555555555555544444.......444444555555554 PP

                                       HHHHHHHHHHHH CS
                          Filament 275 reemarqlreYq 286
                                       re+ +r+l+eY 
  gi|344210119|ref|YP_004786295.1| 267 RER-KRELSEYT 277
                                       433.34444443 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.13
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  52 yekeleelrkqldeltkerarlqleldnl...reeledlrkkyekelnkreevEaelkalrkdldeatlarvdLekk 125
                                        e++l+++r++l+e+ +e + ++ eld+l   r+e+++ r++  + ++  eev+ae++  +  + ++  +r +L ++
  gi|344210119|ref|YP_004786295.1| 336 IESTLQSMRDHLQETVTEIDDIDDELDELtdrRDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSAR 412
                                       6899*******************999998333567788899999999****************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX.....XXXXXXXXXXXXXXXXXX CS
                          Filament 126 vesLkeelaflkkvheeEvkelqkqvseqvlvevdaark.ld.....Lteilkeiraqyeelaek 184
                                       ve+L+e +  l++   +Ev el++++ +++ +e+d  ++  d     ++ i ++ir++ e  a++
  gi|344210119|ref|YP_004786295.1| 413 VEELEERVTSLRTEEFDEVLELHTKA-NELELELDRLESeRDevreeIADIESDIRRNDELAAQR 476
                                       *************************9.88999999743313355555777888888776655544 PP

>> Zw10  Centromere/kinetochore Zw10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   2.2      0.17        47      10      76 ..     159     227 ..     126     238 .. 0.58
   2 ?    2.4   1.2      0.16        44      12      71 ..     336     394 ..     327     399 .. 0.80
   3 ?   13.5   4.6   7.3e-05      0.02      11      83 ..     401     472 ..     395     507 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.17
                              Zw10  10 edlekkisklekkveei...keevskmivkkYseflelsssaeellerveslskeidalkkkveneieqd 76 
                                       +dle +   l   + e+    ++v + i+++  +f++  +  +el + +++l+ + + lk +v n i+++
  gi|344210119|ref|YP_004786295.1| 159 PDLERQQATLRDEITETrdkLQRVEDRIDERDVDFQTTQENRDELETALDELQATRSELK-RVRNDIQSE 227
                                       444444444443333330003456666666666666666666666666666666655543.455555554 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.16
                              Zw10  12 lekkisklekkveeikeevskmivkkYseflelsssaeellerveslskeidalkkkven 71 
                                       +e++ + +  +++e+ +e+ ++i+++ +e+ +  +   e+ +r ++l  +i+ +  ++e 
  gi|344210119|ref|YP_004786295.1| 336 IESTLQSMRDHLQETVTEI-DDIDDELDELTDRRDEIAETRTRARELTATIEEVDAEIER 394
                                       5777888888888888887.5799999999999999999999999999999988888875 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 7.3e-05
                              Zw10  11 dlekkisklekkveeikeevskmivkkYseflelsssaeellerveslskeidalkkkveneieqdlkaavee 83 
                                       dl+ + ++l+ +vee+ e+v++   ++++e lel++ a+el  +++ l++e d + +++ + ie+d++   e 
  gi|344210119|ref|YP_004786295.1| 401 DLRERRNNLSARVEELEERVTSLRTEEFDEVLELHTKANELELELDRLESERDEVREEIAD-IESDIRRNDEL 472
                                       899999***************************************************9975.77777665433 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  12.6     0.045        13      46     153 ..     160     269 ..     139     284 .. 0.53
   2 ?    9.8   5.7    0.0023      0.62      86     175 ..     333     420 ..     320     422 .. 0.92
   3 ?    2.1  10.6      0.51   1.4e+02      55     167 ..     389     496 ..     385     506 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.045
                           DUF4201  46 qlqienqalnkkIeernkeLkrlkkkttk...tvhalthlkeklhmleselselkkelkekeerlaklrkelykvkl 119
                                        l+++ ++l+++I e  ++L+r  +++     + ++++++++ l +   el++ ++elk+  +++++ ++++  ++ 
  gi|344210119|ref|YP_004786295.1| 160 DLERQQATLRDEITETRDKLQRVEDRIDErdvDFQTTQENRDELETALDELQATRSELKRVRNDIQSEQESIAALRD 236
                                       34555555555555555555555555543222455555555555555555555555555555555555555555555 PP

                           DUF4201 120 erdklrkqneklkqqggllrvPaLlkDYdktkek 153
                                       er  l  +++ l ++  + r +aL  D d+  e+
  gi|344210119|ref|YP_004786295.1| 237 ERGSLAVERSGLPESPDE-RLEALESDIDRLRER 269
                                       555555555555555444.555555555555554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0023
                           DUF4201  86 lhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekveekrksvk 162
                                        + +es+l+ +++ l+e  ++++++++el ++  +rd + + +++ ++ ++    +++  + ++++  v ++r++ +
  gi|344210119|ref|YP_004786295.1| 333 PDRIESTLQSMRDHLQETVTEIDDIDDELDELTDRRDEIAETRTRARELTAT--IEEVDAEIERRQTTVVDLRERRN 407
                                       557899**********************************999999999888..7899999**************** PP

                           DUF4201 163 kLrrkvkilemrl 175
                                       +L  +v++le+r+
  gi|344210119|ref|YP_004786295.1| 408 NLSARVEELEERV 420
                                       ***********98 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.51
                           DUF4201  55 nkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqnekl 131
                                       + +Ie+r+  ++ l+++ ++ + ++++l e+ + l++e     +e  e++++ ++l+ el +++ erd +r++ +++
  gi|344210119|ref|YP_004786295.1| 389 DAEIERRQTTVVDLRERRNNLSARVEELEERVTSLRTEE---FDEVLELHTKANELELELDRLESERDEVREEIADI 462
                                       668999999999999999999999999999988887764...46788889999999999999999999999999999 PP

                           DUF4201 132 kqqggllrvPaLlkDYdktkekveekrksvkkLrrk 167
                                       +++    r+ +L    ++ ++++ ++r++++ L+ +
  gi|344210119|ref|YP_004786295.1| 463 ESDI--RRNDELAAQREDVVDELIDLRSRIDRLEAE 496
                                       8764..458888888888888888888888888765 PP

>> FliD_N  Flagellar hook-associated protein 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.29        80      19      51 ..     133     165 ..     116     185 .. 0.66
   2 ?    4.5   1.5       0.2        55      17      53 ..     197     233 ..     178     292 .. 0.70
   3 ?    2.2   0.1       1.1     3e+02      30      76 ..     340     384 ..     330     455 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.29
                                       XXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHH CS
                            FliD_N  19 kldkleqkktklewkqsayrelnsklsnlksal 51 
                                       ++   eq+k++++++ + + +l+ +l +l+ + 
  gi|344210119|ref|YP_004786295.1| 133 QIRAAEQRKEEIDAELDRIASLKRDLPDLERQQ 165
                                       455577888888888888888888877777633 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.2
                                       XXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHH CS
                            FliD_N  17 rakldkleqkktklewkqsayrelnsklsnlksalsa 53 
                                       +   d+le++  +l++ +s+++ +++++++ +++++a
  gi|344210119|ref|YP_004786295.1| 197 QENRDELETALDELQATRSELKRVRNDIQSEQESIAA 233
                                       2334445555555555555555555555555554434 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 1.1
                                       XXXXHHHHHHHHHHHHHHHHHHHHHXX.GGGGGXEEEEECSTTTEEEE CS
                            FliD_N  30 lewkqsayrelnsklsnlksalsalsk.sstfsakkatssdesvvtat 76 
                                       l++ ++ ++e  ++++++ ++l++l++  ++++++    +    +tat
  gi|344210119|ref|YP_004786295.1| 340 LQSMRDHLQETVTEIDDIDDELDELTDrRDEIAETR---TRARELTAT 384
                                       455555555555555555554444444344442211...111112222 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.8      0.14        39     113     153 ..     129     172 ..     125     178 .. 0.79
   2 ?    9.5   7.0    0.0028      0.78      99     170 ..     167     241 ..     146     282 .. 0.84
   3 ?    5.1  10.9     0.065        18      90     180 ..     364     465 ..     329     467 .. 0.72
   4 ?    4.8   5.7     0.079        22      97     172 ..     399     471 ..     397     508 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.14
                            DUF724 113 klekkieeeesekrkleeeid...elekkilelerqlallkekk 153
                                        ++++i+ +e++k+++++e+d    l++   +lerq+a+l+ + 
  gi|344210119|ref|YP_004786295.1| 129 SIHRQIRAAEQRKEEIDAELDriaSLKRDLPDLERQQATLRDEI 172
                                       57899999999999999998866678999999*****9999543 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0028
                            DUF724  99 slkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk...ekkeaadkeiarlkseaekl 170
                                        l+de t+++++++++e +i e + + +  +e+ dele +  el+  +  lk   ++ ++++++ia+l+ e  +l
  gi|344210119|ref|YP_004786295.1| 167 TLRDEITETRDKLQRVEDRIDERDVDFQTTQENRDELETALDELQATRSELKrvrNDIQSEQESIAALRDERGSL 241
                                       578888889999999999999999999999999999999999998887777767677777888888887777665 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.065
                            DUF724  90 lqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk...........ekkea 155
                                       l +r +++ + +++ ++l  ++++++ +ie  ++    l e  ++l+ ++ ele++ ++l+           +k ++
  gi|344210119|ref|YP_004786295.1| 364 LTDRRDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSARVEELEERVTSLRteefdevlelhTKANE 440
                                       33333667777788888888888889999999999999999999999999999999999998888888888777777 PP

                            DUF724 156 adkeiarlkseaekleeeledveqe 180
                                        + e+ rl+se ++++ee+ d+e++
  gi|344210119|ref|YP_004786295.1| 441 LELELDRLESERDEVREEIADIESD 465
                                       7888888888888888888888765 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.079
                            DUF724  97 Llslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaeklee 172
                                       ++ l++++++l  + ++le++++  ++e+    +e+ el  k  ele +l++l +++++  +eia+++s+ ++ +e
  gi|344210119|ref|YP_004786295.1| 399 VVDLRERRNNLSARVEELEERVTSLRTEEF---DEVLELHTKANELELELDRLESERDEVREEIADIESDIRRNDE 471
                                       566777777777777777777776555444...4556777777777777777777777777777777777655444 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3  19.1     0.042        12     273     412 ..     132     272 ..     103     305 .. 0.38
   2 ?    7.3  20.5    0.0026      0.72     673     844 ..     341     503 ..     324     510 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.042
                           DUF3584 273 adeerlaekqeevqeakaelkqqlrtledelkeaidelnqelsaakaklaakeselealeeqkkkyedadieklkad 349
                                        ++++ ++++ee++++  ++ +  r l  +l+ ++++l+ e+ ++++kl++ e+++++ + + +   +++ ++l+  
  gi|344210119|ref|YP_004786295.1| 132 RQIRAAEQRKEEIDAELDRIASLKRDL-PDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQT-TQENRDELETA 206
                                       223333333333333333332222222.2233333333333333333333333333332222222.12222233333 PP

                           DUF3584 350 ldqlpsirseleeleeeldaltekhqdvqekydrr...kqkikeeleeeleklkerleaireekdr 412
                                       ld+l ++rsel+ + ++++   e++ ++  +   +   ++ + e+  e le l+++ + +re k +
  gi|344210119|ref|YP_004786295.1| 207 LDELQATRSELKRVRNDIQSEQESIAALRDERGSLaveRSGLPESPDERLEALESDIDRLRERKRE 272
                                       333333333333333333333333333332222110001122222222222222222223322222 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0026
                           DUF3584 673 kaiaerkqqaeeqlqkldaqlkqleeqqkaaleelkedlseerlekkakwqevvgeldeqlaelkkaieaartqaka 749
                                       +++ ++ q+  ++++++d +l+ l   + + ++e++ +++e +    a ++ev +e++   + +   + ++r++  a
  gi|344210119|ref|YP_004786295.1| 341 QSMRDHLQETVTEIDDIDDELDELTDRR-DEIAETRTRARELT----ATIEEVDAEIERRQTTVVD-LRERRNNLSA 411
                                       2333444444445555555555554433.33455566666666....6666666666666555554.5667888899 PP

                           DUF3584 750 rlkeleeaykreLkskdvDpetvkelkrkieeLekkieriekrreevreYraflqetwlkvdslaeerpalkeqvee 826
                                       r++elee   ++L     D+  v el++k +eLe +++r e++r+evre  a + ++  + d+la +r+  + ++ +
  gi|344210119|ref|YP_004786295.1| 412 RVEELEERV-TSLRTEEFDE--VLELHTKANELELELDRLESERDEVREEIADIESDIRRNDELAAQREDVVDELID 485
                                       999998765.5799999986..6699999999999999999999999999999999999989999999999999999 PP

                           DUF3584 827 lesaaeeleqeltrlied 844
                                       l+s + +le e t + ++
  gi|344210119|ref|YP_004786295.1| 486 LRSRIDRLEAEATDQFNE 503
                                       999988888888776655 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   7.5     0.087        24      10     108 ..     142     240 ..     127     251 .. 0.85
   2 ?   12.2   5.4   0.00051      0.14      15     101 ..     336     422 ..     332     427 .. 0.84
   3 ?    1.5   1.6      0.97   2.7e+02      19      61 ..     438     473 ..     429     510 .. 0.41

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.087
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH.. CS
                        Laminin_II  10 etakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeass 86 
                                       e + + l+ +a l+ +l+ ++ +  ++++++ et +k++     i++     ++ +++ ++L+  l el+  +++ +
  gi|344210119|ref|YP_004786295.1| 142 EEIDAELDRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQENRDELETALDELQATRSELK 218
                                       45555577788899999999999999999999999999999999999999999999999999999999999999999 PP

                                       .HHHHHHHHHHHHHHHHHHHHT CS
                        Laminin_II  87 slsdniseikelIaqARkaAnk 108
                                        + ++i+  +e Ia+ R+   +
  gi|344210119|ref|YP_004786295.1| 219 RVRNDIQSEQESIAALRDERGS 240
                                       9999999999999998886555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00051
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHH CS
                        Laminin_II  15 vleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdn 91 
                                       +++ l+ +   l++t  ++  i+++++e ++  ++  ++   Ar+   ++e++  +++ +  ++  l+e +++ls+ 
  gi|344210119|ref|YP_004786295.1| 336 IESTLQSMRDHLQETVTEIDDIDDELDELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSAR 412
                                       67788889999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       HHHHHHHHHH CS
                        Laminin_II  92 iseikelIaq 101
                                       ++e+ e +  
  gi|344210119|ref|YP_004786295.1| 413 VEELEERVTS 422
                                       9998887665 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.97
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  19 laplsqnlentkeklseinrsveetnekvkdankairdArrsv 61 
                                        ++l+ +l++++++  e++++++ ++ ++       r   +  
  gi|344210119|ref|YP_004786295.1| 438 ANELELELDRLESERDEVREEIADIESDI-------RRNDELA 473
                                       22222333333333333333332222222.......2222222 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   2.4     0.025         7      11      72 ..     138     199 ..     126     209 .. 0.74
   2 ?    2.6   1.4      0.75   2.1e+02       7      70 ..     207     270 ..     200     284 .. 0.63
   3 ?    0.4   0.1       3.8     1e+03      24      50 ..     256     282 ..     249     318 .. 0.51
   4 ?    8.4   1.7     0.012       3.4       6      73 ..     336     409 ..     332     411 .. 0.82
   5 ?    5.1   6.5      0.12        34       3      65 ..     406     472 ..     404     508 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXX CS
                              YabA  11 eeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegken 72 
                                       e+ +e++++ l+++++lk++l +l  + a+L+ e ++ r++l++ e++ +e++ + ++++en
  gi|344210119|ref|YP_004786295.1| 138 EQRKEEIDAELDRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQEN 199
                                       4445677788889999**************************76666666666555555544 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.75
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXX CS
                              YabA   7 fdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegk 70 
                                       +d+l++  ++l+++ +++++ +e++a+l +e  +L +e + l e  +e+ ++ +++  +l+e k
  gi|344210119|ref|YP_004786295.1| 207 LDELQATRSELKRVRNDIQSEQESIAALRDERGSLAVERSGLPESPDERLEALESDIDRLRERK 270
                                       4566666677777778888888888888888888888877776665444444444444444444 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  24 leelkeelaelleenaeLeleneklre 50 
                                       le+l++++ +l e+ +eL+   ++l++
  gi|344210119|ref|YP_004786295.1| 256 LEALESDIDRLRERKRELSEYTTRLQN 282
                                       333333333333333333333333333 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......XXXXXXXXXXXXXXXXXXXXX CS
                              YabA   6 lfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl......eeeekkekekkkelsegkenL 73 
                                       + ++l+++ ++l+e+++e++++ +el el+++ +e+    ++ re+       + e ++++++  +l+e ++nL
  gi|344210119|ref|YP_004786295.1| 336 IESTLQSMRDHLQETVTEIDDIDDELDELTDRRDEIAETRTRARELTatieevDAEIERRQTTVVDLRERRNNL 409
                                       5678999***************************9999988888888777766556666677777778888777 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXX CS
                              YabA   3 kkelfdkleeleeqleelle....eleelkeelaelleenaeLeleneklrerleeeekkekekkke 65 
                                       +++l +++eelee++++l +    e+ el+++ +el  e ++Le e +++re++++ e++ +++++ 
  gi|344210119|ref|YP_004786295.1| 406 RNNLSARVEELEERVTSLRTeefdEVLELHTKANELELELDRLESERDEVREEIADIESDIRRNDEL 472
                                       5789999******999876422226889999**********************94444333333332 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   6.6      0.38     1e+02      15      79 ..     161     220 ..     106     226 .. 0.62
   2 ?    4.2   2.4      0.26        70       8      66 ..     203     270 ..     197     286 .. 0.58
   3 ?    0.8   0.1       2.8   7.7e+02      11      43 ..     255     287 ..     249     316 .. 0.63
   4 ?   12.0   2.0   0.00098      0.27      20      92 ..     338     408 ..     332     413 .. 0.85
   5 ?    3.7   3.2      0.36     1e+02      25      91 ..     423     491 ..     408     501 .. 0.51

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.38
                           DUF2203  15 lkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdl 79 
                                       l++   + ++lr+e++e++++l++ +++ ++  +  + ++ +e ++e+e +++e++++  e+k +
  gi|344210119|ref|YP_004786295.1| 161 LER---QQATLRDEITETRDKLQRVEDRIDE--RDVDFQTTQENRDELETALDELQATRSELKRV 220
                                       222...2223344444444444444444443..44445555666666666666666666666654 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.26
                           DUF2203   8 AnalLpllkelleelralrkeleeleeeleeakaeaekse.............aaeleaeleeleaeieelv 66 
                                        ++ L +l+ + +el+++r+++++ +e++++ ++e+ + +                  ++le+  ++++e  
  gi|344210119|ref|YP_004786295.1| 203 LETALDELQATRSELKRVRNDIQSEQESIAALRDERGSLAversglpespderL----EALESDIDRLRERK 270
                                       456677777777777788888888777777777776554477666766643332....22333333333333 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 2.8
                           DUF2203  11 lLpllkelleelralrkeleeleeeleeakaea 43 
                                        L  l++ +++lr+ ++el e  ++l++    +
  gi|344210119|ref|YP_004786295.1| 255 RLEALESDIDRLRERKRELSEYTTRLQNVVGFN 287
                                       567778888888888888888877777665443 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00098
                           DUF2203  20 eelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdleaglvDFpakldg 92 
                                       + l+++r++l+e+++e++++ +e +  e + ++ e++e +++++el+++iee+ +e+   +  +vD   ++++
  gi|344210119|ref|YP_004786295.1| 338 STLQSMRDHLQETVTEIDDIDDELD--ELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNN 408
                                       4567788888888889999988865..4899999********************************9887776 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.36
                           DUF2203  25 lrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeieelGvevkdleaglvDFpakld 91 
                                       lr+e  + + el+++ +e e +    ++++ e++e  a ie+ +++ +el ++  d+   l+D  +++d
  gi|344210119|ref|YP_004786295.1| 423 LRTEEFDEVLELHTKANELELELdrLESERDEVREEIADIESDIRRNDELAAQREDVVDELIDLRSRID 491
                                       222222222233333333322212244445555555555566666666777888888888888877776 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   5.8      0.14        39     106     194 ..     132     215 ..     126     234 .. 0.53
   2 ?   10.0   2.1    0.0018       0.5     136     194 ..     329     386 ..     254     394 .. 0.69
   3 ?   -0.4   3.9       2.9     8e+02     103     166 ..     401     464 ..     381     510 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.14
                               LXG 106 nglkkakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdqeqksalanlesdlkal 182
                                       +++  a++  ee + e+++i +  +d+ +l e++  +++d++ + ++k+q++ + ++    e + ++++++++ ++l
  gi|344210119|ref|YP_004786295.1| 132 RQIRAAEQRKEEIDAELDRIASLKRDLPDL-ERQQATLRDEITETRDKLQRVEDRID----ERDVDFQTTQENRDEL 203
                                       444444444444444444444444444333.33444455555555555555555554....4455566666666666 PP

                               LXG 183 ktyvseLeemts 194
                                       +t ++eL+++ s
  gi|344210119|ref|YP_004786295.1| 204 ETALDELQATRS 215
                                       666666666544 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0018
                               LXG 136 pelddsevkdslqkakkkvqetiekledfdqeqksalanlesdlkalktyvseLeemts 194
                                       ++++ +++++ lq++++++qet++ ++d+d e++++++  ++ +++  t  +eL+++++
  gi|344210119|ref|YP_004786295.1| 329 SRVKPDRIESTLQSMRDHLQETVTEIDDIDDELDELTDRRDE-IAETRTRARELTATIE 386
                                       6678899**************************988776554.4455555566666665 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.9
                               LXG 103 elenglkkakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdq 166
                                       +l  + +++++ +eel++++ +   +  d v   + + +e++ +l++ +++++e+ e + d++ 
  gi|344210119|ref|YP_004786295.1| 401 DLRERRNNLSARVEELEERVTSLRTEEFDEVLELHTKANELELELDRLESERDEVREEIADIES 464
                                       5666667777777777777777555555555555667777777777777777777777777765 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 ?    4.5   5.7      0.15        42      12      59 ..     129     174 ..     125     185 .. 0.76
   2 ?    2.0   7.0      0.89   2.4e+02       8      60 ..     163     210 ..     147     219 .. 0.65
   3 ?    6.6   0.1     0.034       9.4       9      29 ..     255     275 ..     247     288 .. 0.84
   4 ?    5.9   0.3     0.054        15      41      66 ..     345     370 ..     335     373 .. 0.81
   5 ?    3.7   3.6      0.26        72      13      59 ..     350     394 ..     343     398 .. 0.67
   6 ?    5.3   2.7     0.087        24      11      56 ..     379     419 ..     368     425 .. 0.54
   7 ?    6.3   5.0     0.042        12      13      63 ..     409     451 ..     401     455 .. 0.56
   8 ?    1.3  10.2       1.5   4.3e+02      11      63 ..     439     489 ..     426     503 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.15
                      ABC_tran_CTD  12 eleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLee 59 
                                        + ++I a E++++e++ael   +  +++  l +l +++++l++e+ e
  gi|344210119|ref|YP_004786295.1| 129 SIHRQIRAAEQRKEEIDAELDRIASLKRD--LPDLERQQATLRDEITE 174
                                       57789****************98866555..77777777777776655 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.89
                      ABC_tran_CTD   8 releeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeel 60 
                                       r+ ++l +eI +   +++ +e+++ + +       ++ +++  +ele++L+el
  gi|344210119|ref|YP_004786295.1| 163 RQQATLRDEITETRDKLQRVEDRIDERD-----VDFQTTQENRDELETALDEL 210
                                       3444566666666677777777776666.....34666666666666666665 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.034
                      ABC_tran_CTD   9 eleeleaeIeaLEeeiaelea 29 
                                       +le+le++I++L e++ el +
  gi|344210119|ref|YP_004786295.1| 255 RLEALESDIDRLRERKRELSE 275
                                       688888888888888888865 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.054
                      ABC_tran_CTD  41 eklaelsaeleeleaeLeelyerWee 66 
                                       + l+e+ +e++++++eL+el++r  e
  gi|344210119|ref|YP_004786295.1| 345 DHLQETVTEIDDIDDELDELTDRRDE 370
                                       569******************99665 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.26
                      ABC_tran_CTD  13 leaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLee 59 
                                          eI+ ++ e+ el+++  + +  ++ ++  el+a +ee++ae+e+
  gi|344210119|ref|YP_004786295.1| 350 TVTEIDDIDDELDELTDRRDEIA--ETRTRARELTATIEEVDAEIER 394
                                       44567777777777777666444..6667777777777777777775 PP

  == domain 6  score: 5.3 bits;  conditional E-value: 0.087
                      ABC_tran_CTD  11 eeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleae 56 
                                        el a+Ie+ ++ei+  ++ + d       e+ + lsa+ eele+ 
  gi|344210119|ref|YP_004786295.1| 379 RELTATIEEVDAEIERRQTTVVDLR-----ERRNNLSARVEELEER 419
                                       3455555555555555555555444.....5555555555555554 PP

  == domain 7  score: 6.3 bits;  conditional E-value: 0.042
                      ABC_tran_CTD  13 leaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyer 63 
                                       l a+ e+LEe+ ++l +e          +++ el+++ +ele eL++l+++
  gi|344210119|ref|YP_004786295.1| 409 LSARVEELEERVTSLRTEEF--------DEVLELHTKANELELELDRLESE 451
                                       44455555555555544433........66666666666666666666543 PP

  == domain 8  score: 1.3 bits;  conditional E-value: 1.5
                      ABC_tran_CTD  11 eeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyer 63 
                                        ele e+++LE e  e+ +e+ad e  sd  +  el a+ e++ +eL  l +r
  gi|344210119|ref|YP_004786295.1| 439 NELELELDRLESERDEVREEIADIE--SDIRRNDELAAQREDVVDELIDLRSR 489
                                       47999999**************999..99999999999999888888666555 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   3.2     0.064        18      10      67 ..     170     227 ..     158     233 .. 0.79
   2 ?    7.0   3.7     0.017       4.8       4      91 ..     339     425 ..     336     434 .. 0.67
   3 ?    1.7   1.4      0.75   2.1e+02      11      62 ..     405     460 ..     382     468 .. 0.49
   4 ?    3.8   0.1      0.18        49       4      52 ..     461     510 ..     458     511 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.064
                             Sec34  10 eecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieek 67 
                                       +e++e  ++++++++ ++e   +f++ +e+  +l++a ++l + +++l+++ ++i+++
  gi|344210119|ref|YP_004786295.1| 170 DEITETRDKLQRVEDRIDERDVDFQTTQENRDELETALDELQATRSELKRVRNDIQSE 227
                                       4555556677778888888888999999999999999999999999999999999875 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.017
                             Sec34   4 qLeskeeecdelleqtdealeqLeeleekfksvse...ktsslheaceqlleeqkrleelaeeieekLkyFeeldpi 77 
                                       +L+s +++++e ++++d++ ++L+el+++ ++++e   + ++l ++ e++ +e +r ++++ +++e+    ++l   
  gi|344210119|ref|YP_004786295.1| 339 TLQSMRDHLQETVTEIDDIDDELDELTDRRDEIAEtrtRARELTATIEEVDAEIERRQTTVVDLRERR---NNLSAR 412
                                       79999999999999999999999999998888865111456777777777777777777777766654...344444 PP

                             Sec34  78 trkLnspgsslvks 91 
                                        ++L++  +s  ++
  gi|344210119|ref|YP_004786295.1| 413 VEELEERVTS-LRT 425
                                       4555555555.555 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.75
                             Sec34  11 ecdelleqtdealeqLeele.ekfksv...sektsslheaceqlleeqkrleelae 62 
                                       + ++l ++++e++e +++l+ e+f++v   ++k ++l+ + ++l +e+++++e   
  gi|344210119|ref|YP_004786295.1| 405 RRNNLSARVEELEERVTSLRtEEFDEVlelHTKANELELELDRLESERDEVREEIA 460
                                       33444444444444444443123333311144445555555555555555444444 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.18
                             Sec34   4 qLeskeeecdelleqtdealeqLeeleekfksvsek.tsslheaceqlle 52 
                                        +es  ++ del +q +++ ++L +l+++ ++ +++ t +++e++++ll+
  gi|344210119|ref|YP_004786295.1| 461 DIESDIRRNDELAAQREDVVDELIDLRSRIDRLEAEaTDQFNEKMDDLLD 510
                                       577889999**********************998653889*****99985 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 ?    7.9   6.8     0.011         3      19     102 ..     128     212 ..     114     217 .. 0.69
   2 ?    3.1   3.8      0.33        91      11      89 ..     196     275 ..     192     291 .. 0.66
   3 ?    1.3  10.7       1.2   3.3e+02      14      88 ..     357     432 ..     333     466 .. 0.43
   4 ?    4.1   5.6      0.16        45       3      84 ..     423     500 ..     421     512 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.011
                             Mod_r  19 ealvktlpevkqlkeekeellaenesla...eknlslepeleelrselqekleelkelekefeekeqeldell.qkf 91 
                                        ++     ++++ +++kee+ ae  ++a   ++  +le +   lr+e++e++++l+++e++ +e   + ++   ++ 
  gi|344210119|ref|YP_004786295.1| 128 ASIH---RQIRAAEQRKEEIDAELDRIAslkRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQeNRD 201
                                       4444...45667777777776666555544155555588*************************9999998883444 PP

                             Mod_r  92 spdallarLqt 102
                                        ++++l+ Lq+
  gi|344210119|ref|YP_004786295.1| 202 ELETALDELQA 212
                                       45678888876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.33
                             Mod_r  11 lledeeklealvktl.pevkqlkeekeellaeneslaeknlsl.epeleelrselqekle.elkelekefeekeqel 84 
                                         e+ + le  +++l  +  +lk  + ++  e+es+a   l + + +l  +rs l e+ +  l++le+  +++ ++ 
  gi|344210119|ref|YP_004786295.1| 196 TQENRDELETALDELqATRSELKRVRNDIQSEQESIAA--LRDeRGSLAVERSGLPESPDeRLEALESDIDRLRERK 270
                                       55677778888877766677888888888888888876..3332446777777777777633777777666666666 PP

                             Mod_r  85 dellq 89 
                                        el++
  gi|344210119|ref|YP_004786295.1| 271 RELSE 275
                                       66653 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 1.2
                             Mod_r  14 deeklealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqel.dell 88 
                                        ++ l++l++  +e+ + +++  el a++e++  +   +++++ +lr++ ++    ++ele+++  + +e  de+l
  gi|344210119|ref|YP_004786295.1| 357 IDDELDELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSARVEELEERVTSLRTEEfDEVL 432
                                       2344444444444444444444444444444433333334444444444444444444444444444333223333 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.16
                             Mod_r   3 lSkeeLqelledeeklealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefee 79 
                                       l +ee  e+le + k ++l  +l++   l++e++e+++e+ ++ e+ + +++el  +r+++ ++l  l++  +++e+
  gi|344210119|ref|YP_004786295.1| 423 LRTEEFDEVLELHTKANELELELDR---LESERDEVREEIADI-ESDIRRNDELAAQREDVVDELIDLRSRIDRLEA 495
                                       5689999999999999999987766...777777776666666.667777777777777666666655554444444 PP

                             Mod_r  80 keqel 84 
                                         +++
  gi|344210119|ref|YP_004786295.1| 496 EATDQ 500
                                       43333 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 ?    6.3  11.9     0.023       6.3     154     258 ..     153     282 ..      84     293 .. 0.55
   2 ?    5.6   8.0     0.036       9.9     146     243 ..     337     449 ..     288     498 .. 0.52

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.023
                      Exonuc_VII_L 154 r.........rlekaikrlleekkqrleklasrlkspeellerkrqrldeleerlera..lkkqlkkkrerleelke 219
                                       +         r +  ++  ++e + +l++++ r+ + +  +++ +++ dele+ l++   ++++lk+ r+++++ +e
  gi|344210119|ref|YP_004786295.1| 153 SlkrdlpdleRQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQENRDELETALDELqaTRSELKRVRNDIQSEQE 229
                                       12222222222233334444566666666666664444433333333333333333310023334444444444444 PP

                      Exonuc_VII_L 220 rlkekleekk.....................erlkklkerlelleekkerleeleeklea 258
                                       ++       +                     erl++l++ +++l+e+k++l+e++++l++
  gi|344210119|ref|YP_004786295.1| 230 SI-------AalrdergslaversglpespdERLEALESDIDRLRERKRELSEYTTRLQN 282
                                       44.......022222334444444555555577777777777889999999988888876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.036
                      Exonuc_VII_L 146 eeqleelerrlekaikrll................eekkqrleklasrlkspeellerkrqrldeleerleralkkq 206
                                       e++l++++++l++ +++                   e ++r ++l+ ++++ ++ +er++  + +l+er ++ l+ +
  gi|344210119|ref|YP_004786295.1| 337 ESTLQSMRDHLQETVTEIDdiddeldeltdrrdeiAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNN-LSAR 412
                                       444444444444444321111111111111111113333333333333344444444444444444444444.3334 PP

                      Exonuc_VII_L 207 lkkkrerleelkerlkekleekkerlkklkerlelle 243
                                       +++ +er+++l+++  +++ e +++ ++l+ +l++le
  gi|344210119|ref|YP_004786295.1| 413 VEELEERVTSLRTEEFDEVLELHTKANELELELDRLE 449
                                       4444444444432221222222222233333333333 PP

>> TBK1_CCD1  TANK-binding kinase 1 coiled-coil domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   4.4     0.097        27      92     171 ..     144     221 ..     105     229 .. 0.80
   2 ?    3.0   1.3      0.23        64      77     127 ..     342     392 ..     320     404 .. 0.76
   3 ?    9.4   5.4    0.0025      0.68      52     129 ..     386     461 ..     375     484 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.097
                         TBK1_CCD1  92 epsEldeiselhkkllrlssslerieeslqeiknklipeellsdewvkdegsqsedRnveklkvlldkiteiykqfk 168
                                         +Eld i+ l+  l  l+ +++++ +++ e+ +kl   e   de  +d++ q+   n + l+ +ld++++    +k
  gi|344210119|ref|YP_004786295.1| 144 IDAELDRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDE--RDVDFQTTQENRDELETALDELQATRSELK 218
                                       3458888*****************************996655555..566666666666789999999998888888 PP

                         TBK1_CCD1 169 kdk 171
                                       + +
  gi|344210119|ref|YP_004786295.1| 219 RVR 221
                                       765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.23
                         TBK1_CCD1  77 ekaekllevlmqanlepsEldeiselhkkllrlssslerieeslqeiknkl 127
                                       ++ ++l e ++++     Elde ++ + ++ + ++   ++  +++e++  +
  gi|344210119|ref|YP_004786295.1| 342 SMRDHLQETVTEIDDIDDELDELTDRRDEIAETRTRARELTATIEEVDAEI 392
                                       467789999999999999999977777777777777777777777776655 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0025
                         TBK1_CCD1  52 kedvnkllhkktevelkceiceetlekaekllevlmqanlepsEldeiselhkkllrlssslerieeslqeiknkli 128
                                        e   ++ +++t v+   e  ++ + ++e+l+e ++   +e  E+de+ elh+k ++l+ +l+r+e++  e+ + + 
  gi|344210119|ref|YP_004786295.1| 386 EEVDAEIERRQTTVVDLRERRNNLSARVEELEERVTSLRTE--EFDEVLELHTKANELELELDRLESERDEVREEIA 460
                                       44445556677777766688899999999****99877665..6***************999999999999999886 PP

                         TBK1_CCD1 129 p 129
                                        
  gi|344210119|ref|YP_004786295.1| 461 D 461
                                       6 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4         1   2.8e+02      13      72 ..     211     270 ..     204     280 .. 0.76
   2 ?   10.2   0.5    0.0021      0.57      18      70 ..     346     397 ..     336     420 .. 0.81
   3 ?    5.7   0.4     0.051        14      18      79 ..     444     504 ..     434     507 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1
                              FlxA  13 sgsasqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqqqq 72 
                                       + + s++++ ++ i++ q+++  l ++    + e++   +   + +++l++ I +l + +
  gi|344210119|ref|YP_004786295.1| 211 QATRSELKRVRNDIQSEQESIAALRDERGSLAVERSGLPESPDERLEALESDIDRLRERK 270
                                       567789999999999999999999998666666777777777777777777777766555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0021
                              FlxA  18 qiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqq 70 
                                        +++   +i+++ ++L+el++       e ++++ ++ a I+ + a+I++ q 
  gi|344210119|ref|YP_004786295.1| 346 HLQETVTEIDDIDDELDELTDR-RDEIAETRTRARELTATIEEVDAEIERRQT 397
                                       4555556899999********9.44555579*******************996 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.051
                              FlxA  18 qiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqqqqaekaqek 79 
                                       ++ +L+ + +++ +++ ++ ++    ++e  +q++ +  ++ +l++ I +l+++++++ +ek
  gi|344210119|ref|YP_004786295.1| 444 ELDRLESERDEVREEIADIESD-IRRNDELAAQREDVVDELIDLRSRIDRLEAEATDQFNEK 504
                                       6678888999999999999999.77778899999999999999********99999987765 PP

>> DUF3153  Protein of unknown function (DUF3153)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.3    0.0011       0.3      12      76 ..     153     217 ..     142     269 .. 0.85
   2 ?   -0.7   1.4       3.2   8.7e+02      29     108 ..     407     487 ..     377     499 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0011
                           DUF3153  12 kleqelssasgeqlpwqeeleqrlaelggkveerdeeelrltipflngeeleellnrlvsrasea 76 
                                       +l+++l+   ++q++++ e+ ++  +l+ ++ + de ++ +++  +n +ele+ l +l+   se 
  gi|344210119|ref|YP_004786295.1| 153 SLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQENRDELETALDELQATRSEL 217
                                       689999999**************************************************998883 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.2
                           DUF3153  29 eeleqrlaelggkveerdeeel.rltipflngeeleellnrlvsraseaaglslpepelrlvernlllgveqql.sl 103
                                       ++l++r++el+  v++ + ee+ ++     + +ele  l rl s  +e+  +++ + e ++++++ l + ++++ + 
  gi|344210119|ref|YP_004786295.1| 407 NNLSARVEELEERVTSLRTEEFdEVLELHTKANELELELDRLESERDEV-REEIADIESDIRRNDELAAQREDVvDE 482
                                       4455555555555554444444322222334455555555555555555.566666678888888888777764255 PP

                           DUF3153 104 dlDLr 108
                                        +DLr
  gi|344210119|ref|YP_004786295.1| 483 LIDLR 487
                                       56776 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  23.8   0.00035     0.096     320     580 ..     126     374 ..     115     387 .. 0.82
   2 ?    5.9   7.3     0.011         3     495     582 ..     334     421 ..     327     429 .. 0.88
   3 ?   -3.2  21.0       6.1   1.7e+03     180     321 ..     377     508 ..     369     512 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00035
                              HOOK 320 dlndLrrqvklleernaeYlqktveleeelkkanalrsqlelykkqvqelhkklseeskkadklefelkkleeklea 396
                                       d++ + rq++ +e+r         e++ el + ++l+  l  + +q   l++   e   k +++e  + +    +++
  gi|344210119|ref|YP_004786295.1| 126 DVASIHRQIRAAEQRK-------EEIDAELDRIASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQT 195
                                       5666778887777655.......69999************************************************* PP

                              HOOK 397 lqkekerllaerdaLketneELkcaqlqqkelsqadalaskssssgenlaae..llpaevreklirLqhENKmLklk 471
                                        q +++ l +  d L+ t  ELk  +   ++  +++ +     ++  +la e   lp    e+l  L+++  +L+++
  gi|344210119|ref|YP_004786295.1| 196 TQENRDELETALDELQATRSELKRVRNDIQS--EQE-SIAALRDERGSLAVErsGLPESPDERLEALESDIDRLRER 269
                                       **********************995443333..223.3333333445565553389******************887 PP

                              HOOK 472 qegseeekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaed.ssllkkkleehleklk 547
                                       +++  +e  t+lq+       + + L  e+r  ++ i    + v +++ +l + gsk+   +  ++ k ++    l+
  gi|344210119|ref|YP_004786295.1| 270 KREL-SEYTTRLQNVVG---FNEELLSGEHREITDAIDAKPESVGDITDQLYK-GSKTTCwTCGSRVKPDRIESTLQ 341
                                       7766.777777888777...5667899*********************99987.77777646777778888999999 PP

                              HOOK 548 evqeelqkkkeqleelepklssnkqkieeleea 580
                                       ++ + lq+    +++++ +l++ + + +e+ e+
  gi|344210119|ref|YP_004786295.1| 342 SMRDHLQETVTEIDDIDDELDELTDRRDEIAET 374
                                       999999999999***999999999999988775 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.011
                              HOOK 495 neLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkleehleklkevqeelqkkkeqleelepklssnk 571
                                       +++e+  ++ +++++e  ++++++  +l+e   + ++ ++++ +  e+   ++ev++e+++++ ++ +l ++ ++ +
  gi|344210119|ref|YP_004786295.1| 334 DRIESTLQSMRDHLQETVTEIDDIDDELDELTDRRDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLS 410
                                       677888899999999999999999999999999999999999999999*****************999999999999 PP

                              HOOK 572 qkieeleeaLk 582
                                        ++eelee  +
  gi|344210119|ref|YP_004786295.1| 411 ARVEELEERVT 421
                                       *****999764 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 6.1
                              HOOK 180 ekdelaQrcheldkqlsllqeEknaLlaenkklqerlselengeesgtiqltskkylelqkqleqlqeelfrlEtar 256
                                          el+  ++e+d ++   q     L++  ++l++r++ele+   s  +       lel+++ ++l+ el rlE+ r
  gi|344210119|ref|YP_004786295.1| 377 RARELTATIEEVDAEIERRQTTVVDLRERRNNLSARVEELEERVTSLRT-EEFDEVLELHTKANELELELDRLESER 452
                                       4445555555555555555555555555555555555555533332222.133455777777788888888888888 PP

                              HOOK 257 ddyrlkceelekevlelqqrneeltslaeEaqaLkDEvDvLresadkvkkleatvetykkkledl 321
                                       d++r  ++++e ++     rn+el+++ e      DE+  Lr+  d+++  e + + +  k++dl
  gi|344210119|ref|YP_004786295.1| 453 DEVREEIADIESDIR----RNDELAAQRE---DVVDELIDLRSRIDRLEA-E-ATDQFNEKMDDL 508
                                       888877777777774....5555543332...223444444444444332.1.234555555555 PP

>> Baculo_p24  Baculovirus P24 capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.3    0.0084       2.3      77     170 ..     137     233 ..     125     241 .. 0.66
   2 ?    1.5   3.2      0.78   2.1e+02     106     174 ..     350     426 ..     328     512 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0084
                        Baculo_p24  77 ynlsdsahppeyyvlkqLvrDL..lvGaqseavdplkdiktqlctlqecleesnvlvnsttesssn.enieslreil 150
                                        ++ +++  +e+  + +L rDL  l  +q    d++++ +++l+++++ ++e +v  ++t+e+ ++ e+  +  +  
  gi|344210119|ref|YP_004786295.1| 137 AEQRKEEIDAELDRIASLKRDLpdLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQENRDElETALDELQAT 213
                                       55555555666666777777774445566679999***************999987776666665443333444455 PP

                        Baculo_p24 151 rseeasllsnlnsllesiks 170
                                       rse + +  +++s  esi  
  gi|344210119|ref|YP_004786295.1| 214 RSELKRVRNDIQSEQESIAA 233
                                       66667777777776666655 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.78
                        Baculo_p24 106 avdplkdiktqlctlqecleesnvlvn......sttesssn.....enieslreilrseeasllsnlnsllesiksl 171
                                       +v +++di ++l +l +  +e  ++ +      +t e   +     e  ++    lr+ +++l + +++l e + sl
  gi|344210119|ref|YP_004786295.1| 350 TVTEIDDIDDELDELTDRRDEIAETRTrareltATIE---EvdaeiERRQTTVVDLRERRNNLSARVEELEERVTSL 423
                                       5555566666555555544333322223333222222...1223355556666667888888888888888888887 PP

                        Baculo_p24 172 qad 174
                                        ++
  gi|344210119|ref|YP_004786295.1| 424 RTE 426
                                       654 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.6    0.0052       1.4     100     175 ..     151     232 ..     137     233 .. 0.87
   2 ?   -1.3   0.0         6   1.6e+03     105     163 ..     254     312 ..     250     320 .. 0.75
   3 ?    3.0   0.5       0.3        82     107     171 ..     340     410 ..     332     415 .. 0.58
   4 ?    2.4   0.1      0.46   1.3e+02     111     174 ..     403     466 ..     397     471 .. 0.52
   5 ?   -0.0   0.0       2.4   6.7e+02      99     127 ..     475     503 ..     470     513 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0052
                      Bacillus_HBL 100 kaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdv......deltsilagdsgvisqlqneiedl 170
                                        a+l+ +l +L+++  +   e++++  +L++ ++++++ + +F+t+       +++   l+++  +++ ++n+i++ 
  gi|344210119|ref|YP_004786295.1| 151 IASLKRDLPDLERQQATLRDEITETRDKLQRVEDRIDERDVDFQTTQenrdelETALDELQATRSELKRVRNDIQSE 227
                                       57899***************************************999788777888888999999999999999999 PP

                      Bacillus_HBL 171 qgkik 175
                                       q++i+
  gi|344210119|ref|YP_004786295.1| 228 QESIA 232
                                       99886 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 6
                      Bacillus_HBL 105 ellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisql 163
                                       e+le+L+++i    +  ++l++  ++l++ +  +++ ++ +  e+t  + ++   + ++
  gi|344210119|ref|YP_004786295.1| 254 ERLEALESDIDRLRERKRELSEYTTRLQNVVGFNEELLSGEHREITDAIDAKPESVGDI 312
                                       67888888888888888888888888888888888888877777777777766666555 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.3
                      Bacillus_HBL 107 lekLqeeiqqnqke...vkqlikeLkklklklakds...knFktdvdeltsilagdsgvisqlqneiedlq 171
                                       l+ +++++q+   e   +++ + eL++ ++++a+     ++++++++e+++ ++  + ++ +l+++ ++l 
  gi|344210119|ref|YP_004786295.1| 340 LQSMRDHLQETVTEiddIDDELDELTDRRDEIAETRtraRELTATIEEVDAEIERRQTTVVDLRERRNNLS 410
                                       55555555544444000455666666666666654311156777777778888888877777777766665 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.46
                      Bacillus_HBL 111 qeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqgki 174
                                       +e  ++ ++ v++l + +++l+++   ++ ++ t+++el+  l   + + +++++ei+d+++ i
  gi|344210119|ref|YP_004786295.1| 403 RERRNNLSARVEELEERVTSLRTEEFDEVLELHTKANELELELDRLESERDEVREEIADIESDI 466
                                       4444445555555555555555555555555555555555555555555555555555555554 PP

  == domain 5  score: -0.0 bits;  conditional E-value: 2.4
                      Bacillus_HBL  99 dkaellellekLqeeiqqnqkevkqlike 127
                                       +++++++ l +L++ i   ++e++++ +e
  gi|344210119|ref|YP_004786295.1| 475 QREDVVDELIDLRSRIDRLEAEATDQFNE 503
                                       68899999999999999999999888765 PP

>> AKNA  AT-hook-containing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2     0.023       6.4      11      67 ..     226     282 ..     218     286 .. 0.86
   2 ?    4.4   0.3      0.21        59      34      90 ..     424     480 ..     409     485 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.023
                              AKNA  11 leeeylkglrsetlaqklssskgqpgkfdps.releaeIyqlgqrleeLkdqtdqlkq 67 
                                        e+e + +lr+e        s g p+  d     le  I +l++r  eL++ t  l++
  gi|344210119|ref|YP_004786295.1| 226 SEQESIAALRDERGSLAVERS-GLPESPDERlEALESDIDRLRERKRELSEYTTRLQN 282
                                       79999****************.9988877752569******************99997 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.21
                              AKNA  34 qpgkfdpsreleaeIyqlgqrleeLkdqtdqlkqkveefskdiaqdspsplqdarlp 90 
                                         ++fd   el+++   l+  l+ L    d  ++++    +di+ +  +  q+++++
  gi|344210119|ref|YP_004786295.1| 424 RTEEFDEVLELHTKANELELELDRLESERDEVREEIADIESDIRRNDELAAQREDVV 480
                                       56789999999999999********************99999988877777776665 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.6       3.8     1e+03      78     106 ..     123     151 ..     101     158 .. 0.59
   2 ?   -0.0  19.6       4.1   1.1e+03      20     117 ..     163     284 ..     131     285 .. 0.76
   3 ?   10.1   6.2    0.0029       0.8      36     107 ..     340     417 ..     332     435 .. 0.69
   4 ?    1.1   4.9       1.8     5e+02      36     100 ..     448     494 ..     425     506 .. 0.48

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 3.8
                           DUF4200  78 keaeikklkaeietlkseiekleekleey 106
                                       +  +++ ++ +i + ++++e+ +++l++ 
  gi|344210119|ref|YP_004786295.1| 123 RPVDVASIHRQIRAAEQRKEEIDAELDRI 151
                                       44566667777777777777766666654 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 4.1
                           DUF4200  20 eeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlk... 93 
                                        + ++l +++++ +++l++ e ++ e+ + f+   +en ++ + al + +  r + k+  ++i+  +++i++l+   
  gi|344210119|ref|YP_004786295.1| 163 RQQATLRDEITETRDKLQRVEDRIDERDVDFQ-TTQENRDELETALDELQATRSELKRVRNDIQSEQESIAALRder 238
                                       44455666777777777777777777777775.46788888888888888888888888888888888888888888 PP

                           DUF4200  94 ......................seiekleekleeykkYeefLekvv 117
                                                             s+i++l e+ +e+++Y + L++vv
  gi|344210119|ref|YP_004786295.1| 239 gslaversglpespderlealeSDIDRLRERKRELSEYTTRLQNVV 284
                                       8888888888888888888888999999999999999999999997 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0029
                           DUF4200  36 lekkeqeleedllkfdkflkend......akraralkkaeeerklkkekeaeikklkaeietlkseiekleekleey 106
                                       l+  +  l+e++ + d    e d      ++ a+ + +a e +  ++e +aei++ ++ +++l+++++ l +++ee+
  gi|344210119|ref|YP_004786295.1| 340 LQSMRDHLQETVTEIDDIDDELDeltdrrDEIAETRTRARELTATIEEVDAEIERRQTTVVDLRERRNNLSARVEEL 416
                                       44444455555555554444444000000445556667777777889****************************98 PP

                           DUF4200 107 k 107
                                       +
  gi|344210119|ref|YP_004786295.1| 417 E 417
                                       7 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 1.8
                           DUF4200  36 lekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseiekle 100
                                       le ++ e +                  + +  +e+  ++++e +a+ ++  +e+ +l+s+i++le
  gi|344210119|ref|YP_004786295.1| 448 LESERDEVR------------------EEIADIESDIRRNDELAAQREDVVDELIDLRSRIDRLE 494
                                       222222222..................23333344444444444444455555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2037  (0.113615); expected 358.6 (0.02)
Passed bias filter:                      897  (0.0500307); expected 358.6 (0.02)
Passed Vit filter:                       232  (0.0129399); expected 17.9 (0.001)
Passed Fwd filter:                       158  (0.00881254); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              65  [number of targets reported over threshold]
# CPU time: 2.35u 0.38s 00:00:02.73 Elapsed: 00:00:00.67
# Mc/sec: 2891.23
//
Query:       gi|344210120|ref|YP_004786296.1|  [L=198]
Description: hypothetical protein HAH_5179 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   14.3   0.2      0.081   12.8   0.2    1.8  1  SCAB-ABD       Actin-binding domain of plant-specific actin-b
      0.054   13.4   0.0      0.098   12.6   0.0    1.4  1  zinc_ribbon_4  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> SCAB-ABD  Actin-binding domain of plant-specific actin-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2     9e-06     0.081       8      36 ..      25      53 ..      22      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9e-06
                          SCAB-ABD  8 EtadLvdqhkRLSVRDLasKFekglaAAa 36
                                      E a L   + R S RDLa +F++ l  Aa
  gi|344210120|ref|YP_004786296.1| 25 EHAWLGKNRERQSLRDLADRFNQALLVAA 53
                                      6677888999*************995554 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.1e-05     0.098       2      16 ..     174     188 ..     174     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                     zinc_ribbon_4   2 kitCpsCkakyeidd 16 
                                       +i+C+ C+++y i+d
  gi|344210120|ref|YP_004786296.1| 174 DIRCQDCGTRYGISD 188
                                       59***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1356.09
//
Query:       gi|344210121|ref|YP_004786297.1|  [L=205]
Description: hypothetical protein HAH_5180 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1559.91
//
Query:       gi|344210122|ref|YP_004786298.1|  [L=436]
Description: hypothetical protein HAH_5181 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   13.2   0.0       0.15   12.3   0.0    1.4  1  DUF2951   Protein of unknown function (DUF2951)
        0.1   12.7   0.1       0.52   10.4   0.0    2.2  2  DUF357    Protein of unknown function (DUF357)


Domain annotation for each model (and alignments):
>> DUF2951  Protein of unknown function (DUF2951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.7e-05      0.15      46      94 ..     328     377 ..     315     380 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.7e-05
                           DUF2951  46 ktleelrkekeideknkkkndknirdikmwvlglvgtil.sslviallkt 94 
                                       ++l+ ++  +e de  +  ++k +rdi+    g + + l s+   al +t
  gi|344210122|ref|YP_004786298.1| 328 RALDRIQSRREADELARPSDAKTVRDIRQTAYGALTAALeSTSRSALART 377
                                       799*************************9999977766613444555555 PP

>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   5.7e-05      0.52      10      45 ..     204     241 ..     196     244 .. 0.86
   2 ?   -2.3   0.0      0.56     5e+03       6      31 ..     362     387 ..     360     389 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.7e-05
                                       HHHHH.....TS---HHH..HHHHHHHHHHHHHHHHHH CS
                            DUF357  10 lekvkiapdeesplgeaa..eevlemaesYleDakyfl 45 
                                        +++++ p ees+l  +a   e+ e a++Yl Da++ +
  gi|344210122|ref|YP_004786298.1| 204 ASDMDVLPREESELLSVAewGETAESAQAYLDDARHLR 241
                                       466789999999999999888**************987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.56
                                       HHHHHHHHH.....TS---HHHHHHH CS
                            DUF357   6 leealekvkiapdeesplgeaaeevl 31 
                                       l+ ale+ + ++  ++ l +a+++v+
  gi|344210122|ref|YP_004786298.1| 362 LTAALESTSRSALARTVLVDAGHKVM 387
                                       66788888888888888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2887.87
//
Query:       gi|344210123|ref|YP_004786299.1|  [L=882]
Description: sacrosine dehydrogenase/glycine cleavage T protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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-62  211.6   0.1      2e-62  210.9   0.1    1.4  1  GCV_T          Aminomethyltransferase folate-binding domain
    2.2e-43  149.2   0.1    2.2e-43  149.2   0.1    2.2  3  DAO            FAD dependent oxidoreductase
    6.8e-19   67.9   0.2    2.1e-18   66.4   0.2    1.9  1  FAO_M          FAD dependent oxidoreductase central domain
    1.3e-10   41.1   0.0    3.1e-10   39.8   0.0    1.7  1  GCV_T_C        Glycine cleavage T-protein C-terminal barrel d
    6.7e-06   25.5   0.0      0.024   13.9   0.0    2.4  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      2e-05   24.0   0.0     0.0086   15.4   0.0    2.5  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    0.00014   22.0   0.0    0.00025   21.2   0.0    1.4  1  SoxG           Sarcosine oxidase, gamma subunit family
    0.00047   20.2   0.9       0.94    9.5   0.1    3.2  3  NAD_binding_9  FAD-NAD(P)-binding
    0.00086   19.5   0.0     0.0033   17.6   0.0    2.0  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0019   17.3   0.1     0.0032   16.6   0.1    1.3  1  FAD_binding_2  FAD binding domain
  ------ inclusion threshold ------
      0.016   13.9   0.0      0.034   12.9   0.0    1.5  2  HI0933_like    HI0933-like protein
       0.17   11.2   0.1       0.51    9.6   0.0    1.7  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal 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 !  210.9   0.1   1.3e-65     2e-62       2     256 ..     473     754 ..     472     755 .. 0.94

  Alignments for each domain:
  == domain 1  score: 210.9 bits;  conditional E-value: 1.3e-65
                             GCV_T   2 ydrhkalgakfvefagwemPvqYa...........................sesikaehlavreaaglfDvShmgki 51 
                                       y+ +  l a+f+e agwe+P++Y+                           s +i aehl++re+++++    ++ +
  gi|344210123|ref|YP_004786299.1| 473 YEKQADLDAEFFEAAGWERPQWYEsnsdlldryedelaefrrpnewdsrwwSPNILAEHLHTREHVSMIGDMGFSIF 549
                                       7788999************************************************************876666**** PP

                             GCV_T  52 evsGpdaaalLqrlltndisklkpgkatytlllnedGgvidDlivarldedefllvvnaankekdlawlekaaekkd 128
                                       +++G d++++L+r+ + +i+ +++gk  yt +l e+Gg+++Dl++arl+ +++++v+ +a+   d +w+   + ++d
  gi|344210123|ref|YP_004786299.1| 550 DFRGSDVVDYLERMAVGRID-VDVGKTVYTPILAENGGFVSDLTIARLGPKHYRVVTGGAAGGSDRSWFGG-HIPDD 624
                                       ********************.889***********************************************.777** PP

                             GCV_T 129 ldvevedvteelallalqGPkarevlskllgadlselkffsfaevela.ggkkvlvsRtgytGedGfeiyipaeeae 204
                                        dv++ d++e+l++l ++GP+ar++++ +++ d+s   f +++  e++ g+++++++R++y Ge+G+eiy p  +++
  gi|344210123|ref|YP_004786299.1| 625 ADVTMIDRSESLCTLGVWGPNARDMVEGVTEEDMSHDAFEPYTAQEITvGEVDAWAMRLSYIGEQGWEIYAPMGQGR 701
                                       ******************************999888455555555555779************************** PP

                             GCV_T 205 elweaLleagkeegvkpaGlgArdtl.RlEaglrlyghdldeettPleaglgw 256
                                       +lw+ L+eag++++v+paG+g + t  RlE+g+rl+gh+l+ e++P eagl +
  gi|344210123|ref|YP_004786299.1| 702 RLWDVLWEAGQDHNVRPAGMGVYGTTgRLEKGYRLFGHELELEYNPAEAGLTF 754
                                       ***********************7654***********************986 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.2   0.1   1.5e-46   2.2e-43       3     352 .]      51     412 ..      49     412 .. 0.84
   2 ?   -3.1   0.3       2.9   4.3e+03      79     118 ..     487     525 ..     456     535 .. 0.60
   3 ?   -1.0   0.0       0.7     1e+03      61     105 ..     697     736 ..     674     776 .. 0.75

  Alignments for each domain:
  == domain 1  score: 149.2 bits;  conditional E-value: 1.5e-46
                                       EEECTSHHHHHHHHHHHHTT...EEEEESSSSTTS.SGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHH CS
                               DAO   3 viiGGGiiGlstAyeLarrg...Vtllekgdiags.gaSgrnsgllhsglrylpeaselarlslealeelreleeel 75 
                                       v iGGGi+G s Ay+Lar g   + +l+kg+++   g++g++s +l++ +++ +   e+  l+++++e +++++   
  gi|344210123|ref|YP_004786299.1|  51 VLIGGGIVGNSLAYHLARMGredISILDKGPFPDPgGSTGHASNFLMP-VEHSK---EMTHLTRRSIEQYKDMDT-- 121
                                       77**************999999********776644************.54455...677999999999999984.. PP

                                       SSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT..STTTS.EEEEETTEEEEEHHHHH CS
                               DAO  76 gididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa..lpgll.galfypdtgqvdpaklt 149
                                            + ++G + +a++e+  e+l++++++++++g +aell++eev++l p   + +l+ ++++++++g++dp ++ 
  gi|344210123|ref|YP_004786299.1| 122 -----FTNSGGIEVARTEARVEELKRRIQSAKAWGEPAELLTPEEVEALVPYvnT-DLVkAGFYSTGAGTCDPLRAG 192
                                       .....889********9999***********99******************9733.666377888889*****9987 PP

                                       HHHHHHHHHT...T-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTT.CTTTSEEEEE CS
                               DAO 150 aalaraaeal...Gveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gll.keldlpispv 220
                                         ++++a +    G ++  +tev +l  edg ++ v  +t+ g++ +ad vV+aaG+ws +l +++  e+  p++p+
  gi|344210123|ref|YP_004786299.1| 193 EVMRARADEYtdgGLHVSPNTEVLDLHVEDGSIAAV--ETDrGTV-TADEVVIAAGLWSPKLaEMAgVEI--PLTPA 264
                                       777666644444399**********98899******..8888987.5599**********6658887666..***** PP

                                       EEEEEEEEECCT.HSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSE...............EETTCSSTSCS CS
                               DAO 221 rgqvlvlkplse.klvspaailpvpetdddgrgvyvtprkdgrvlvGgtad...............eesgdddpevd 281
                                        +q++ + p+s  +  + +  +pv   +d ++ +y ++   + + vG+  +                + ++++p+ +
  gi|344210123|ref|YP_004786299.1| 265 VHQMVSVGPISFfEDYEGEISFPV--VRDMDTQMYERQHG-NDLEVGSYQHrpilwdvedipsideAPLSPTQPPLT 338
                                       **********99444444455555..55667777888876.45*****999*******9999987744445557999 PP

                                       HHHHHHHHHHHHHHSGGG.CG....EEEEEEEEEE.ETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHHH CS
                               DAO 282 eedidellealrklfPql.gd....vlrkwaGlrp.lpdglpligetpgvkglylatGhsghGltlapatGkllael 352
                                       ++++++ +  + +++P+l +d    ++++  Gl+  +pdg pl+g+   v+gl+ ++ +    ++ apa+G+++a++
  gi|344210123|ref|YP_004786299.1| 339 DDAFEQSMADALEIVPELlDDpeagIRHEIDGLLSqTPDGAPLLGPLQDVDGLWSCAAI---WIKEAPAIGEAVAQW 412
                                       9****************64224455889999****67*********77899********...*************86 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.9
                                       TSEEEEEEEEEESSHHHHHHHHHHHHHH.HHTTTTEEEEEH CS
                               DAO  79 idyrrtGllslaadeeelealdkllall.leagldaellda 118
                                        +++r+  +   +  + l++ +++la+  +++  d++++++
  gi|344210123|ref|YP_004786299.1| 487 AGWERPQWYESNS--DLLDRYEDELAEFrRPNEWDSRWWSP 525
                                       4455555555533..24555555555554455556667666 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.7
                                       HHHHHHHHHHHHHHHSSTTSEEEEEEEEEESSHHHHHHHHHHHHH CS
                               DAO  61 slealeelreleeelgididyrrtGllslaadeeelealdkllal 105
                                       + +++++++ l e  g d  +r+ G+ +++++     +l+k ++l
  gi|344210123|ref|YP_004786299.1| 697 MGQGRRLWDVLWEA-GQDHNVRPAGMGVYGTTG----RLEKGYRL 736
                                       45799*******98.9999*******9999754....44444433 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 !   66.4   0.2   1.4e-21   2.1e-18       2      56 .]     416     470 ..     415     470 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 1.4e-21
                             FAO_M   2 GepsiDlwevDirRFgdlhnnreylrervaesygkvYsipyPreelesgRnlrtS 56 
                                       G ++iDl++ D++RF ++ n+r ++++r+ e ++k Y+i++P e+++s+R lrtS
  gi|344210123|ref|YP_004786299.1| 416 GWSDIDLHGADVNRFYEYGNSRSFVKDRASEGFQKIYDIVHPAEQYQSARELRTS 470
                                       889***************************************************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 !   39.8   0.0   2.1e-13   3.1e-10      11      73 ..     801     864 ..     780     874 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 2.1e-13
                           GCV_T_C  11 gapll.rggepilrdgevvGhvTSgaysptlgksialAyvkaelaklgtevevevrgkrvpaev 73 
                                       ++p+l + g+ +++d+ +  +vTS++ +p++gk + +Ay+++ +a+ g +++ve +g+++p++v
  gi|344210123|ref|YP_004786299.1| 801 NEPVLdENGDVLVDDEGRRSYVTSAGTGPSVGKHLLMAYLPQSHAEEGRSLQVEYMGQQYPVTV 864
                                       3345544444445555667*****************************************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 !   13.9   0.0   1.6e-05     0.024     125     176 ..      28      82 ..       8     147 .. 0.77
   2 !    9.1   0.0   0.00046      0.69      61     251 ..     200     258 ..     163     272 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                                       ECCSECHHHHHHCCSS-T..SEEEEES-SHHHHHHHHHHHHHT-E.EEEEESSSS CS
                                       xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                       Pyr_redox_2 125 klvrtldsaealklkllp..krivvvGgGyiGvElAaalaklgke.vtlveardr 176
                                        +vr  +   a++++ lp  +++v +GgG +G  lA +la++g e + +++ ++ 
  gi|344210123|ref|YP_004786299.1|  28 SSVRQHTGETAMSSNSLPsaAKTVLIGGGIVGNSLAYHLARMGREdISILDKGPF 82 
                                       45566666777777777799999********************998999998775 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00046
                                       HCHHHH.CCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.TCTTC.TTBEECCSECHHHHH CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  61 kklnqg.ielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdl.gipGvaenvgklvrtldsaea 135
                                       ++++ g +++  ++ev+++  + + +      e d  ++++d++v+A G ++ +l  + Gv                
  gi|344210123|ref|YP_004786299.1| 200 DEYTDGgLHVSPNTEVLDLHVEDGSIAAV---ETDRGTVTADEVVIAAGLWSPKLaEMAGV---------------- 257
                                       34444445555555555555555555552...23334566666666666433333355555................ PP

                                       HCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 136 lklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgn 212
                                                                                                                    
  gi|344210123|ref|YP_004786299.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       TEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 213 geklevvledgeeidadlvvvavGvrpstelleeklgle 251
                                                                             e
  gi|344210123|ref|YP_004786299.1| 258 --------------------------------------E 258
                                       ......................................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 !    5.9   0.0    0.0043       6.5       1      30 [.      51      80 ..      51      86 .. 0.94
   2 !   15.4   0.0   5.8e-06    0.0086      95     147 ..     206     258 ..     188     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0043
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                      + iG+G  G + a++l ++g ed+ il+kg
  gi|344210123|ref|YP_004786299.1| 51 VLIGGGIVGNSLAYHLARMGREDISILDKG 80
                                      57***************************9 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 5.8e-06
                       Pyr_redox_3  95 elpiklfeeVesvkkedeg.fevetsketyeAkkviiAtGefdkPnklnipGee 147
                                        l++  ++eV +++ ed++   vet+++t++A++v+iA+G +  P++ ++ G e
  gi|344210123|ref|YP_004786299.1| 206 GLHVSPNTEVLDLHVEDGSiAAVETDRGTVTADEVVIAAGLW-SPKLAEMAGVE 258
                                       6999**********97655399******************95.68888888876 PP

>> SoxG  Sarcosine oxidase, gamma subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.7e-07   0.00025      30     146 ..     589     712 ..     570     713 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.7e-07
                              SoxG  30 skesvlwlaPdeflvid.qegkaa.laalaealaela..svvdlShgrvlisisGakaeavlakltaiDlsadaFpv 102
                                       s+ ++  l+P ++ v+  + ++++    +   + + a  ++ d S     + + G++a+ ++  +t  D+s daF  
  gi|344210123|ref|YP_004786299.1| 589 SDLTIARLGPKHYRVVTgGAAGGSdRSWFGGHIPDDAdvTMIDRSESLCTLGVWGPNARDMVEGVTEEDMSHDAFEP 665
                                       4448999********997444444155555556554447999*********************************99 PP

                              SoxG 103 Gaaaatilgkvev...vilrtgsdafevlvfrsFaeslwkaLldasa 146
                                         a++  +g+v +    +  +g+  +e++      + lw+ L +a +
  gi|344210123|ref|YP_004786299.1| 666 YTAQEITVGEVDAwamRLSYIGEQGWEIYAPMGQGRRLWDVLWEAGQ 712
                                       999988888776511156689********************999865 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 !    6.8   0.0    0.0042       6.3       1      72 [.      51     122 ..      51     148 .. 0.73
   2 !    9.5   0.1   0.00063      0.94     121     154 ..     212     245 ..     192     246 .. 0.85
   3 ?    0.1   0.0      0.48   7.1e+02      24      66 ..     623     665 ..     619     692 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0042
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvwrtdqseelllNv.pasemslftddp....ptfae 71 
                                       +++G+G+ G +++ +L++      + +i + d+ ++  +g+    +  +++l+ v +++em+++t ++    +++++
  gi|344210123|ref|YP_004786299.1|  51 VLIGGGIVGNSLAYHLARM----GREDISILDKGPFpDPGGSTGHA--SNFLMPVeHSKEMTHLTRRSieqyKDMDT 121
                                       68****************9....59999999998886666654444..45566552577888888877766655555 PP

                     NAD_binding_9  72 W 72 
                                       +
  gi|344210123|ref|YP_004786299.1| 122 F 122
                                       4 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00063
                     NAD_binding_9 121 raevvdleeradgqavlladgaslaadaVvLAlG 154
                                       ++ev+dl+ ++++ a +++d  +++ad+Vv+A G
  gi|344210123|ref|YP_004786299.1| 212 NTEVLDLHVEDGSIAAVETDRGTVTADEVVIAAG 245
                                       789*****************************98 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.48
                     NAD_binding_9  24 spleitlfdpsep.gagrvwrtdqseelllNvpasemslftddp 66 
                                       ++ ++t++d+se+    +vw ++  + +   v+ ++ms+ + +p
  gi|344210123|ref|YP_004786299.1| 623 DDADVTMIDRSESlCTLGVWGPNA-RDMVEGVTEEDMSHDAFEP 665
                                       5789******6665889*****95.6677788888888777666 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 !   17.6   0.0   2.2e-06    0.0033       2      34 ..      53      88 ..      52     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.2e-06
                                      E--SHHHHHHHHHHHCCTE.EEEEE-SS..SSSSGG CS
                     NAD_binding_8  2 vGaGlsGlvaAylLakagf.dvlllekr..drlGGr 34
                                      +G+G+ G ++Ay+La+ g+ d+ +l+k+  +++GG 
  gi|344210123|ref|YP_004786299.1| 53 IGGGIVGNSLAYHLARMGReDISILDKGpfPDPGGS 88
                                      9****************8868******955568875 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.2e-06    0.0032       3     209 ..      51     253 ..      49     271 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.2e-06
                                       EEE--SHHHHHHHHHHHHTTT.-EEEEESSS...GGGSGGGG--S-EE-TT..SSGGSTC.CHHHH.HHHHHHHHTT CS
                     FAD_binding_2   3 iViGsGlAGLaAAleaaeaGl.kvavvekeq...efggatawsqGgidavlspeqkkagikdspel.hrtdtlkald 74 
                                       + iG+G+ G + A+ +a+ G+ ++ +++k++   + g++ ++s   + +  s+e+  +   +s+e+   +dt+++++
  gi|344210123|ref|YP_004786299.1|  51 VLIGGGIVGNSLAYHLARMGReDISILDKGPfpdPGGSTGHASNFLMPVEHSKEMTHLTR-RSIEQyKDMDTFTNSG 126
                                       77****************************833234557777787888888888877755.5444315567777776 PP

                                       T-S-HHHHHHHHHTHHHHHHHHHHTT----B.CCTS.....SB-EEE-TT-SSTEEEE-.STT-......HHHHHHH CS
                     FAD_binding_2  75 eladqplveafveaapeavdeLeelgvpfsr.tedg.....pvdvrelGglsatartlhdaadarretlvtghalla 145
                                       +  + ++ ea ve+ ++ ++  +++g p    t+++     p+  ++l +      t++++ d+         +++ 
  gi|344210123|ref|YP_004786299.1| 127 GI-EVARTEARVEELKRRIQSAKAWGEPAELlTPEEvealvPYVNTDLVKAGFY-STGAGTCDP-----LRAGEVMR 196
                                       44.999*******************99998853333668887777777666666.788889998.....56677777 PP

                                       HHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..... CS
                     FAD_binding_2 146 rlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallke 209
                                       + ++++ + g+++ ++te+++L vedg +  ++       ++  ++a+ vv+a+g ++  +l e
  gi|344210123|ref|YP_004786299.1| 197 ARADEYTDGGLHVSPNTEVLDLHVEDGSIAAVETD----RGT--VTADEVVIAAGLWSP-KLAE 253
                                       7777887999*****************99886544....554..5699******99984.4444 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       2.9   4.4e+03       3      32 ..      50      80 ..      49      81 .. 0.79
   2 ?   12.9   0.0   2.2e-05     0.034     103     164 ..     186     246 ..     125     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.9
                                      EEEE--SHHHHHHHHHHHHTT-.-EEEE-SS CS
                       HI0933_like  3 viviGgGaAGlmaAisaakrgk.rVllleka 32
                                      ++ iGgG  G   A ++a+ g+ ++ +l+k+
  gi|344210123|ref|YP_004786299.1| 50 TVLIGGGIVGNSLAYHLARMGReDISILDKG 80
                                      789*******999999987776257888875 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.2e-05
                                       ETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 103 pvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       ++  +a ++++a   e ++ g ++  +tev +++ e++++  v+t ++++++ad++v+A G 
  gi|344210123|ref|YP_004786299.1| 186 CDPLRAGEVMRARADEYTDGGLHVSPNTEVLDLHVEDGSIAAVET-DRGTVTADEVVIAAGL 246
                                       67778999*************************************.9************884 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 ?    9.6   0.0   0.00034      0.51      12      59 ..      32      79 ..      26      82 .. 0.72
   2 ?   -2.1   0.1       1.3     2e+03     124     152 ..     215     245 ..     209     256 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00034
                                      GCTSEEETTCEETCB---EEEEESTSHHHHHHHHHHHHTT-.EEEEEES CS
                       AlaDh_PNT_C 12 ffggkgtlaGgvpgvepakvlviGgGvaGlqAiatakglga.kVtvlDv 59
                                      +++g++ + +     ++ak++ iGgG++G + +   +++g  ++ +lD+
  gi|344210123|ref|YP_004786299.1| 32 QHTGETAMSSNSL-PSAAKTVLIGGGIVGNSLAYHLARMGReDISILDK 79
                                      5555555444432.489*************9998888888525777775 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                                       EEETTGGGT..-SBTT--TBBTTSEEEEETT CS
                       AlaDh_PNT_C 124 ivDvAidqG..Gnvetsrltthgepvveekg 152
                                       + D+ ++ G    vet r t  +++vv   g
  gi|344210123|ref|YP_004786299.1| 215 VLDLHVEDGsiAAVETDRGTVTADEVVIAAG 245
                                       7899999995567888899988888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (882 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.44
# Mc/sec: 5969.25
//
Query:       gi|344210124|ref|YP_004786300.1|  [L=257]
Description: electron transfer flavoprotein subunit beta [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-32  110.7   2.2    1.1e-31  110.2   2.2    1.1  1  ETF       Electron transfer flavoprotein domain


Domain annotation for each model (and alignments):
>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.2   2.2   5.9e-36   1.1e-31       6     174 ..      28     204 ..      25     211 .. 0.93

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 5.9e-36
                                       -EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHHH CS
                               ETF   6 ehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeatakala 82 
                                       +++ + +++p+ + a+e+A ++++ ++g+ t++++G+  a+e+lr+ la m ad++ l++++   ++++  ta+ala
  gi|344210124|ref|YP_004786300.1|  28 TSHLGFTISPHEECAVEEAIQVADDHDGTATVMSLGSVDADEQLRTGLA-MTADEATLLETDGE-EWRPRETAAALA 102
                                       5667889******************99**********************.***********985.6*********** PP

                                       HHHHHC.....--SEEEEESSCCH...HHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSS CS
                               ETF  83 alikke.....dpdlvlagataig...kqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlp 151
                                       +++        ++dl l+g+++ +    qv+ r+A++L+vp+++ v++l++e+g+++++R++ g  g+ ev e+dlp
  gi|344210124|ref|YP_004786300.1| 103 DALSGDagtdpEFDLLLFGNESADvanHQVGVRVAERLDVPFVAGVSDLTIEDGTAVAERDVTG--GT-EVYELDLP 176
                                       ****99888777***********669**************************9***********..**.******** PP

                                       EEEEE-TTSS--.....--S-TT---EE CS
                               ETF 152 avltvrpgafep.....aaimaakkkev 174
                                       a + vr+g++ p     +a+m+a+k+ +
  gi|344210124|ref|YP_004786300.1| 177 AAVGVREGLNTPryasmRAKMQARKQSI 204
                                       *************999988999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.32s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1628.82
//
Query:       gi|344210125|ref|YP_004786301.1|  [L=322]
Description: electron transfer flavor protein alpha subunit-like protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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  113.2   1.0    4.3e-33  113.2   1.0    2.0  2  ETF_alpha  Electron transfer flavoprotein FAD-binding domain
    2.7e-27   95.8   2.4      3e-27   95.7   1.6    1.5  2  ETF        Electron transfer flavoprotein 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 ?   -1.2   0.1      0.24   2.1e+03      20      36 ..      19      35 ..      10      47 .. 0.83
   2 !  113.2   1.0   4.8e-37   4.3e-33       2      83 ..     199     280 ..     198     281 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.24
                                      GGHHHHHHHHHHHT-EE CS
                         ETF_alpha 20 enlelleelaealgaav 36
                                      e+l l++ela+a++aa+
  gi|344210125|ref|YP_004786301.1| 19 EALTLARELATATDAAL 35
                                      67789999999999875 PP

  == domain 2  score: 113.2 bits;  conditional E-value: 4.8e-37
                                       -TTT-S-EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE-HHHHTTTSS-CCCB-SSSS-----S-EEEES----HHHH CS
                         ETF_alpha   2 dLeeakvvvsgGrGlkskenlelleelaealgaavgasRavvdagwipeerqvGqtGktvaPklyiavGisGaiqhl 78 
                                       +L ea+vvv+gGrG++ +e+++ le la+ lg++vgasRa+v++gw p++ q+GqtG++++P+ly+a+GisGa+qh+
  gi|344210125|ref|YP_004786301.1| 199 SLGEARVVVGGGRGVGGPEDYDKLETLADSLGGTVGASRAAVNEGWRPHNDQIGQTGTKISPDLYVACGISGAVQHM 275
                                       799************************************************************************** PP

                                       GGGTT CS
                         ETF_alpha  79 aGmke 83 
                                       +G+k 
  gi|344210125|ref|YP_004786301.1| 276 VGCKG 280
                                       ***97 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   1.6   3.4e-31     3e-27       2     175 ..       3     172 ..       2     179 .. 0.93
   2 ?   -3.5   0.0       0.9   8.1e+03      50      67 ..     273     290 ..     266     297 .. 0.75

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 3.4e-31
                                       EEEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHH CS
                               ETF   2 lvlaehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeata 78 
                                       l l+eh+ +g+  + +leal+ Ar+l+ ++++ + av +G   +  al e l ++G++++++v d++l++y +ea+a
  gi|344210125|ref|YP_004786301.1|   3 LSLVEHA-GGSPEEPSLEALTLARELATATDAALEAVAFGA--ESAALGEKLGDYGVETLHHVGDERLDTYAPEAWA 76 
                                       7899**7.********************999**********..44459***************************** PP

                                       HHHHHHHHHC--SEEEEESSCCHHHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSSEEEE CS
                               ETF  79 kalaalikkedpdlvlagataigkqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlpavlt 155
                                       + +a+l+ + dpd v+a+ t  g++v++ ++a+ ++p+++++ ++e+  +   + R+  gg+ +++++  + ++++t
  gi|344210125|ref|YP_004786301.1|  77 ESIAQLLDATDPDAVVAPGTDRGQEVLAHVGARRDLPMAANCLDVEAG-DVYELSRQRWGGSLVEHTRLDSDTKLVT 152
                                       ***********************************************8.89*************999999******* PP

                                       E-TTSS----S-TT---EEE CS
                               ETF 156 vrpgafepaaimaakkkeve 175
                                        ++  f p+ + ++ + +v+
  gi|344210125|ref|YP_004786301.1| 153 AAEHEFSPETATETVESTVQ 172
                                       ********766666555555 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.9
                                       HHHHHHCT-SEEEEEE-G CS
                               ETF  50 realaamGadkvilvddp 67 
                                       ++ + ++Gad+++ ++++
  gi|344210125|ref|YP_004786301.1| 273 QHMVGCKGADNILAINTD 290
                                       555677899999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2373.81
//
Query:       gi|344210126|ref|YP_004786302.1|  [L=126]
Description: hypothetical protein HAH_5185 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   18.5   3.6     0.0017   18.1   3.6    1.2  1  Cupin_2   Cupin domain
  ------ inclusion threshold ------
      0.025   14.5   0.1      0.051   13.5   0.1    1.5  2  Cupin_7   ChrR Cupin-like 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 !   18.1   3.6   1.9e-07    0.0017       3      69 ..      42     107 ..      40     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.9e-07
                                       EEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEE CS
                           Cupin_2   3 velppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllv 69 
                                       v ++p  ++ +h+H+g+ e ++V    g + v+g ++++ +G +v + + t  ++ N+ +e  ++l 
  gi|344210126|ref|YP_004786302.1|  42 VIVEPDSVTTPHTHDGQ-EEVFVATTGGQIAVEGDVHDVPEGGVVRVHPDTVRNLCNHIEETHVWLA 107
                                       6799999999*******.66666666688999999********************999999888875 PP

>> Cupin_7  ChrR Cupin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.7e-06     0.051      23      51 ..      36      64 ..      19      96 .. 0.76
   2 ?   -1.4   0.0      0.26   2.3e+03      27      48 ..      83     104 ..      71     109 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-06
                                      -EEEEEEEE-TTEE---EE-TT-EEEEEE CS
                           Cupin_7 23 aratslvryapgsafsahkHpggeeilVL 51
                                      +  ++ v ++p+s+ ++h+H+g ee++V 
  gi|344210126|ref|YP_004786302.1| 36 EMRVNQVIVEPDSVTTPHTHDGQEEVFVA 64
                                      566788999******************95 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.26
                                       EEEEE-TTEE---EE-TT-EEE CS
                           Cupin_7  27 slvryapgsafsahkHpggeei 48 
                                        +vr++p+++ +  +H +  ++
  gi|344210126|ref|YP_004786302.1|  83 GVVRVHPDTVRNLCNHIEETHV 104
                                       5788888888777777665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 850.73
//
Query:       gi|344210127|ref|YP_004786303.1|  [L=197]
Description: formimidoyltetrahydrofolate cyclodeaminase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-42  144.6   7.2    3.5e-42  144.2   7.2    1.1  1  FTCD_C    Formiminotransferase-cyclodeaminase
  ------ inclusion threshold ------
       0.12   12.7   3.5        0.3   11.5   1.3    2.1  2  DUF3995   Protein of unknown function (DUF3995)
       0.23   12.0   5.1       0.14   12.7   0.7    2.2  2  MccV      Microcin V bacteriocin


Domain annotation for each model (and alignments):
>> FTCD_C  Formiminotransferase-cyclodeaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.2   7.2   5.9e-46   3.5e-42       2     181 ..       8     178 ..       7     179 .. 0.97

  Alignments for each domain:
  == domain 1  score: 144.2 bits;  conditional E-value: 5.9e-46
                                       HHHHHHHHHSSSSSS-HHHHHHHHHHHHHHHHHHHHHTTTT-TT-GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            FTCD_C   2 ieefleelaskspaPGGGsvaAlvgalgaaLgsmvanltlgkkkyedveeemeellekleelrkellelideDaeaF 78 
                                       i+efl+++as + +P GG+vaA+ ga+gaaL++mv+  t+g    e+ ++e++e+ + l + r++ll+l+deDa+  
  gi|344210127|ref|YP_004786303.1|   8 ISEFLDDVASGQVTPSGGAVAAVGGAMGAALCEMVCIHTVGTDGSEAAADELSEVGDTLADRRERLLALADEDAATV 84 
                                       78*************************************************************************** PP

                                       HHHHTTTT..........S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-GGGHHHHHHHHHHHHHHHHH CS
                            FTCD_C  79 nevmeayklpketeeekaareeaiqealkkavevPlelarkalellelleelaekgnknavSDagvaaklleaaveg 155
                                       ++v +a++  +         ++++q+a k+ +evPle+a+ +l+++e+++++ +kg + av Da+v+a+l+ aa+++
  gi|344210127|ref|YP_004786303.1|  85 DAVGAAIESGD---------DDRMQAASKRSTEVPLETAEVCLDVVEHARTVTAKGTPVAVPDAAVGALLAAAALQA 152
                                       *******9866.........569****************************************************** PP

                                       HHHHHHHHHTT---HHHHHHHHHHHH CS
                            FTCD_C 156 allnVkiNlksikDeefaeelkaeae 181
                                       ++ +V++Nl +i+De+f++++k++a+
  gi|344210127|ref|YP_004786303.1| 153 SVATVRANLDMIDDESFVAAMKQRAD 178
                                       ***********************987 PP

>> DUF3995  Protein of unknown function (DUF3995)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.074   4.4e+02      32      51 ..      18      37 ..       5      52 .. 0.75
   2 ?   11.5   1.3   4.9e-05       0.3      25      59 ..     119     156 ..     108     173 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.074
                           DUF3995 32 gsavPsavatlavallllaa 51
                                      g+ +Ps +a++av+++++aa
  gi|344210127|ref|YP_004786303.1| 18 GQVTPSGGAVAAVGGAMGAA 37
                                      44489999999999988776 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.9e-05
                           DUF3995  25 avvgekegsa...vPsavatlavallllaaAllvlala 59 
                                        vv+++++ +   +P+av  +av++ll+aaAl + + +
  gi|344210127|ref|YP_004786303.1| 119 DVVEHARTVTakgTPVAVPDAAVGALLAAAALQASVAT 156
                                       45555554445779*****************9877655 PP

>> MccV  Microcin V bacteriocin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   2.3e-05      0.14      22      80 ..      14      73 ..       9      91 .. 0.67
   2 ?    1.3   0.3     0.086   5.1e+02      24      61 ..     124     158 ..     104     188 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                              MccV 22 diakgigaaag...tfvaGaiGaivggivagavydvastktpdaalspsGlggtlkqkPegl 80
                                      d+a g  + +g   + v+Ga+Ga+++ +v+ +   v++  + +aa + s +g+tl  + e l
  gi|344210127|ref|YP_004786303.1| 14 DVASGQVTPSGgavAAVGGAMGAALCEMVCIH--TVGTDGSEAAADELSEVGDTLADRRERL 73
                                      566555554441114689***********955..5555555555666666677776666655 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.086
                              MccV  24 akgigaaagtfvaGaiGaivggivagavydvastktpd 61 
                                       a++++a+++  va  + a+vg++ a+a+ + as +t+ 
  gi|344210127|ref|YP_004786303.1| 124 ARTVTAKGTP-VA-VPDAAVGALLAAAALQ-ASVATVR 158
                                       4555444333.33.2344455544444433.2222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1528.32
//
Query:       gi|344210128|ref|YP_004786304.1|  [L=581]
Description: formyltetrahydrofolate synthetase [Haloarcula hispanica ATCC 33960]
Scores for 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-240  796.9   0.0     8e-240  796.7   0.0    1.0  1  FTHFS     Formate--tetrahydrofolate ligase


Domain annotation for each model (and alignments):
>> FTHFS  Formate--tetrahydrofolate ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  796.7   0.0  4.5e-244    8e-240       2     554 .]      19     581 .]      18     581 .] 0.98

  Alignments for each domain:
  == domain 1  score: 796.7 bits;  conditional E-value: 4.5e-244
                                       -HHHHHHCS----HHHHHHCTT--CCCEEEBSTTEEEE-CHHCCTCTTTS..-.-EEEEEEESS--TT--SHHHHHH CS
                             FTHFS   2 sdieiaqeaklkpieeiaeklglkeeelelyGkykakvslkvlerllkek..kkgklilvtaitPtplGeGKtttti 76 
                                       +d++iaq+++++pi e+ e  gl  ++l+ +G+y+akv+++++erl +++  k+ +l+lvt++tPtp GeGKt+tt+
  gi|344210128|ref|YP_004786304.1|  19 TDYDIAQSTEMEPIWELVEPWGLGLDDLQYFGEYTAKVKQHAIERLREQAedKEQNLVLVTGMTPTPKGEGKTVTTV 95 
                                       89*****************************************9775544115699********************* PP

                                       HHHHHHHHTT--EEEEE----SHHHHCST--SCEETTEEEESHHHHHTTTTSHHHHHHHHHHHHHHHHHHHHHTTTT CS
                             FTHFS  77 gLaqalnklgkkavaalRepslGPvfgiKGgAaGGGysqvvPmedinLhltGDihaitaannllaalidnrifhene 153
                                       gL q+ln++g++a++a+RepslGPvfg+KGgAaGGG sqv+PmedinLh+tGD+ha+t+a+nl+aa++d++i ++++
  gi|344210128|ref|YP_004786304.1|  96 GLGQTLNHVGEEAMIAIREPSLGPVFGVKGGAAGGGRSQVLPMEDINLHFTGDLHALTSAHNLIAAMLDAKISQGDD 172
                                       ***************************************************************************** PP

                                       T-EECCCE---EEESS--GGGSSEEES-SSTTS---EEE-EEEGGGSHHHHHHHH-SSHHHHHHHHHC-EEEEETTS CS
                             FTHFS 154 ldidpkkitwkrvlDvndraLRkivvglggkekgvpretgfditvasEimailaLakdledlkerlgrivvaytkdg 230
                                       l+id ++++w r++D+ndraLR+ vvglggk+ g+pre++f +t+asE+ma+l+La+dl dlker++ri+vay++dg
  gi|344210128|ref|YP_004786304.1| 173 LNIDINNVSWPRAIDMNDRALRETVVGLGGKTGGTPREDSFLLTAASELMAVLCLASDLGDLKERVSRIIVAYDEDG 249
                                       ***************************************************************************** PP

                                       -EEECCCCT-HHHHHHHTTTTTS-EEEEETT--EEEE-----SSSS--B--HHHHHHHHHH-SEEEEEBSSSTTTHH CS
                             FTHFS 231 epvtaedlkvagalavllkdaikPnlvqtlegtpalvHggPFAniahGcnsviatklalkladyvvtEaGFgadlga 307
                                       +pvt+ed++++g  ++ll+daikPn+vqt+egtpalvHggPFAniahG+ns++a+k+a+ + dy vtEaGFg+dlga
  gi|344210128|ref|YP_004786304.1| 250 DPVTVEDIEATGPATMLLRDAIKPNVVQTIEGTPALVHGGPFANIAHGTNSLVADKTAFGMGDYLVTEAGFGSDLGA 326
                                       ***************************************************************************** PP

                                       HHHHHTHHHHHT---SEEEEEEEHHHHHHHTT....--CCCTTS--HHHHHHHHHHHHHHHHHHCTTT--EEEEEE- CS
                             FTHFS 308 ekfldikcrasglkpdavvlvatvraLklhgg....vekeelkeenlealekGlanlekhienvkkfgvpvvvaink 380
                                       ekf+d+ cr+++++p+avvlva+vraLk+hg     v+ +e++e  +ea+e+G++nl+kh +n++kfgvpvvv++n+
  gi|344210128|ref|YP_004786304.1| 327 EKFMDVVCRKGDMTPNAVVLVASVRALKYHGLdqwpVDYDEIDEAGVEAVEAGFSNLDKHATNLQKFGVPVVVSVNR 403
                                       *******************************87777777************************************** PP

                                       -TT--HHHHHHHHHHH.HCTTSEEEEE-HHHHGGGGGHHHHHHHHHHCC...--.---SS-TTS-HHHHHHHHHHHT CS
                             FTHFS 381 fktDteaelelvkela.eakavevalsevwakGgeGalelaeavveale...ekefkflYdlelsieekietiakei 453
                                       f++Dt++e++++ +++ e+ +v++a s+v+++G+eG+++lae+v+ea+e   e++f++lYd+e+si+eki+t+a+ei
  gi|344210128|ref|YP_004786304.1| 404 FPDDTDEEIQAILDHCrEDLGVRAAESNVFSDGSEGGVDLAENVIEATEesnEEDFRMLYDDEDSIKEKIHTVATEI 480
                                       ****************9999*****************************653366********************** PP

                                       T--SEEEE-HHHHHHHHHHHHTTCTTS-EEEE--SSSSSSSTT--SS--S-EEEEEEEEEETTTTEEEEESST--SS CS
                             FTHFS 454 YgadgvelseeakkklkklekqgldklpvciaKtqySlsddpklkgapegftltvrevrlsaGagfivalageimtm 530
                                       Ygad+v+++  a ++++++++ ++d++pv+++Kt  Slsdd+++kgapeg++l+++ev  saGagf+val+++  tm
  gi|344210128|ref|YP_004786304.1| 481 YGADDVKYTGGALDDIEQMNELDFDDYPVVMSKTFHSLSDDASQKGAPEGWELEISEVYPSAGAGFLVALTADALTM 557
                                       ***************************************************************************** PP

                                       ----SS-GGGC-EE-TTSEEES-- CS
                             FTHFS 531 PGlpkkpaaekidvdeegkieGlf 554
                                       PGlp++paa ++d+de+g+i+Glf
  gi|344210128|ref|YP_004786304.1| 558 PGLPARPAAADMDIDEDGNISGLF 581
                                       ***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (581 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 4226.20
//
Query:       gi|344210129|ref|YP_004786305.1|  [L=799]
Description: dihydropteroate synthase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-81  272.9   0.8    4.3e-81  272.2   0.8    1.4  1  Pterin_bind   Pterin binding enzyme
    5.6e-12   46.0   0.0    1.3e-11   44.9   0.0    1.7  1  Mur_ligase_M  Mur ligase middle domain
    1.7e-06   28.2   0.0    5.5e-06   26.6   0.0    1.9  1  Mur_ligase_C  Mur ligase family, glutamate ligase domain
  ------ inclusion threshold ------
      0.021   14.5   0.3      0.073   12.7   0.3    1.9  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b


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 !  272.2   0.8   9.6e-85   4.3e-81       1     244 []     537     774 ..     537     774 .. 0.98

  Alignments for each domain:
  == domain 1  score: 272.2 bits;  conditional E-value: 9.6e-85
                                       EEEEETTTTTCHCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEE CS
                       Pterin_bind   1 mgilNvtpdsfsdggkfedldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpis 77 
                                       mgilNvtpdsf+dgg+++  d a+++a++m+e+GAdi+DiggestrPga++v +e+e++rvvpv+ea+++  ++++s
  gi|344210129|ref|YP_004786305.1| 537 MGILNVTPDSFYDGGEYNRRDLAVSHAEQMIESGADIVDIGGESTRPGADPVAVETEIDRVVPVIEAVSSL-NTTVS 612
                                       9*******************************************************************997.9**** PP

                                       EE-S-HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHHH CS
                       Pterin_bind  78 iDttkaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflearv 154
                                       +Dt ka va aAl+agadivNdvsg++ dp+m  +va+++a v++mh+ + p +  ++  +y+dvv++v + l++++
  gi|344210129|ref|YP_004786305.1| 613 VDTRKAAVADAALDAGADIVNDVSGLS-DPEMRFVVADHDASVILMHSLSAPVDPGRTV-TYDDVVDDVLRDLTEQI 687
                                       ***************************.*********************9999888887.***************** PP

                                       HHHHHTT--GGGEEEETTTTSSTTHHHHHHHHHTHHHHHHTTSSEBEEEGTTGHHHHHHHCTTCHGHHHHHHHHHHH CS
                       Pterin_bind 155 eaaeeaGvaperillDpgigfgkteehnlellrrldelrealevpvllGvSrksflgrllelgkaeeRdagtaafla 231
                                         ae+aG+++e+i++Dpg gfgk++ +++el++rl+e+ +al++pvl+G+Srks+  ++ ++g  ++R   t+a++a
  gi|344210129|ref|YP_004786305.1| 688 LLAEQAGIDREQIIVDPGCGFGKNAAESFELVDRLHEF-HALGCPVLVGHSRKSMFADMSDAG--ADRLPPTLATTA 761
                                       **************************************.*******************87545..7*********** PP

                                       HHHHTT-SEEEES CS
                       Pterin_bind 232 laaaaGadivrVh 244
                                       laa++Gad+vrVh
  gi|344210129|ref|YP_004786305.1| 762 LAAERGADAVRVH 774
                                       ************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 !   44.9   0.0   2.9e-15   1.3e-11       1     191 [.      44     266 ..      44     267 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 2.9e-15
                                       EESSS-HHHHHHHHHHHHHCT...EEEEETTC........................................SS-TH CS
                      Mur_ligase_M   1 vTGtnGKTTtteliaaileka...gkvigtvg........................................ttnne 34 
                                       ++G+nGK +t++++++++++a   ++++++ g                                         t  e
  gi|344210129|ref|YP_004786305.1|  44 IAGSNGKGSTAQMTESVIRAAgldVGLFTSPGlngfreqvtvnggripkervtefveqiepcidrlaaeddkPTHFE 120
                                       89*******************66666666666**************************************6644555 PP

                                       HHHHHHHHHHHHTT-SEEEEE--HCHHHC.TTTCCHCBESEEEE---TSTTHHHH.SSHHHHHHHHHHHHHTSETTC CS
                      Mur_ligase_M  35 iglpktlaemekkeaeyavlEvsshglge.krlegllkpdvavitnispdHldfh.gtlenyaeaKaelferlkeeg 109
                                       + + ++l++++ +++++avlEv+    g  +  ++ ++p + ++t+is +H d + +t+e++a+ Ka+   r     
  gi|344210129|ref|YP_004786305.1| 121 VLTALALYHFDVEDVDVAVLEVGIG--GRyDATSA-VDPVASAVTSISLEHTDLLgDTVEKIARDKAQVAPRDA--- 191
                                       5556677788889************..55334444.9****************98799*********9886444... PP

                                       EEEEETTSC...CHHHHHCTCCTCEEEEESSSTSECEEEEEEEEETTEEEEEEEEETTEEEEEEESSCSCHHHHHHH CS
                      Mur_ligase_M 110 iavinaddpyakelikklkkakvkvvtfglekeaedlraknieeksegteiellevkggeleieipllGkhnvyNal 186
                                        +v+           ++++    +++t+g e+ +   + +n  +++ +++i+l+  ++  le +++llG+h+++Na 
  gi|344210129|ref|YP_004786305.1| 192 PLVTGTTGA----ALDAIQGI-TDTITVGGEGAD-VTAVENGMRSAVENRISLT-GPDWALESNLKLLGQHQAENAG 261
                                       577775555....44444444.468999999976.3344466677788888676.57888****************9 PP

                                       HHHHH CS
                      Mur_ligase_M 187 aaiaa 191
                                       +a+ +
  gi|344210129|ref|YP_004786305.1| 262 VAATL 266
                                       99876 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 !   26.6   0.0   1.2e-09   5.5e-06       2      63 ..     288     340 ..     287     362 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.2e-09
                                       TTSSEEEEETTTEEEEEET--SHHHHHHHHHHHHHHSSSSEEEEEEEESTT.CCSCHCTHHH CS
                      Mur_ligase_C   2 kgRlevvgeadgvtvidDyahnpdslsaalkalreiapdkrlilvfgpggelgertrtfhde 63 
                                       +gR+e+ ++  +++v+ D  hnp++++ + ++++ + ++  l++vf ++++   ++++   +
  gi|344210129|ref|YP_004786305.1| 288 PGRFEIRST--DPMVVLDGSHNPGAMETLTTLIERY-EYDDLHVVFAAMQD---KEYE---R 340
                                       8*******9..9**************9888888555.889**********9...6655...2 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 ?   12.7   0.3   1.6e-05     0.073      63     147 ..     296     395 ..     285     399 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                                       TS-EEEEE-C.HHHHHHCHHHHHHHHHH.T--EEEEEEE--CCCHH.............S..TC--T-CCHHHCCCS CS
                      TPP_enzyme_N  63 gkpgvvlvts.gpGatnaltalaeAkvd.riPllvlsgdrptslrg.............qgvlqqeldqlalfrpvt 124
                                         p+vvl  s  pGa+ +lt l+e +    + +++ +++ ++++r              ++    + +  +l++ + 
  gi|344210129|ref|YP_004786305.1| 296 TDPMVVLDGShNPGAMETLTTLIERYEYdDLHVVFAAMQDKEYERMiatlpavetafaaRPEVDRAASTGSLAAAFE 372
                                       45777776666*************99653889999888888888889999999877666555554557777788888 PP

                                       SEEEE-SSGGGHHHHHHHHHHHH CS
                      TPP_enzyme_N 125 kyaervtspeelpealrrAirta 147
                                         a +v+++e++pea +rA++ta
  gi|344210129|ref|YP_004786305.1| 373 GQAAQVQQVESVPEATERAVATA 395
                                       88*******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (799 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 5820.14
//
Query:       gi|344210130|ref|YP_004786306.1|  [L=77]
Description: hypothetical protein HAH_5189 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   13.1   0.3        0.1   12.6   0.3    1.2  1  FixQ      Cbb3-type cytochrome oxidase component FixQ


Domain annotation for each model (and alignments):
>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   5.7e-06       0.1       8      32 ..      18      42 ..      13      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.7e-06
                              FixQ  8 gfadswgllflvllfygvviyafrp 32
                                      ++a  +g+++l+l+++g+ ++a+++
  gi|344210130|ref|YP_004786306.1| 18 QVAAVAGTVVLLLMLVGLGAFAYKS 42
                                      678899*****************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 498.08
//
Query:       gi|344210131|ref|YP_004786307.1|  [L=171]
Description: hypothetical protein HAH_5190 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0028   18.0   9.0     0.0034   17.7   0.7    2.9  3  Lar_restr_allev  Restriction alleviation protein Lar
     0.0034   17.3   5.0       0.34   10.9   0.2    2.4  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.011   15.9   0.4      0.011   15.9   0.4    2.2  2  zf-piccolo       Piccolo Zn-finger
      0.018   15.1   0.8      0.018   15.1   0.8    1.9  2  Zn_Tnp_IS91      Transposase zinc-binding domain
      0.039   14.0   7.6       0.33   11.0   3.1    2.7  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.05   13.6   7.6       0.59   10.2   4.6    2.2  2  zinc-ribbons_6   zinc-ribbons
       0.35   10.3   2.3       0.29   10.5   0.2    1.9  2  zf_Rg            Reverse gyrase zinc finger
       0.43   10.9  10.2        8.2    6.7   4.5    2.3  2  IBR              IBR domain, a half RING-finger domain
       0.45   11.3   4.8         28    5.6   4.8    2.4  2  zinc_ribbon_15   zinc-ribbon family
       0.48   10.5   9.1        4.1    7.5   1.8    2.4  2  DZR              Double zinc ribbon
       0.53    9.8   6.3        2.1    7.9   0.7    3.0  3  TF_Zn_Ribbon     TFIIB zinc-binding
       0.64   10.0   8.2         36    4.4   0.3    4.0  4  zinc_ribbon_4    zinc-ribbon domain
       0.77    9.9   4.3        2.8    8.1   0.1    2.8  3  TRAF6_Z2         TNF receptor-associated factor 6 zinc finger
        1.2    8.9   8.8        8.9    6.1   0.6    3.5  3  YacG             DNA gyrase inhibitor YacG
        4.1    7.1  10.4        7.2    6.3   0.1    3.9  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
        6.2    6.9  10.7        1.1    9.2   3.0    2.9  3  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
        6.5    6.7   9.3        9.4    6.2   0.0    3.2  3  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
          9    6.2   8.5        9.4    6.1   0.0    3.3  4  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger


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 ?    3.1   0.1      0.12   1.2e+02      28      36 ..      85      93 ..      51     105 .. 0.71
   2 ?    1.5   0.2      0.39   3.9e+02       5      14 ..     105     114 ..     101     120 .. 0.80
   3 !   17.7   0.7   3.4e-06    0.0034       5      39 ..     127     159 ..     125     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.12
                   Lar_restr_allev 28 cvyCadCga 36
                                      +v+C  C+ 
  gi|344210131|ref|YP_004786307.1| 85 TVECPRCES 93
                                      777777776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.39
                   Lar_restr_allev   5 pCPfCggrav 14 
                                       +CP C g+  
  gi|344210131|ref|YP_004786307.1| 105 DCPRCVGEYS 114
                                       7****99876 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 3.4e-06
                   Lar_restr_allev   5 pCPfCggravlersqrvvaeigqcvyCadCgastp 39 
                                        CP C +r ++++++  + +i ++ +C+dC +  +
  gi|344210131|ref|YP_004786307.1| 127 TCPVCRSRMEHGQRHPERFDIPEWATCTDCRY--H 159
                                       7******************************9..2 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 !   10.9   0.2   0.00034      0.34      29      59 ..      86     116 ..      82     124 .. 0.88
   2 !    7.9   0.8    0.0029       2.8      30      56 ..     127     160 ..     126     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                    OrfB_Zn_ribbon  29 ktCseCgsknkealsgrtfkCpnCgfeadrD 59 
                                        +C++C s+  + ++++   Cp+C  e+  D
  gi|344210131|ref|YP_004786307.1|  86 VECPRCESEIFQHNARDSIDCPRCVGEYSHD 116
                                       58**********9***********9998777 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0029
                    OrfB_Zn_ribbon  30 tCseCgsknke.......alsgrtfkCpnCgfea 56 
                                       tC++C s++++        + +++ +C++C +++
  gi|344210131|ref|YP_004786307.1| 127 TCPVCRSRMEHgqrhperFDIPEWATCTDCRYHW 160
                                       8*********996666554555666899999886 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.4       0.6     6e+02       3      14 ..      88      99 ..      79     112 .. 0.63
   2 ?   15.9   0.4   1.1e-05     0.011       2      27 ..     127     157 ..     126     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.6
                        zf-piccolo  3 CplCktelnvgs 14
                                      Cp C+ e+  ++
  gi|344210131|ref|YP_004786307.1| 88 CPRCESEIFQHN 99
                                      777776665553 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.1e-05
                        zf-piccolo   2 lCplCktelnvgskep.....pnyntCteCk 27 
                                       +Cp+C+ +++ g+++p     p++ tCt+C+
  gi|344210131|ref|YP_004786307.1| 127 TCPVCRSRMEHGQRHPerfdiPEWATCTDCR 157
                                       7*****999999977677999*********8 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.8   1.8e-05     0.018      38      83 ..      84     129 ..      75     135 .. 0.86
   2 ?   -1.8   0.1       3.3   3.3e+03      41      51 ..     152     162 ..     149     168 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                       Zn_Tnp_IS91  38 aryeCeeCghekivyfsCksrhCpsCqkkateewlekqqeellpvp 83 
                                       a++eC+ C++e + ++   s  Cp+C  +++++  +++q   l +p
  gi|344210131|ref|YP_004786307.1|  84 ATVECPRCESEIFQHNARDSIDCPRCVGEYSHDEFADLQLLYLTCP 129
                                       6789*****9999988888888*********999998888877777 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.3
                       Zn_Tnp_IS91  41 eCeeCghekiv 51 
                                        C++C+ +  +
  gi|344210131|ref|YP_004786307.1| 152 TCTDCRYHWEF 162
                                       58888766554 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   3.1   0.00033      0.33      66      95 ..      81     112 ..      59     149 .. 0.81
   2 ?    2.7   0.1      0.12   1.2e+02      68      84 ..     148     164 ..     143     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00033
                                       EE--EEEETTTS-EEECHH.H.HHS-TTTSSS CS
                              HypA  66 evpvkvrCreCgkefelee.k.alrCpkCgsa 95 
                                       + p++v+C +C++e+ +++ + ++ Cp+C ++
  gi|344210131|ref|YP_004786307.1|  81 RPPATVECPRCESEIFQHNaRdSIDCPRCVGE 112
                                       6789999****999875553458899999654 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.12
                                       --EEEETTTS-EEECHH CS
                              HypA  68 pvkvrCreCgkefelee 84 
                                       p  ++C++C++++e e+
  gi|344210131|ref|YP_004786307.1| 148 PEWATCTDCRYHWEFEH 164
                                       55689*******99664 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.6   0.00059      0.59       2      40 ..      87     136 ..      86     137 .. 0.76
   2 ?    7.4   0.8    0.0042       4.2       2      26 ..     127     160 ..     126     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00059
                                       --SSS-S--EE-S..SEEE-TTT--........EEEEE.EE-SSS-S--- CS
                    zinc-ribbons_6   2 kCpeCqqelekrg..eqyhCeaCqe........dlkke.alCpeCeqele 40 
                                       +Cp+C++e+ +++  +++ C  C          dl+    +Cp C++++e
  gi|344210131|ref|YP_004786307.1|  87 ECPRCESEIFQHNarDSIDCPRCVGeyshdefaDLQLLyLTCPVCRSRME 136
                                       7********96655689******986777766655544146999999887 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0042
                                       --SSS-S--EE-S.........SEEE-TTT--EE CS
                    zinc-ribbons_6   2 kCpeCqqelekrg.........eqyhCeaCqedl 26 
                                       +Cp C + +e+ +         e ++C  C+ + 
  gi|344210131|ref|YP_004786307.1| 127 TCPVCRSRMEHGQrhperfdipEWATCTDCRYHW 160
                                       7*********766689999999999999998765 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2    0.0003      0.29      10      43 ..      88     122 ..      85     127 .. 0.90
   2 ?   -1.3   0.1       1.5   1.5e+03       9      14 ..     127     132 ..     122     138 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0003
                             zf_Rg  10 CPNCgGdisdeRlekGLpCkrClPke.gdvckaLk 43 
                                       CP C+ +i +  +   + C rC+ +  +d + +L+
  gi|344210131|ref|YP_004786307.1|  88 CPRCESEIFQHNARDSIDCPRCVGEYsHDEFADLQ 122
                                       ***********************998899998886 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                             zf_Rg   9 lCPNCg 14 
                                        CP C 
  gi|344210131|ref|YP_004786307.1| 127 TCPVCR 132
                                       699996 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 ?    6.7   4.5    0.0082       8.2      16      47 ..      83     112 ..      78     135 .. 0.70
   2 ?    6.4   2.0      0.01        10      18      48 ..     125     160 ..     112     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0082
                               IBR  16 pnlkwCprpdCeaiieksegcksvtCskCgfe 47 
                                       p ++ Cp   Ce+ i + +  +s+ C++C  e
  gi|344210131|ref|YP_004786307.1|  83 PATVECP--RCESEIFQHNARDSIDCPRCVGE 112
                                       56899**..8*976655555566677777554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.01
                               IBR  18 lkwCprpdCeaiiekseg.cks......vtCskCgfef 48 
                                       +  Cp   C + +e+ +   ++      +tC++C++ +
  gi|344210131|ref|YP_004786307.1| 125 YLTCP--VCRSRMEHGQRhPERfdipewATCTDCRYHW 160
                                       56799..9999998888843337788889999999865 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.9       0.2     2e+02      65      85 ..      85     109 ..      55     110 .. 0.63
   2 ?    5.6   4.8     0.028        28      36      81 ..     124     166 ..      76     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.2
                    zinc_ribbon_15  65 kkeCknCgkeveeefky....CpkC 85 
                                       + eC++C++e+ ++++     Cp+C
  gi|344210131|ref|YP_004786307.1|  85 TVECPRCESEIFQHNARdsidCPRC 109
                                       5678888877754432222226666 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.028
                    zinc_ribbon_15  36 pylacskCkslleaskelgkeiekkessekkeCknCgkeveeefky 81 
                                        yl+c  C+s++e+ +   ++ e+ +  e  +C +C+ + e e +y
  gi|344210131|ref|YP_004786307.1| 124 LYLTCPVCRSRMEHGQ---RHPERFDIPEWATCTDCRYHWEFEHSY 166
                                       5899999999999998...444445566789999999988877666 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.8    0.0042       4.1      10      34 ..      83     109 ..      78     120 .. 0.61
   2 ?    5.6   9.2     0.017        16       1      44 [.      88     141 ..      88     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0042
                               DZR  10 pdarfCseCgtklkavaa..edrCpsC 34 
                                       p    C++C +++ + +a  ++ Cp+C
  gi|344210131|ref|YP_004786307.1|  83 PATVECPRCESEIFQHNArdSIDCPRC 109
                                       555556666666654444566666666 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.017
                               DZR   1 CpqCgee....lppdarfCseCgtklkavaa.........edrCpsCgekvdpearf 44 
                                       Cp+C++e    +  d++ C++C  + +   +           +Cp C + ++ ++r 
  gi|344210131|ref|YP_004786307.1|  88 CPRCESEifqhNARDSIDCPRCVGEYS---HdefadlqllYLTCPVCRSRMEHGQRH 141
                                       9***9998888999999*****99987...224689999999999999998887765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.7    0.0021       2.1       3      32 ..      88     117 ..      86     123 .. 0.77
   2 ?    3.5   0.1     0.051        51       2       9 ..     127     134 ..     126     141 .. 0.87
   3 ?   -0.4   0.0      0.83   8.3e+02      21      25 ..     152     156 ..     145     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0021
                                       ETTTTCEECHEETSTTCEEESSS.SBEEEEC CS
                      TF_Zn_Ribbon   3 CPnCgstnlveDpergelvCtdC.GlVledn 32 
                                       CP C s+ +   ++r  + C++C G+   d+
  gi|344210131|ref|YP_004786307.1|  88 CPRCESE-IFQHNARDSIDCPRCvGEYSHDE 117
                                       *****98.55556777779****99876665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.051
                                       EETTTTCE CS
                      TF_Zn_Ribbon   2 kCPnCgst 9  
                                       +CP+C s+
  gi|344210131|ref|YP_004786307.1| 127 TCPVCRSR 134
                                       7****987 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.83
                                       EESSS CS
                      TF_Zn_Ribbon  21 vCtdC 25 
                                       +CtdC
  gi|344210131|ref|YP_004786307.1| 152 TCTDC 156
                                       79999 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   0.3     0.037        36       3      10 ..      86      93 ..      84      95 .. 0.77
   2 ?    3.2   0.1     0.088        87       3      12 ..     104     113 ..     103     120 .. 0.81
   3 ?    1.6   0.1      0.26   2.6e+02       4       9 ..     127     132 ..     124     136 .. 0.60
   4 ?    2.9   0.1       0.1     1e+02      25      35 ..     150     160 ..     146     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.037
                     zinc_ribbon_4  3 itCpsCka 10
                                      ++Cp+C++
  gi|344210131|ref|YP_004786307.1| 86 VECPRCES 93
                                      68888875 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.088
                     zinc_ribbon_4   3 itCpsCkaky 12 
                                       i Cp+C  +y
  gi|344210131|ref|YP_004786307.1| 104 IDCPRCVGEY 113
                                       7899997666 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.26
                     zinc_ribbon_4   4 tCpsCk 9  
                                       tCp C 
  gi|344210131|ref|YP_004786307.1| 127 TCPVCR 132
                                       555554 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.1
                     zinc_ribbon_4  25 kvrCskCghvF 35 
                                       +++C+ C+  +
  gi|344210131|ref|YP_004786307.1| 150 WATCTDCRYHW 160
                                       579****9988 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 ?    8.1   0.1    0.0028       2.8       2      16 ..      84      99 ..      84     100 .. 0.72
   2 ?    2.3   0.0      0.18   1.8e+02       4      11 ..     104     111 ..     103     114 .. 0.81
   3 ?   -1.7   0.2       3.4   3.4e+03       6       9 ..     128     131 ..     126     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0028
                          TRAF6_Z2  2 alVeCPQCQr.aFQKn 16
                                      a VeCP C    FQ n
  gi|344210131|ref|YP_004786307.1| 84 ATVECPRCESeIFQHN 99
                                      68******74246665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.18
                          TRAF6_Z2   4 VeCPQCQr 11 
                                       ++CP C +
  gi|344210131|ref|YP_004786307.1| 104 IDCPRCVG 111
                                       68****66 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.4
                          TRAF6_Z2   6 CPQC 9  
                                       CP C
  gi|344210131|ref|YP_004786307.1| 128 CPVC 131
                                       9999 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.022        22       1      12 [.      86      97 ..      86     103 .. 0.79
   2 ?    1.7   0.0      0.22   2.2e+02       1      10 [.     104     113 ..     104     119 .. 0.76
   3 ?    6.1   0.6    0.0089       8.9       2      19 ..     127     144 ..     126     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.022
                              YacG  1 vkCPtCkkevew 12
                                      v+CP C++e+  
  gi|344210131|ref|YP_004786307.1| 86 VECPRCESEIFQ 97
                                      89****998755 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.22
                              YacG   1 vkCPtCkkev 10 
                                       ++CP C  e 
  gi|344210131|ref|YP_004786307.1| 104 IDCPRCVGEY 113
                                       58****8765 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0089
                              YacG   2 kCPtCkkevewseenpfr 19 
                                       +CP+C++++e  +++p r
  gi|344210131|ref|YP_004786307.1| 127 TCPVCRSRMEHGQRHPER 144
                                       7********999988765 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0072       7.2       2      12 ..      85      95 ..      84     101 .. 0.84
   2 ?    3.6   0.1     0.051        51       1      14 [.     102     115 ..     102     119 .. 0.71
   3 ?    1.8   0.1      0.18   1.8e+02       4      15 ..     127     138 ..     125     141 .. 0.81
   4 ?   -1.2   0.2       1.6   1.5e+03       4       9 ..     152     157 ..     149     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0072
                            zf_UBZ  2 tylCerCgkei 12
                                      t+ C+rC +ei
  gi|344210131|ref|YP_004786307.1| 85 TVECPRCESEI 95
                                      789****9998 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.051
                            zf_UBZ   1 dtylCerCgkeipe 14 
                                       d++ C+rC  e ++
  gi|344210131|ref|YP_004786307.1| 102 DSIDCPRCVGEYSH 115
                                       6789****665555 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.18
                            zf_UBZ   4 lCerCgkeipes 15 
                                       +C+ C +++++ 
  gi|344210131|ref|YP_004786307.1| 127 TCPVCRSRMEHG 138
                                       8*****999875 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 1.6
                            zf_UBZ   4 lCerCg 9  
                                       +C +C 
  gi|344210131|ref|YP_004786307.1| 152 TCTDCR 157
                                       8****5 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 ?    4.6   0.4     0.031        31      26      37 ..      81      92 ..      71      95 .. 0.78
   2 ?    9.2   3.0    0.0011       1.1      11      39 ..      86     112 ..      82     114 .. 0.81
   3 ?   -0.7   1.2       1.4   1.4e+03      32      37 ..     127     132 ..     120     158 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.031
                                      ......E-TTTT CS
                         Anti-TRAP 26 eprasleCPkCs 37
                                       p a++eCP+C+
  gi|344210131|ref|YP_004786307.1| 81 RPPATVECPRCE 92
                                      46789******7 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0011
                                       EE-TTTTTTSEETTE......E-TTTTTS CS
                         Anti-TRAP  11 tkCdaCngsGkiepeeprasleCPkCsGk 39 
                                       ++C+ C+   +i   + r s++CP+C G+
  gi|344210131|ref|YP_004786307.1|  86 VECPRCES--EIFQHNARDSIDCPRCVGE 112
                                       57999997..5666667*********995 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.4
                                       E-TTTT CS
                         Anti-TRAP  32 eCPkCs 37 
                                        CP C 
  gi|344210131|ref|YP_004786307.1| 127 TCPVCR 132
                                       455554 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 ?    2.1   2.5      0.18   1.8e+02      26      46 ..      88     112 ..      84     116 .. 0.73
   2 ?    6.2   0.0    0.0094       9.4      39      48 ..     127     136 ..     119     138 .. 0.83
   3 ?    0.7   0.1      0.49   4.9e+02      24      33 ..     151     160 ..     149     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.18
                                       -HHHHHHHHH....TT-B-TTT--B CS
                        zf-C3HC4_3  26 CeeCaekllk....rkkkCpiCrrp 46 
                                       C +C +++ +     +  Cp C  +
  gi|344210131|ref|YP_004786307.1|  88 CPRCESEIFQhnarDSIDCPRCVGE 112
                                       7788888877777777788888665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0094
                                       B-TTT--B-- CS
                        zf-C3HC4_3  39 kCpiCrrpie 48 
                                       +Cp+Cr+ +e
  gi|344210131|ref|YP_004786307.1| 127 TCPVCRSRME 136
                                       7999998765 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.49
                                       EE-HHHHHHH CS
                        zf-C3HC4_3  24 vlCeeCaekl 33 
                                       ++C +C  ++
  gi|344210131|ref|YP_004786307.1| 151 ATCTDCRYHW 160
                                       5899998887 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 ?    6.1   0.0    0.0094       9.4       2      14 ..      86      98 ..      85     102 .. 0.81
   2 ?    1.2   0.1      0.32   3.2e+02       2       9 ..     104     111 ..     103     113 .. 0.79
   3 ?    2.6   0.1      0.12   1.2e+02       3      11 ..     127     135 ..     126     142 .. 0.89
   4 ?   -3.5   0.1       9.4   9.3e+03       6      32 ..     155     158 ..     151     160 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0094
                                      EE-SSS--EEEEE CS
                    zf-C4_Topoisom  2 ekCPkCggdLvlk 14
                                      ++CP C +++ + 
  gi|344210131|ref|YP_004786307.1| 86 VECPRCESEIFQH 98
                                      69******99876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.32
                                       EE-SSS-- CS
                    zf-C4_Topoisom   2 ekCPkCgg 9  
                                       ++CP C g
  gi|344210131|ref|YP_004786307.1| 104 IDCPRCVG 111
                                       58****65 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.12
                                       E-SSS--EE CS
                    zf-C4_Topoisom   3 kCPkCggdL 11 
                                       +CP C++ +
  gi|344210131|ref|YP_004786307.1| 127 TCPVCRSRM 135
                                       7*****988 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 9.4
                                       SS--EEEEEE-SSSEEEEESST.T--- CS
                    zf-C4_Topoisom   6 kCggdLvlkrgkkGkFvGCsnYPeCkf 32 
                                                               C++
  gi|344210131|ref|YP_004786307.1| 155 D-----------------------CRY 158
                                       4.......................554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); 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):              18  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1086.32
//
Query:       gi|344210132|ref|YP_004786308.1|  [L=202]
Description: hypothetical protein HAH_5191 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   14.8  13.1       0.01   14.8  13.1    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 ?    2.8   8.1    0.0025        46     246     338 ..       7     110 ..       1     123 [. 0.72
   2 ?   14.8  13.1   5.6e-07      0.01     249     315 ..     118     184 ..     110     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.0025
                             MFS_1 246 aglllallalvgailallagrlsdrlgr..rrrlllallllllaalglallavt....ssavllll....vlvliGf 312
                                       +g+++ +++l++ ++ +++g+l+  +g    r+l   ++++l++++g ++l +     ++++ ++     + vl+G+
  gi|344210132|ref|YP_004786308.1|   7 VGVAPTVPGLAATVVNPVVGQLMPGVGTelSRPLRGLVSFVLVLVAGALVLRLRrnyvDESIDAISdspaMAVLYGI 83 
                                       566688999999999********776665566888888888888888888888877775555555588889999999 PP

                             MFS_1 313 .glgfvfpsllalasdlappeeagtas 338
                                        g+ +v +  l+ a+ la  + ag ++
  gi|344210132|ref|YP_004786308.1|  84 aGYVIVGIVGLYGATTLARLSVAGGVF 110
                                       999999888888888888544444443 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 5.6e-07
                             MFS_1 249 llallalvgailallagrls.drlgrrrrlllallllllaalglallavtssavllllvlvliGfglg 315
                                        +a++ +++ +++l++g l+ d +g+rr+++  l++++l+a++++ll+++ s v +l +++ +G+g++
  gi|344210132|ref|YP_004786308.1| 118 SSAFVLVLTSFGFLVVGTLLtDIFGSRRPTYGLLIGAFLSAVSWVLLSPAGSIVSSL-AIAAFGIGGS 184
                                       356666666677888888888*****************************5555555.6777788443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1288.97
//
Query:       gi|344210133|ref|YP_004786309.1|  [L=586]
Description: glycine betaine transporter [Haloarcula hispanica ATCC 33960]
Scores for 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-179  595.5  45.5     7e-179  595.3  45.5    1.0  1  BCCT          BCCT, betaine/carnitine/choline family transpor
  ------ inclusion threshold ------
       0.53   10.1   0.0       0.53   10.1   0.0    3.2  3  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr


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 !  595.3  45.5  7.8e-183    7e-179       1     484 [.      44     538 ..      44     539 .. 0.97

  Alignments for each domain:
  == domain 1  score: 595.3 bits;  conditional E-value: 7.8e-183
                              BCCT   1 vflvslliivlfvllalvfpealeevlsslnswilekfgwlylllvllflvfllvlafskygkikLGkddekpefst 77 
                                       vf v+l+ii+lf++++++  ++++++ + l+++i ++fgw+yll+v++f+++ll++afskyg+i++G+ ++++efs 
  gi|344210133|ref|YP_004786309.1|  44 VFPVALAIIALFIAVTILLGDTAASAYTWLFNTIGDTFGWFYLLAVNVFIITLLYFAFSKYGNIRIGGVEAEKEFSD 120
                                       7899************************************************************************* PP

                              BCCT  78 lsWfamlfaaglgigllfwgvaEplahylspp..pgaeagteeaaqeAlaytffhwGlhaWaiyalvalalayfayr 152
                                       +sW+amlf+ag+gigl+f++v+Epl+++++pp  +gaeagt +aa+ A+a+tffhwG+h+Wa+y lv+l la+f+++
  gi|344210133|ref|YP_004786309.1| 121 FSWMAMLFSAGMGIGLMFFSVSEPLYYFQNPPsfFGAEAGTGAAASAAMAQTFFHWGFHPWAVYGLVGLGLAFFSFN 197
                                       ******************************9987777**************************************** PP

                              BCCT 153 kglpltissalypllgeringllgkvvDvlavlatvfGvatslGlgvlqinaglselfg.......ieesltvqlai 222
                                       +glplt++s++ pllgeri+g+ g+++D+++v+at+fG++tslGlgv q+n+gls++ g       ++++++ q+a+
  gi|344210133|ref|YP_004786309.1| 198 RGLPLTFRSIFWPLLGERIYGWPGHIIDLVTVFATLFGLSTSLGLGVAQVNTGLSYVGGdmlgavsVPTGTWPQVAL 274
                                       **********************************************************999999777999999**** PP

                              BCCT 223 ivvitalatvsavsGldkGikrlSnlnlvlalllllfvllvGptlfilntfvqslgdylqnlvalslatdaae.eae 298
                                       i+ it++at+s+++Gld G+krlS+lnl+l+++ll f+++vGpt++i+ t++++lg+y+ n++al + t++ + +a+
  gi|344210133|ref|YP_004786309.1| 275 IAGITLIATLSVAAGLDGGVKRLSTLNLYLMFALLGFLVIVGPTVYIFGTWAEGLGAYFGNILALGFFTGTLNeAAN 351
                                       *********************************************************************99762445 PP

                              BCCT 299 ewlasWTvFyWawwiawapfvGlFiAriSrGRtiRefilgvllvptlvtflwftvlGgtaielelegeaelaea.ae 374
                                       +  ++WTvFyW+wwiaw+pfvG+FiAriS+GR++Ref+lgvl++p+++++lw++v+Gg+a+  +l g++++ ++ +e
  gi|344210133|ref|YP_004786309.1| 352 GTPTAWTVFYWGWWIAWSPFVGMFIARISKGRSVREFVLGVLFLPSMFSTLWLSVFGGSAMFNSLLGNGQALATyNE 428
                                       89***************************************************************99997777669* PP

                              BCCT 375 asveaalfalleqlplgsilsvlavvliiiffvTsaDSatlvlatltsggdenpprkqrvfWgvllgavaavlllag 451
                                        ++++a+falleq+plg +  ++a++l+i+ffvTs+DS++lv++ ltsgg++++pr+qr+fW++++g+va +ll+ g
  gi|344210133|ref|YP_004786309.1| 429 VGQTVAMFALLEQFPLGVVSGLIATLLVITFFVTSSDSGSLVIDHLTSGGKHDVPRTQRIFWALTEGLVASILLIGG 505
                                       ***************************************************************************** PP

                              BCCT 452 glealqsasiiaalPftlvlllmvvsllkalre 484
                                       gl+alq+a+i+++lPf+++l+lm+++++  l++
  gi|344210133|ref|YP_004786309.1| 506 GLTALQTAAITTGLPFAFILCLMCYTVYLGLDN 538
                                       **************************9987765 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   0.0   5.9e-05      0.53      26      62 ..      25      61 ..      17      68 .. 0.89
   2 ?   -0.1   0.6     0.077   6.9e+02     113     132 ..     264     283 ..     223     297 .. 0.66
   3 ?    0.5   0.6      0.05   4.5e+02      74     140 ..     445     512 ..     433     518 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5.9e-05
                      Trp_oprn_chp 26 dalggprtvalsGadwapaltalAlvllAaavAvlav 62
                                      d + g+++++++G d+ p++ ++Al+++A ++Av+++
  gi|344210133|ref|YP_004786309.1| 25 DREPGDTNIQAAGFDIHPVVFPVALAIIALFIAVTIL 61
                                      556679999************************9876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.077
                      Trp_oprn_chp 113 veltawpvlalaggvlllla 132
                                       v + +wp +al++g+ l+++
  gi|344210133|ref|YP_004786309.1| 264 VPTGTWPQVALIAGITLIAT 283
                                       22344999999999877653 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.05
                      Trp_oprn_chp  74 lalagagaavaalslltdpadaaraaaaaatgvasaaaavelta...wpvlalaggvllllagvllllra 140
                                        +++g++a++ +++ +++++d+      +  ++++++++v  t+   w++   + + +ll++g l++l+ 
  gi|344210133|ref|YP_004786309.1| 445 GVVSGLIATLLVITFFVTSSDSGSLVIDH--LTSGGKHDVPRTQrifWALTEGLVASILLIGGGLTALQT 512
                                       45666667777777766666665555533..556677777766667777777777777777776666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); 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:                         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: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3612.55
//
Query:       gi|344210134|ref|YP_004786310.1|  [L=42]
Description: hypothetical protein HAH_5193 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.099   12.3   0.3        0.1   12.3   0.3    1.0  1  TMEM72    Transmembrane protein family 72


Domain annotation for each model (and alignments):
>> TMEM72  Transmembrane protein family 72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   5.8e-06       0.1      21      56 ..       2      37 ..       1      41 [. 0.94

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.8e-06
                            TMEM72 21 aivLigvGvelllkgefkslavylllsgvavsvlEi 56
                                      a+ L+gvG   ++ g+f+ +++  l +++++ + E+
  gi|344210134|ref|YP_004786310.1|  2 AALLMGVGLVGMTVGDFRLAGFSFLSASLVIYIRET 37
                                      799******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); 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: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 271.67
//
Query:       gi|344210135|ref|YP_004786311.1|  [L=147]
Description: universal stress protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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-30  105.0   0.0    5.5e-30  104.7   0.0    1.0  1  Usp           Universal stress protein family
     0.0082   15.6   0.2       0.01   15.3   0.2    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


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 !  104.7   0.0   6.2e-34   5.5e-30       1     138 [.       1     138 [.       1     139 [. 0.95

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 6.2e-34
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.HHHHHH CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.akaaae 76 
                                       my++IlV++Dgs+e+++ +e+++ela+a ga++++l+vid +  + + ++++++ee ++e++   +e +a +   a+
  gi|344210135|ref|YP_004786311.1|   1 MYDHILVPYDGSDEARRGAEHGIELAAALGATVHALYVIDLPGTPRALALRDDEEEMREEYRNYGEEVLAnLGNVAQ 77 
                                       9*****************************************9999999999988888888888777777799**** PP

                                       CTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEE CS
                               Usp  77 aggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVl 138
                                       ++gv+ +++ + g p+eei+e+ae+ed d iV+Gs  r++l   llG ++++v+r +++pV+
  gi|344210135|ref|YP_004786311.1|  78 EHGVDYKTHFKTGAPSEEIVEFAENEDMDAIVLGSAFRGKLGN-LLGGTTDKVVRTSSIPVI 138
                                       *************************************999997.89***************7 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   0.2   1.1e-06      0.01      66     147 ..      13      99 ..       2     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHHHHHHHHHHTBSEEEEEBCC.........GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--T CS
                      AP_endonuc_2  66 eesvdalkraielaaaLGapllvlhpGt.........agagpkgseeeawerlaeslneladyaekegvklalEtla 133
                                       +e+++ +++ ielaaaLGa +  l + +           + +++ +ee ++   e+l  l+ +a+++gv    +  +
  gi|344210135|ref|YP_004786311.1|  13 DEARRGAEHGIELAAALGATVHALYVIDlpgtpralaLRDDEEEMREEYRNYGEEVLANLGNVAQEHGVDYKTHFKT 89 
                                       456999**************97777665666688776445666666688888889**************99888888 PP

                                       TTTSSSTCHHHHHH CS
                      AP_endonuc_2 134 gsgvelgdeelarl 147
                                       g+++    ee++++
  gi|344210135|ref|YP_004786311.1|  90 GAPS----EEIVEF 99 
                                       8887....444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1028.71
//
Query:       gi|344210136|ref|YP_004786312.1|  [L=420]
Description: threonine dehydratase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-78  262.6   5.7    6.4e-78  262.1   5.7    1.2  1  PALP      Pyridoxal-phosphate dependent enzyme
    1.4e-07   31.1   0.4    1.4e-07   31.1   0.4    2.0  2  ACT       ACT domain
    9.2e-06   26.2   1.0      2e-05   25.1   0.1    2.1  2  ACT_4     ACT domain
  ------ inclusion threshold ------
      0.017   15.1   0.0      0.037   14.0   0.0    1.6  1  ACT_6     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 !  262.1   5.7   1.4e-81   6.4e-78       4     294 .]      28     313 ..      26     313 .. 0.98

  Alignments for each domain:
  == domain 1  score: 262.1 bits;  conditional E-value: 1.4e-81
                                       CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-E CS
                              PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlk 80 
                                       ++++TP+ r+ +l + + +++ lK+E+l+ tgSfK+Rga + +++     g +  v+as+GNh++++A+aa + G +
  gi|344210136|ref|YP_004786312.1|  28 VVKKTPVERSTSLGEFVDAEVHLKMEHLQWTGSFKTRGAFNKISQDVAD-GVESFVAASAGNHAQGVALAATKCGAE 103
                                       5789*****************************************7777.7************************** PP

                                       EEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTT CS
                              PALP  81 vtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggk 157
                                       +ti++p++a+++k++++r +G  v++vg+d++e++++a+++ +e ++a +v+ +d+ ++i+g+gt+g E++ ++ ++
  gi|344210136|ref|YP_004786312.1| 104 STIFMPENAPQAKIDATRGYGGSVELVGNDFQETMSHAKAVVEE-TDAEFVHAYDDLDIIAGQGTLGTEMYHDC-PD 178
                                       ********************************************.*****************************.6* PP

                                       EEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHHS CS
                              PALP 158 pdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafelld 234
                                       +d+v+vp+GgGgli+G+++++k+  p++rv+gv+++g++++++sl++g +v +++ dtiadg+a+g  se ++ +++
  gi|344210136|ref|YP_004786312.1| 179 VDTVIVPIGGGGLISGVSTAVKHLSPETRVVGVQATGAETVHESLDKGIPVVLDEVDTIADGIATGGISETTLNIIE 255
                                       ***************************************************************************** PP

                                       EEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 235 rlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                       + vde+vtvsd ++++a+ ll +r++ vve ++aa++aa+ l +  +++++ +v+ +l+g
  gi|344210136|ref|YP_004786312.1| 256 ANVDEVVTVSDTDIAQAILLLMERAKQVVEGAGAASVAAV-LSDSLDVSGE-TVMPLLCG 313
                                       ****************************************.**********.99999987 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1         2   8.8e+03      26      36 ..     251     261 ..     243     272 .. 0.55
   2 !   31.1   0.4   3.2e-11   1.4e-07       3      64 ..     338     403 ..     336     405 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2
                                       SEEEEEEEEEE CS
                               ACT  26 iNidsieqrss 36 
                                       +Ni+ +++ ++
  gi|344210136|ref|YP_004786312.1| 251 LNIIEANVDEV 261
                                       55555555444 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 3.2e-11
                                       EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT....ECEEEEEEEEEEHHHHHHHHHHHHT CS
                               ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedk....vagivfvvivvdeedleevlealkk 64 
                                       lrv+  D+PG++ +++g++a+ g Ni+ + + +s ++     a +vf v++ ++e++++++ a+++
  gi|344210136|ref|YP_004786312.1| 338 LRVRIDDQPGVMEEISGVIARQGANIHDVRHERSVENleigEAYLVFNVETSGAEHAQTIITAIRD 403
                                       8999**********************************9999999999999999999999988886 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.3     1e+04      27      41 ..     246     260 ..     243     273 .. 0.70
   2 !   25.1   0.1   4.4e-09     2e-05       6      71 ..     335     403 ..     330     413 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.3
                             ACT_4  27 iseekanivsvnakt 41 
                                       ise++ ni + n+++
  gi|344210136|ref|YP_004786312.1| 246 ISETTLNIIEANVDE 260
                                       677777777777665 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 4.4e-09
                             ACT_4   6 tvrleveaedrkglLaditqviseekanivsvnaktrkk...dglaeikitveVkdvehLsrviakLra 71 
                                         +l+v   d++g++ +i+ vi+ ++ani++v+ +   +    g a + ++ve + +eh +++i+++r 
  gi|344210136|ref|YP_004786312.1| 335 LLQLRVRIDDQPGVMEEISGVIARQGANIHDVRHERSVEnleIGEAYLVFNVETSGAEHAQTIITAIRD 403
                                       5789****************************988865555568899********************96 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   8.2e-06     0.037      10      34 ..     343     367 ..     334     379 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.2e-06
                             ACT_6  10 pdrpGltasLtsvlaefgvnilDie 34 
                                       +d+pG+  ++++v+a+ g+ni D++
  gi|344210136|ref|YP_004786312.1| 343 DDQPGVMEEISGVIARQGANIHDVR 367
                                       8**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3031.37
//
Query:       gi|344210137|ref|YP_004786313.1|  [L=850]
Description: sacrosine dehydrogenase/glycine cleavage T protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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  256.8   0.0    2.6e-76  256.4   0.0    1.2  1  GCV_T          Aminomethyltransferase folate-binding domain
    2.1e-38  132.8   1.7    5.4e-38  131.5   1.5    1.7  2  DAO            FAD dependent oxidoreductase
    7.4e-17   61.1   0.2    2.2e-16   59.6   0.1    1.9  2  GCV_T_C        Glycine cleavage T-protein C-terminal barrel d
    3.9e-13   49.5   0.2      1e-12   48.1   0.2    1.8  1  FAO_M          FAD dependent oxidoreductase central domain
    1.7e-05   25.0   0.1    6.8e-05   23.0   0.1    2.1  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    2.7e-05   24.3   0.0    0.00048   20.3   0.0    2.3  2  SoxG           Sarcosine oxidase, gamma subunit family
    5.1e-05   22.5   0.3    9.8e-05   21.6   0.3    1.6  1  FAD_binding_2  FAD binding domain
    0.00019   20.7   0.1     0.0022   17.3   0.1    2.2  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    0.00085   19.8   0.4     0.0063   17.0   0.4    2.3  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.001   18.4   0.1       0.02   14.2   0.1    2.2  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
     0.0014   18.3   0.0     0.0026   17.4   0.0    1.5  1  ApbA           Ketopantoate reductase PanE/ApbA
     0.0037   16.7   0.0     0.0066   15.8   0.0    1.3  1  ThiF           ThiF family
     0.0082   15.5   0.0      0.015   14.7   0.0    1.4  1  GMC_oxred_N    GMC oxidoreductase
  ------ inclusion threshold ------
      0.038   13.0   0.5      0.068   12.2   0.5    1.4  1  Lycopene_cycl  Lycopene cyclase protein
      0.056   12.1   0.1        2.1    6.9   0.2    2.2  2  HI0933_like    HI0933-like protein
      0.071   13.2   0.0       0.14   12.2   0.0    1.4  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
      0.082   13.2   0.1       0.19   12.0   0.1    1.6  1  TrkA_N         TrkA-N domain
      0.087   12.1   0.1       0.17   11.1   0.1    1.3  1  Thi4           Thi4 family
       0.11   12.4   0.7        9.1    6.3   0.3    2.5  2  NAD_binding_9  FAD-NAD(P)-binding


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 !  256.4   0.0   2.8e-79   2.6e-76       2     256 ..     463     739 ..     462     740 .. 0.94

  Alignments for each domain:
  == domain 1  score: 256.4 bits;  conditional E-value: 2.8e-79
                             GCV_T   2 ydrhkalgakfvefagwemPvqYa........................sesikaehlavreaaglfDvShmgkievs 54 
                                       y+++k+lga+f + +gwe P++Y+                        s+   aehl++r ++++fD+++++ i v+
  gi|344210137|ref|YP_004786313.1| 463 YHQQKELGAEFYQSGGWETPQWYEsnadlvekyddripaqdgwqginrSKIEAAEHLHTRDKVSMFDMTTFSSIMVE 539
                                       8899*******************************************99999************************* PP

                             GCV_T  55 GpdaaalLqrlltndisklkpgkatytlllnedGgvidDlivarldedefllvvnaankekdl.awlekaaekkdld 130
                                       G++++a+Lqr+++nd++ l++g+++y+lllne Gg+++D++v++ld++ef++++ ++n+  ++  +le+  ++++++
  gi|344210137|ref|YP_004786313.1| 540 GEGSQAFLQRVCSNDMD-LDVGQVRYSLLLNEGGGILADITVVKLDDEEFMVTTGGGNSPGIHgGHLED-EAPETVS 614
                                       *****************.999****************************************99899999.6757777 PP

                             GCV_T 131 vevedvteelallalqGPkarevlskllgadlselkffsfaevela..ggkkvlvsRtgytGedGfeiyipaeeaee 205
                                       v+ve+   + +++ l+GP++r +l+++++ d+++ + f++++ +++   +++v+++R++y+Ge+G+e+++p+e++++
  gi|344210137|ref|YP_004786313.1| 615 VHVEE--GAKSTIGLWGPNSRLLLQRCTDTDVTN-EGFPYFSAKQMyvDDVPVIALRVSYVGELGWELWVPTEYGQR 688
                                       77777..7789*****************888666.55555555555555**************************** PP

                             GCV_T 206 lweaLleagkeegvkpaGlgArdtlRlEaglrlyghdldeettPleaglgw 256
                                       lwe+L +ag++ gv+p+G gA+ ++RlE+g+rl+g+d+d++ +P+eagl +
  gi|344210137|ref|YP_004786313.1| 689 LWETLQDAGEDLGVRPMGGGALSSMRLEKGYRLWGTDIDTDSNPFEAGLPF 739
                                       ************************************************976 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.5   1.5   5.7e-41   5.4e-38       1     352 []      11     397 ..      11     397 .. 0.77
   2 ?   -1.9   0.0         2   1.9e+03      60      90 ..     682     711 ..     569     756 .. 0.68

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 5.7e-41
                                       EEEEECTSHHHHHHHHHHHHTT...EEEEESSSSTTS.SGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg...Vtllekgdiags.gaSgrnsgllhsglrylpeaselarlslealeelrelee 73 
                                       d v+iG+G +G+s+Ay+L++ g   V+++++g+ + + g+S ++ g+  +     p++  + + ++++ ++l + + 
  gi|344210137|ref|YP_004786313.1|  11 DTVVIGAGAVGCSVAYHLTELGaedVAVIDQGPLPVTgGSSVHAPGIMFQ-T--SPSK-IQTKTAYYTSRLLSDAD- 82 
                                       89*****************99999********887763777777777755.4..3433.22366666655554444. PP

                                       HHSSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTE.EEEEHHHHHHHSTT..STTTSEEEEETTEEEEEHHH CS
                               DAO  74 elgididyrrtGllslaadeeelealdkllallleaglda.elldaeevrelepa..lpgllgalfypdtgqvdpak 147
                                              y++ G + +a++ee ++ l+++++ ++++gl++ +ll++eev e  p+   +++lg++++p++g+vd   
  gi|344210137|ref|YP_004786313.1|  83 ------VYDEVGGIEVARSEERMDFLRRRVEWATSYGLPEpQLLSPEEVTEHLPMvdEDEILGGYYSPTDGRVDGIG 153
                                       ......49**********99999999999999999***8879*************64449***************** PP

                                       HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTTCTTTSEEEEEEEE CS
                               DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdllgllkeldlpispvrgq 223
                                       +++++++      + ++ +tevt+l+  +g +  v  +t+ g++d+ +  V+a++ w  ++g+l  ldlpi pv +q
  gi|344210137|ref|YP_004786313.1| 154 ALQWYMENS---SASFYGNTEVTDLDVSGGEINAV--ETDqGRIDC-ERAVIATNNWGYQTGQLAGLDLPIAPVEHQ 224
                                       ****96665...588**********9988888888..777798554.66******9*667744456688******** PP

                                       EEEEEECCT.HSTGSGCSEEEEE.......EEETTTTEEEEEE..........TTSEEEEEESSE............ CS
                               DAO 224 vlvlkplse.klvspaailpvpe.......tdddgrgvyvtpr..........kdgrvlvGgtad............ 270
                                       ++v++p +e +  ++  +    +       + d++   y+  +           d+++++ +++d            
  gi|344210137|ref|YP_004786313.1| 225 YVVTEPMDElADAESSVG----DnttgldvPGDRSIAEYM--SegphqpvgrdQDHSLYFRTHGDalgmgsynhetl 295
                                       ******999433333333....233357553333333333..23455666655677888888888999988888999 PP

                                       .....................EETTCSSTSCSHHHHHH.HHHHHHHHSGGGCGEEE..EEEEEEE.ETTSSEEEEEE CS
                               DAO 271 .....................eesgdddpevdeedide.llealrklfPqlgdvlr..kwaGlrp.lpdglpliget 322
                                                            + +++++  ++ + +d+   +a  +l+P+ +dv++  +  G+   +pdg+p +get
  gi|344210137|ref|YP_004786313.1| 296 svdpeamgknseehqasvrgfTKEHWET--PTHRGRDKsAKQAFDELLPATQDVEYeaTENGIFVfTPDGMPAVGET 370
                                       9999999999977777665544444444..4444444459999*******88888655888*888669********9 PP

                                       ETEEEEEEEEECTTTHHHHHHHHHHHHHHH CS
                               DAO 323 pgvkglylatGhsghGltlapatGkllael 352
                                        +v+gl+    +    +t++ + G++lae+
  gi|344210137|ref|YP_004786313.1| 371 AQVDGLWTGLAI---WWTHSGGYGRILAEW 397
                                       99*********9...99***********97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHHHHSSTTSEEEEEEEEEE CS
                               DAO  60 lslealeelreleeelgididyrrtGllsla 90 
                                        +++++++++ l++  g d+++r+ G   l 
  gi|344210137|ref|YP_004786313.1| 682 PTEYGQRLWETLQDA-GEDLGVRPMGGGALS 711
                                       456788999999987.889998887776664 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 ?   -3.2   0.0       8.9   8.4e+03      34      49 ..     140     155 ..     137     184 .. 0.76
   2 !   59.6   0.1   2.3e-19   2.2e-16       6      80 .]     768     842 ..     764     842 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.9
                           GCV_T_C  34 gaysptlgksialAyv 49 
                                       g+yspt g+  +++ +
  gi|344210137|ref|YP_004786313.1| 140 GYYSPTDGRVDGIGAL 155
                                       7999998887776655 PP

  == domain 2  score: 59.6 bits;  conditional E-value: 2.3e-19
                           GCV_T_C   6 lelddgapllrggepilrdgevvGhvTSgaysptlgksialAyvkaelaklgtevevevrgkrvpaevvkkpfyD 80 
                                       ++ldd ++++  g p+l+dge +G+v  g y+++++ sia+ yv++e+a++gt+v+++  g++++a+v ++p++D
  gi|344210137|ref|YP_004786313.1| 768 VTLDDSTDIMLSGRPVLKDGEAIGYVQAGNYGYSIDESIAYTYVPTEYAEAGTSVQIQCEGETYDATVRDEPLFD 842
                                       5677777777****************************************************************9 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 !   48.1   0.2   1.1e-15     1e-12       5      56 .]     409     460 ..     407     460 .. 0.98

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 1.1e-15
                             FAO_M   5 siDlwevDirRFgdlhnnreylrervaesygkvYsipyPreelesgRnlrtS 56 
                                       ++D+ ++++rRF+++++ ++y  +r+a  y +vYsi+ Pr+++++ R+lrtS
  gi|344210137|ref|YP_004786313.1| 409 PVDTGGIHVRRFEPHAGEKDYFVDRGAKRYEQVYSIVEPRWQPDDHRGLRTS 460
                                       7899***********************************************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 !   23.0   0.1   7.2e-08   6.8e-05       1      54 [.      14      68 ..      14      80 .. 0.86
   2 ?   -2.5   0.0       6.5   6.1e+03      45      66 ..     673     694 ..     670     696 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 7.2e-08
                                      EE--SHHHHHHHHHHHCCTE.EEEEE-SSSSSSGGG-EECETTCEECTS---EEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagf.dvlllekrdrlGGraasyevpgvrvdygahifhg 54
                                      ++GaG+ G++ Ay+L++ g+ dv ++++++ +    +s++ pg+ +++ ++ + +
  gi|344210137|ref|YP_004786313.1| 14 VIGAGAVGCSVAYHLTELGAeDVAVIDQGPLPVTGGSSVHAPGIMFQTSPSKIQT 68
                                      8*****************9978*******88777779999999999999988866 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.5
                                       ECTS---EEETTHHHHCHHHHC CS
                     NAD_binding_8  45 vdygahifhgsgyypnvrrllr 66 
                                        ++g+  + +++y +++++ l+
  gi|344210137|ref|YP_004786313.1| 673 GELGWELWVPTEYGQRLWETLQ 694
                                       5799999999999999999877 PP

>> SoxG  Sarcosine oxidase, gamma subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.39   3.7e+02      75      98 ..     535     558 ..     511     567 .. 0.82
   2 !   20.3   0.0   5.1e-07   0.00048      64     146 ..     613     698 ..     571     699 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.39
                              SoxG  75 lisisGakaeavlakltaiDlsad 98 
                                        i ++G  ++a l+++++ D+ +d
  gi|344210137|ref|YP_004786313.1| 535 SIMVEGEGSQAFLQRVCSNDMDLD 558
                                       5899*****************998 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 5.1e-07
                              SoxG  64 asvvdlShgrvlisisGakaeavlakltaiDlsadaFpvGaaaatilgkvevvil...rtgsdafevlvfrsFaesl 137
                                        sv    +++  i + G++++ +l++ t  D+  + Fp   a++  +++v v  l     g+  +e+ v   + + l
  gi|344210137|ref|YP_004786313.1| 613 VSVHVEEGAKSTIGLWGPNSRLLLQRCTDTDVTNEGFPYFSAKQMYVDDVPVIALrvsYVGELGWELWVPTEYGQRL 689
                                       455556688999*************************************987655233689**************** PP

                              SoxG 138 wkaLldasa 146
                                       w++L+da +
  gi|344210137|ref|YP_004786313.1| 690 WETLQDAGE 698
                                       ******987 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.3     1e-07   9.8e-05       1      49 [.      11      62 ..      11     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1e-07
                                      SEEEE--SHHHHHHHHHHHHTTT.-EEEEESSS..GGGSGGGG--S-EE-TT CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGl.kvavvekeq..efggatawsqGgidavl 49
                                      D +ViG+G+ G++ A+ ++e G+ +vav+++++  ++gg+++ + G ++  +
  gi|344210137|ref|YP_004786313.1| 11 DTVVIGAGAVGCSVAYHLTELGAeDVAVIDQGPlpVTGGSSVHAPGIMFQTS 62
                                      89*****************************95438999*****99998666 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 !   17.3   0.1   2.3e-06    0.0022     143     175 ..      10      43 ..       2      54 .. 0.86
   2 ?    0.4   0.0      0.32     3e+02     196     235 ..     162     201 ..     139     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.3e-06
                                       SEEEEES-SHHHHHHHHHHHHHT-E.EEEEESSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                       Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgke.vtlveard 175
                                       +++vv+G+G++G+ +A +l++lg+e v ++++++
  gi|344210137|ref|YP_004786313.1|  10 ADTVVIGAGAVGCSVAYHLTELGAEdVAVIDQGP 43 
                                       789*******************9999****9887 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.32
                                       TTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 196 eGvevklgtsvkeidgngeklevvledgeeidadlvvvav 235
                                       +   ++ +t+v+++d  g ++  v++d+ +id++  v+a+
  gi|344210137|ref|YP_004786313.1| 162 SSASFYGNTEVTDLDVSGGEINAVETDQGRIDCERAVIAT 201
                                       4444555666666666666555666666666666666554 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.4   6.7e-06    0.0063       2      32 ..      12      43 ..      11      49 .. 0.88
   2 ?   -0.9   0.0       2.7   2.6e+03      46      78 ..     155     187 ..     153     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.7e-06
                                      EEEECSSHHHHHHHHHHHHTT.SEEEEEESSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelg.kkVtvversd 32
                                       vv+G+G +g+ +A  l+elg  +V v++ ++
  gi|344210137|ref|YP_004786313.1| 12 TVVIGAGAVGCSVAYHLTELGaEDVAVIDQGP 43
                                      69*******************55999998776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.7
                                       HHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox  46 lqeklekngievllntkveeiegsedgvesvkl 78 
                                       lq ++e+    ++ nt+v+ ++ s+ ++++v++
  gi|344210137|ref|YP_004786313.1| 155 LQWYMENSSASFYGNTEVTDLDVSGGEINAVET 187
                                       566888889999**********99988888876 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 !   14.2   0.1   2.1e-05      0.02       1      31 [.      13      43 ..      13      69 .. 0.93
   2 ?    1.8   0.0      0.12   1.2e+02     100     135 ..     168     204 ..     118     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                      ++iGaG+ G ++a++l ++g ed+ ++++g 
  gi|344210137|ref|YP_004786313.1| 13 VVIGAGAVGCSVAYHLTELGAEDVAVIDQGP 43
                                      79**************************995 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.12
                       Pyr_redox_3 100 lfeeVesvkke.degfevetsketyeAkkviiAtGef 135
                                        ++eV++++ + +e   vet+++ + +++ +iAt  +
  gi|344210137|ref|YP_004786313.1| 168 GNTEVTDLDVSgGEINAVETDQGRIDCERAVIATNNW 204
                                       5788888888515668899999999999999999654 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.8e-06    0.0026       2      31 ..      13      43 ..      12      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.8e-06
                                      EEES-SHHHHHHHHHHHH.HTHCEEEE-SCH CS
                              ApbA  2 ailGaGaiGsllaakLak.agadvtlilrsr 31
                                      +++GaGa+G+ +a++L++  ++dv +i++++
  gi|344210137|ref|YP_004786313.1| 13 VVIGAGAVGCSVAYHLTElGAEDVAVIDQGP 43
                                      69****************78888*9999887 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.9e-06    0.0066      19      50 ..      10      41 ..       6      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.9e-06
                                      SEEEEE--SHHHHHHHHHHHHHTTTEEEEEES CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 19 skvllvGaGglGsellknLalsGvgkltlvDn 50
                                      + ++++GaG++G+ ++  L  +G + + ++D+
  gi|344210137|ref|YP_004786313.1| 10 ADTVVIGAGAVGCSVAYHLTELGAEDVAVIDQ 41
                                      5679***************************8 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.5e-05     0.015       2      58 ..      11      69 ..      10      84 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                       GMC_oxred_N  2 delveggGsagsvvAaRLsedpstsvlvleaggreknrl..imvlalalklidkklnta 58
                                      d +v+g+G++g+ vA+ L+e +++ v v++ g+            +++++++ +k++t+
  gi|344210137|ref|YP_004786313.1| 11 DTVVIGAGAVGCSVAYHLTELGAEDVAVIDQGPLPVTGGssVHAPGIMFQTSPSKIQTK 69
                                      889*****************************988887754344444444444444444 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   7.2e-05     0.068       1      39 [.      11      48 ..      11      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.2e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfp 39
                                      D vviGaG+ g+s+A +lte   +  v +i+ +p ++ +
  gi|344210137|ref|YP_004786313.1| 11 DTVVIGAGAVGCSVAYHLTELG-AEDVAVIDQGPLPVTG 48
                                      88****************5544.4479999999988665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2    0.0022       2.1       2      33 ..      11      43 ..      10      47 .. 0.86
   2 ?    2.8   0.0     0.042        40     114     162 ..     154     201 ..     144     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0022
                                      SEEEE--SHHHHHHHHHHHHTT-.-EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgk.rVlllekak 33
                                      d++viG+Ga G   A ++ + g+ +V+++++++
  gi|344210137|ref|YP_004786313.1| 11 DTVVIGAGAVGCSVAYHLTELGAeDVAVIDQGP 43
                                      79****************8877527****9975 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.042
                                       HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE-- CS
                       HI0933_like 114 allkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAt 162
                                       al+  ++++  +++ +tev++++ + +++  v+t +++++ +++ v+At
  gi|344210137|ref|YP_004786313.1| 154 ALQWYMENSSASFYGNTEVTDLDVSGGEINAVET-DQGRIDCERAVIAT 201
                                       566678888999999*******************.9************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 ?   12.2   0.0   0.00015      0.14      12      42 ..       9      39 ..       4      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                      T-EEEEES-SHHHHHHHHHHHCCT-CEEEEE CS
                      Shikimate_DH 12 ekkvlliGaGemaelvakhLlakgvkkvvva 42
                                      ++  ++iGaG ++  va hL + g+++v+v+
  gi|344210137|ref|YP_004786313.1|  9 RADTVVIGAGAVGCSVAYHLTELGAEDVAVI 39
                                      56789***********************997 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   0.1    0.0002      0.19       2      30 ..      13      42 ..      12      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                                      EEES-SHHHHHHHHHHHH.TTEEEEEEESS CS
                            TrkA_N  2 iiiGlGrvGrslaeeLse.ggkdvvvidkd 30
                                      ++iG+G vG s+a  L+e g +dv vid+ 
  gi|344210137|ref|YP_004786313.1| 13 VVIGAGAVGCSVAYHLTElGAEDVAVIDQG 42
                                      8*****************99999*****85 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00018      0.17      18      64 ..      10      59 ..       7      70 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS.SS--TTT..TTTSTTB CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailers.vspGGGa..wlGGqlf 64
                                      +D v++GaG+ G + ay l++     va++++  + + GG+     G +f
  gi|344210137|ref|YP_004786313.1| 10 ADTVVIGAGAVGCSVAYHLTELGAEDVAVIDQGpLPVTGGSsvHAPGIMF 59
                                      799******************98889999998435555554114456666 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   0.3    0.0096       9.1       1      33 [.      13      41 ..      13      56 .. 0.80
   2 ?    3.8   0.0     0.055        52     119     153 ..     166     201 ..     154     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0096
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp 33
                                      +++GaG+ G +v+ +L +        ++ ++d+
  gi|344210137|ref|YP_004786313.1| 13 VVIGAGAVGCSVAYHLTELG----AEDVAVIDQ 41
                                      69***************994....666777776 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.055
                     NAD_binding_9 119 vh.raevvdleeradgqavlladgaslaadaVvLAl 153
                                       ++ ++ev+dl+ ++++   +++d+ ++++++ v+A+
  gi|344210137|ref|YP_004786313.1| 166 FYgNTEVTDLDVSGGEINAVETDQGRIDCERAVIAT 201
                                       54378************999***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (850 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 5513.02
//
Query:       gi|344210138|ref|YP_004786314.1|  [L=856]
Description: sacrosine dehydrogenase/glycine cleavage T protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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-81  272.9   0.1    3.6e-81  272.3   0.1    1.3  1  GCV_T          Aminomethyltransferase folate-binding domain
    2.1e-50  172.3   0.8    4.9e-50  171.1   0.8    1.7  1  DAO            FAD dependent oxidoreductase
      8e-15   54.5   0.0    2.5e-14   53.0   0.0    1.9  1  GCV_T_C        Glycine cleavage T-protein C-terminal barrel d
    2.7e-13   50.0   0.4    7.5e-13   48.6   0.4    1.8  1  FAO_M          FAD dependent oxidoreductase central domain
    2.5e-06   27.7   0.0    4.8e-06   26.8   0.0    1.5  1  SoxG           Sarcosine oxidase, gamma subunit family
    3.5e-05   24.0   0.1    0.00016   21.8   0.0    2.3  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    3.6e-05   24.2   0.3     0.0047   17.4   0.1    2.5  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    4.1e-05   22.9   0.3    4.1e-05   22.9   0.3    2.1  3  FAD_binding_2  FAD binding domain
    0.00013   21.3   0.7     0.0031   16.8   0.0    2.2  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
     0.0054   17.0   0.1      0.055   13.7   0.0    2.4  2  TrkA_N         TrkA-N domain
      0.007   15.7   0.1      0.016   14.6   0.1    1.5  1  ThiF           ThiF family
  ------ inclusion threshold ------
      0.016   14.5   0.6        0.3   10.3   0.3    2.3  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
      0.023   14.4   0.1      0.044   13.4   0.1    1.4  1  ApbA           Ketopantoate reductase PanE/ApbA
      0.037   13.1   2.5       0.19   10.8   0.2    2.2  2  Lycopene_cycl  Lycopene cyclase protein
      0.046   13.1   0.0      0.084   12.2   0.0    1.4  1  GMC_oxred_N    GMC oxidoreductase
      0.049   13.6   0.4        8.1    6.4   0.0    3.2  3  NAD_binding_9  FAD-NAD(P)-binding
      0.066   11.9   0.2       0.74    8.4   0.0    2.0  2  HI0933_like    HI0933-like protein


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 !  272.3   0.1   3.4e-84   3.6e-81       1     257 []     476     754 ..     476     754 .. 0.96

  Alignments for each domain:
  == domain 1  score: 272.3 bits;  conditional E-value: 3.4e-84
                             GCV_T   1 lydrhkalgakfvefagwemPvqYa........................sesikaehlavreaaglfDvShmgkiev 53 
                                       +y+ hk+  a++++ agwe P++++                        s    ae+l+vre++gl+D+++++k+ev
  gi|344210138|ref|YP_004786314.1| 476 MYHTHKKYDAELWAEAGWEEPHWFDsnadllaeygdqipdregweakywSPIEGAEALNVRENVGLHDMTSFNKMEV 552
                                       5899*********************************************9*************************** PP

                             GCV_T  54 sGpdaaalLqrlltndisklkpgkatytlllnedGgvidDlivarldedefllvvnaankekdl.awlekaaekkdl 129
                                        G da +++q+l+tnd++ +++g+++ytl++ne Ggv +D++v+r+ded++ll++++ +  + + aw+++ +     
  gi|344210138|ref|YP_004786314.1| 553 IGGDAGEFVQYLCTNDMD-IDVGDVKYTLMCNEAGGVRADITVTRTDEDRYLLLTTGREVGNNHvAWVRE-QS--PD 625
                                       ******************.889*****************************99999988765554***99.44..8* PP

                             GCV_T 130 dvevedvteelallalqGPkarevlskllgadlselkffsfaevela..ggkkvlvsRtgytGedGfeiyipaeeae 204
                                       dv v+dvt++la++   GP+ar+vlsk++++dls+ ++f+f++ +++  ++++v+++R++y Ge+G+e+y+p+e++e
  gi|344210138|ref|YP_004786314.1| 626 DVVVNDVTSSLAAMVCTGPNARKVLSKITDVDLSD-DAFPFFTSQQFfvKNIPVTALRVSYAGELGWEFYTPSEYGE 701
                                       *********************************99.88888887777799*************************** PP

                             GCV_T 205 elweaLleagkeegvkpaGlgArdtlRlEaglrlyghdldeettPleaglgwa 257
                                       +lwe ++eag+e+g++p+G gA+++lR+E+g+rl+g+dl++e++P+eaglgwa
  gi|344210138|ref|YP_004786314.1| 702 RLWEHIMEAGEEYGIRPYGNGALNSLRIEKGFRLWGKDLHTEHNPYEAGLGWA 754
                                       ****************************************************6 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.1   0.8   4.7e-53   4.9e-50       1     352 []      12     410 ..      12     410 .. 0.80

  Alignments for each domain:
  == domain 1  score: 171.1 bits;  conditional E-value: 4.7e-53
                                       EEEEECTSHHHHHHHHHHHHTT...EEEEESSSSTTS.SGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg...Vtllekgdiags.gaSgrnsgllhsglrylpeaselarlslealeelrelee 73 
                                       d vi+G+Gi+G+ +Ay+L++ g   V+++++g+ + + g+S ++ g+  +  ++++    l +++ ++++++ +le+
  gi|344210138|ref|YP_004786314.1|  12 DTVIVGAGIVGCNIAYQLTALGredVVVVDQGPMPTTgGSSTHAPGIMFQ-TAEPK---VLSQFADYSRRLYSDLEG 84 
                                       89****************999899********999974777777777755.55344...567999999999988888 PP

                                       HHSSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTE.EEEEHHHHHHHSTT..STTTSEEEEETTEEEEEHHH CS
                               DAO  74 elgididyrrtGllslaadeeelealdkllallleaglda.elldaeevrelepa..lpgllgalfypdtgqvdpak 147
                                         g    y +tG + +a++ee ++ l+++++ ++++g++  +ll++eev e  p    ++++g++++p++gqv    
  gi|344210138|ref|YP_004786314.1|  85 ADGQ-QAYNETGGIEVARSEERMDFLQRRVEYAKAWGIEDpQLLSPEEVTEHLPLvdADQIKGGYYSPTDGQVSGVV 160
                                       8775.46***********9999999******9999***5559************96444****************** PP

                                       HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTT.CTTTSEEEEEE CS
                               DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gll.keldlpispvr 221
                                       ++ alar+a ++G++++ +t+ +++e  dg v+ v + t+ g++ +++ vV+a+++w+++l ++l   l  p++pv 
  gi|344210138|ref|YP_004786314.1| 161 ACDALAREAMDGGAKFVPHTRTEDVETADGEVQAV-V-TEnGSI-ECNEVVVATNIWARQLgEKLdVHL--PVTPVE 232
                                       *************************99999*9999.5.554875.4588**********6655554555..****** PP

                                       EEEEEEEECCTHSTGSGCSEEEEE.........EEETTTTEEEEEETTSEEEEEESSE................... CS
                               DAO 222 gqvlvlkplseklvspaailpvpe.........tdddgrgvyvtprkdgrvlvGgtad................... 270
                                       +q+ +++ l+e  +s+  i  +p                       k  r+lvG++                     
  gi|344210138|ref|YP_004786314.1| 233 HQYTMTESLDELADSAVDITDHPLfenyenvsgE------------KAKRLLVGPDRPilrdqdnamyyrnhgdsyg 297
                                       ******9999944444333333322233333330............4456666665556666666666666666777 PP

                                       ...............................EETTCSSTSCSHHHHHH.HHHHHHHHSGGG..CGEEEEEEEEEE.E CS
                               DAO 271 ...............................eesgdddpevdeedide.llealrklfPql..gdvlrkwaGlrp.l 312
                                                                      ++++ d+ ++ +++ d+  ++a  +l+P+   +++++k+ G+ +  
  gi|344210138|ref|YP_004786314.1| 298 igsynhepivpdpqdlggndpdgeqgsvhefTDYHMDN-ATHPDRPDKaPRQASDELLPATagKELEHKYNGMFAeS 373
                                       77777799999999999999999988887665555555.6666666665788888999*944588**********56 PP

                                       TTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHHH CS
                               DAO 313 pdglpligetpgvkglylatGhsghGltlapatGkllael 352
                                       p+glp++g++ +++gl+ a+ +    +t+a ++Gk+lae+
  gi|344210138|ref|YP_004786314.1| 374 PNGLPVMGPVQEYDGLWTAAAI---WVTHAGGAGKALAEW 410
                                       9********999**********...*************97 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 !   53.0   0.0   2.3e-17   2.5e-14       2      78 ..     779     855 ..     778     856 .] 0.96

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 2.3e-17
                           GCV_T_C   2 rlvglelddgapllrggepilrdgevvGhvTSgaysptlgksialAyvkaelaklgtevevevrgkrvpaevvkkpf 78 
                                       + ++l+ldd+++++  + p+l+++e++G++ S+ y++t g  +a+ y+++e+a++gt+ve+   g+r++a+v ++p+
  gi|344210138|ref|YP_004786314.1| 779 KVACLTLDDEDAVVLDNKPVLDGDETIGYLHSAEYGYTEGACVAYTYLPPEYAEPGTSVEILYEGERYDATVREEPL 855
                                       5789****99999********999*************************************************9997 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 !   48.6   0.4   7.1e-16   7.5e-13       5      55 ..     422     473 ..     420     483 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 7.1e-16
                             FAO_M   5 siDlwevDirRFgdlhnnreylrervaesygkvYsipyPreeles.gRnlrt 55 
                                       +iDl ++D++RF+++ +++++ r+ + e+y+ vY+i++P++ +++ +R++r+
  gi|344210138|ref|YP_004786314.1| 422 PIDLAHCDVNRFDEHEGSWDFARDIGGEEYRIVYNIMHPKWVWTDkQRDIRR 473
                                       8****************************************988779*9998 PP

>> SoxG  Sarcosine oxidase, gamma subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   4.6e-09   4.8e-06      26     147 .]     586     713 ..     573     713 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 4.6e-09
                              SoxG  26 kgvaskesvlwlaPdeflvid...qegkaalaalaealaelasvvdlShgrvlisisGakaeavlakltaiDlsada 99 
                                       +gv  + +v     d++l++    + g++ +a ++e   +   v d+     ++  +G++a++vl+k t +Dls da
  gi|344210138|ref|YP_004786314.1| 586 GGVRADITVTRTDEDRYLLLTtgrEVGNNHVAWVREQSPDDVVVNDVTSSLAAMVCTGPNARKVLSKITDVDLSDDA 662
                                       44444448888889999999966333444455555555556788899999999************************ PP

                              SoxG 100 FpvGaaaatilgkvevvil...rtgsdafevlvfrsFaeslwkaLldasae 147
                                       Fp   +++  ++++ v+ l     g+  +e +    + e lw+ +++a +e
  gi|344210138|ref|YP_004786314.1| 663 FPFFTSQQFFVKNIPVTALrvsYAGELGWEFYTPSEYGERLWEHIMEAGEE 713
                                       *************999877233568999****************9999876 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 !   21.8   0.0   1.6e-07   0.00016       1      46 [.      15      61 ..      15      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.6e-07
                                      EE--SHHHHHHHHHHHCCTE.EEEEE-SSSSSSGGG-EECETTCEEC CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagf.dvlllekrdrlGGraasyevpgvrvd 46
                                      IvGaG+ G+ +Ay L+  g+ dv+++++++ +    +s + pg+ ++
  gi|344210138|ref|YP_004786314.1| 15 IVGAGIVGCNIAYQLTALGReDVVVVDQGPMPTTGGSSTHAPGIMFQ 61
                                      9*****************8868*******987766677777776666 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   4.5e-06    0.0047       2      34 ..      13      46 ..      12      55 .. 0.88
   2 ?    4.1   0.0     0.066        70      44      80 ..     163     199 ..     157     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.5e-06
                                      EEEECSSHHHHHHHHHHHHTT.SEEEEEESSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelg.kkVtvversdkl 34
                                       v+vG+G +g+  A  l++lg  +V vv+ ++++
  gi|344210138|ref|YP_004786314.1| 13 TVIVGAGIVGCNIAYQLTALGrEDVVVVDQGPMP 46
                                      69*******************6689999988776 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.066
                                       HHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEET CS
                         Pyr_redox  44 kilqeklekngievllntkveeiegsedgvesvklkd 80 
                                       ++l+++  + g +++ +t++e +e+ + +v++v++++
  gi|344210138|ref|YP_004786314.1| 163 DALAREAMDGGAKFVPHTRTEDVETADGEVQAVVTEN 199
                                       5677888899**************88877****9986 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.3   3.9e-08   4.1e-05       1     204 [.      12     216 ..      12     239 .. 0.71
   2 ?   -1.8   0.1       1.2   1.2e+03      70     113 ..     399     442 ..     384     483 .. 0.58
   3 ?   -2.6   0.0       2.1   2.2e+03     216     287 ..     529     609 ..     514     645 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.9e-08
                                       SEEEE--SHHHHHHHHHHHHTTT.-EEEEESSS..GGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTT CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGl.kvavvekeq..efggatawsqGgidavlspeqkkagikdspelhrtdtlkald 74 
                                       D +++G+G+ G+  A++++  G+ +v+vv++++   +gg+++ + G ++  ++p+  ++   d  +    d+ +a +
  gi|344210138|ref|YP_004786314.1|  12 DTVIVGAGIVGCNIAYQLTALGReDVVVVDQGPmpTTGGSSTHAPGIMFQTAEPKVLSQFA-DYSRRLYSDLEGADG 87 
                                       89*****************************86326899*************777744444.655555555555555 PP

                                       T-S-HHHHHHHHHTHHHHHHHHHHT....T----B...........CCTS...SB-EEE-TT-SSTEEEE-.STT-. CS
                     FAD_binding_2  75 eladqplveafveaapeavdeLeel....gvpfsr...........tedg...pvdvrelGglsatartlhdaadar 133
                                       ++a  +   + v++++e +d+L++                      +  +   ++ + +  + +    + ++ ++  
  gi|344210138|ref|YP_004786314.1|  88 QQAYNETGGIEVARSEERMDFLQRRveyaK----AwgiedpqllspE--EvteHLPLVDADQIKGG-YYSPTDGQ-- 155
                                       5569999999999**********9966441....2333333344331..13334444444444444.22222333.. PP

                                       .....HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 134 retlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                           v+g   + +l+++a + g +f ++t+ +++ + dg+v  +v e   +g+++    + vv+at  + r
  gi|344210138|ref|YP_004786314.1| 156 ----VSGVVACDALAREAMDGGAKFVPHTRTEDVETADGEVQAVVTE---NGSIEC---NEVVVATNIWAR 216
                                       ....488888899999998888********************99888...666553...677777777766 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                                       HHHTTT-S-HHHHHHHHHTHHHHHHHHHHTT----BCCTSSB-E CS
                     FAD_binding_2  70 lkaldeladqplveafveaapeavdeLeelgvpfsrtedgpvdv 113
                                        +++++ a ++++e +v + pe    L+++ v  + + +g +d 
  gi|344210138|ref|YP_004786314.1| 399 HAGGAGKALAEWMEHGVPRLPEGPIDLAHCDVNRFDEHEGSWDF 442
                                       33444444455555555555555555555544444444444443 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.1
                                       SSSBSSGTT-S-HHHHHHHCTTSS.EES..TT-EEEEEEEET....TTTB..B--THHHHTT-EEE-TTSSBTH... CS
                     FAD_binding_2 216 eaettnapavtGdglalalragaa.lnddrmeevqfhPtslvpirdgsgi..LitealrgeGgilvdkdGrrFm... 286
                                        ae++n+  + G   +++   +++ +++d+ e+vq++ t+ ++i  g     L+   +   Gg+  d +++r     
  gi|344210138|ref|YP_004786314.1| 529 GAEALNVRENVGLH-DMTSFNKMEvIGGDAGEFVQYLCTNDMDIDVGDVKytLM---CNEAGGVRADITVTRTDedr 601
                                       55666666666654.446666777777777777777777777665555545555...77777766666666633444 PP

                                       .......G CS
                     FAD_binding_2 287 .......n 287
                                               
  gi|344210138|ref|YP_004786314.1| 602 ylllttgR 609
                                       44444440 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 !   16.8   0.0   2.9e-06    0.0031     141     176 ..       9      45 ..       2      55 .. 0.86
   2 ?    2.5   0.1     0.065        69     189     235 ..     165     211 ..     160     229 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.9e-06
                                       -TSEEEEES-SHHHHHHHHHHHHHT-E.EEEEESSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                       Pyr_redox_2 141 lpkrivvvGgGyiGvElAaalaklgke.vtlveardr 176
                                       +++++v+vG+G +G+ +A +l+ lg e v++v++++ 
  gi|344210138|ref|YP_004786314.1|   9 TQADTVIVGAGIVGCNIAYQLTALGREdVVVVDQGPM 45 
                                       45789*********************99999998875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.065
                                       HHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 189 leealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvav 235
                                       l+++  + G +++ +t+ ++++  + +++ v +++ +i++  vvva+
  gi|344210138|ref|YP_004786314.1| 165 LAREAMDGGAKFVPHTRTEDVETADGEVQAVVTENGSIECNEVVVAT 211
                                       5566667799999999*999999999899555555569999999997 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   0.0   5.2e-05     0.055       2      32 ..      14      45 ..      13      71 .. 0.81
   2 ?    0.1   0.0      0.88   9.3e+02      42      98 ..     569     623 ..     548     633 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.2e-05
                                      EEES-SHHHHHHHHHHHH.TTEEEEEEESSHH CS
                            TrkA_N  2 iiiGlGrvGrslaeeLse.ggkdvvvidkdee 32
                                      +i+G+G vG ++a +L++ g +dvvv+d+ + 
  gi|344210138|ref|YP_004786314.1| 14 VIVGAGIVGCNIAYQLTAlGREDVVVVDQGPM 45
                                      8*****************99999*****9775 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.88
                                       SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHHHHHHHHTSSSEEEEEESS CS
                            TrkA_N  42 levvvgdatdeevLeeagiekadaviaatgddeanilavllakelnpkkkiiaraqd 98 
                                       +++ vgd+  + +  eag  +ad+ ++ t  de+  l++ + +e  ++   ++r q+
  gi|344210138|ref|YP_004786314.1| 569 MDIDVGDVKYTLMCNEAGGVRADITVTRT--DEDRYLLLTTGREVGNNHVAWVREQS 623
                                       55667888888888888888888555555..55555555566665555445555555 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   1.5e-05     0.016      19      50 ..      11      42 ..       5      45 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                                      SEEEEE--SHHHHHHHHHHHHHTTTEEEEEES CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 19 skvllvGaGglGsellknLalsGvgkltlvDn 50
                                      + +++vGaG +G++++ +L ++G + + +vD+
  gi|344210138|ref|YP_004786314.1| 11 ADTVIVGAGIVGCNIAYQLTALGREDVVVVDQ 42
                                      5689***************************8 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 ?   10.3   0.3   0.00028       0.3       1      31 [.      14      44 ..      14      49 .. 0.94
   2 ?    1.8   0.0      0.11   1.2e+02     102     132 ..     180     211 ..     123     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00028
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                      +I+GaG  G ++a++l  +g ed++++++g 
  gi|344210138|ref|YP_004786314.1| 14 VIVGAGIVGCNIAYQLTALGREDVVVVDQGP 44
                                      7***************************985 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.11
                       Pyr_redox_3 102 eeVesvkked.egfevetsketyeAkkviiAt 132
                                       ++ e+v+ +d e   v t+++++e+++v++At
  gi|344210138|ref|YP_004786314.1| 180 TRTEDVETADgEVQAVVTENGSIECNEVVVAT 211
                                       5667788855155889***************9 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   4.1e-05     0.044       2      31 ..      14      44 ..      13      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-05
                                      EEES-SHHHHHHHHHHHH.HTHCEEEE-SCH CS
                              ApbA  2 ailGaGaiGsllaakLak.agadvtlilrsr 31
                                      +i+GaG +G+ +a++L++   +dv+++++++
  gi|344210138|ref|YP_004786314.1| 14 VIVGAGIVGCNIAYQLTAlGREDVVVVDQGP 44
                                      69**************996777799998765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00018      0.19       1      38 [.      12      48 ..      12      57 .. 0.85
   2 ?    2.0   0.2     0.084        89      93     143 ..     165     215 ..     154     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsllf 38
                                      D v++GaG  g+ +A +l  a  +  vv+++ +p +  
  gi|344210138|ref|YP_004786314.1| 12 DTVIVGAGIVGCNIAYQL-TALGREDVVVVDQGPMPTT 48
                                      88****************.5566778999*99998855 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.084
                     Lycopene_cycl  93 llerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglas 143
                                       l+++ +++g+k++  + ++ +e  +ge+++v+ ++  i++  vv+a+ + +
  gi|344210138|ref|YP_004786314.1| 165 LAREAMDGGAKFVPHTRTEDVETADGEVQAVVTENGSIECNEVVVATNIWA 215
                                       566777888998865555444555569999999999**********97655 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     8e-05     0.084       2      40 ..      12      50 ..      11      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8e-05
                       GMC_oxred_N  2 delveggGsagsvvAaRLsedpstsvlvleaggreknrl 40
                                      d +++g+G++g+ +A+ L++ +++ v+v++ g+  +   
  gi|344210138|ref|YP_004786314.1| 12 DTVIVGAGIVGCNIAYQLTALGREDVVVVDQGPMPTTGG 50
                                      889*****************************9876665 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 ?    6.4   0.0    0.0077       8.1       1      36 [.      14      45 ..      14     113 .. 0.81
   2 ?    3.0   0.2     0.084        89     120     153 ..     178     211 ..     161     213 .. 0.80
   3 ?   -0.3   0.0      0.87   9.1e+02      57      99 ..     548     602 ..     536     624 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0077
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep 36
                                      +ivGaG+ G  ++ +L a      + ++ ++d+ ++
  gi|344210138|ref|YP_004786314.1| 14 VIVGAGIVGCNIAYQLTAL----GREDVVVVDQGPM 45
                                      7*****************9....5899999998665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.084
                     NAD_binding_9 120 hraevvdleeradgqavlladgaslaadaVvLAl 153
                                        +++ +d+e+++++++ + +++ s+++++Vv+A+
  gi|344210138|ref|YP_004786314.1| 178 PHTRTEDVETADGEVQAVVTENGSIECNEVVVAT 211
                                       3779999**99999999999999*********98 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.87
                     NAD_binding_9  57 semslftddpptfaeWlrerga............lee.aeeldpddfvpRalyGrY 99 
                                       ++m+++  d  +f+++l++++               + a +++ d  v+R    rY
  gi|344210138|ref|YP_004786314.1| 548 NKMEVIGGDAGEFVQYLCTNDMdidvgdvkytlmC-NeAGGVRADITVTRTDEDRY 602
                                       67888888889999999998876555554433331.03455555555555555555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2      0.11   1.2e+02       2      33 ..      12      44 ..      11      48 .. 0.82
   2 ?    8.4   0.0    0.0007      0.74     113     162 ..     163     211 ..     147     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.11
                                      SEEEE--SHHHHHHHHHHHHTT.--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrg.krVlllekak 33
                                      d++++G+G  G   A ++ + g ++V+++++++
  gi|344210138|ref|YP_004786314.1| 12 DTVIVGAGIVGCNIAYQLTALGrEDVVVVDQGP 44
                                      79****************666515799999876 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0007
                                       HHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE-- CS
                       HI0933_like 113 dallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAt 162
                                       dal +e+ + g k+  +t+ ++ve+ ++++  v t +++++e++++v+At
  gi|344210138|ref|YP_004786314.1| 163 DALAREAMDGGAKFVPHTRTEDVETADGEVQAVVT-ENGSIECNEVVVAT 211
                                       789********************999999888888.9************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (856 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 5851.87
//
Query:       gi|344210139|ref|YP_004786315.1|  [L=373]
Description: serine protease [Haloarcula hispanica ATCC 33960]
Scores for complete 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  142.3   0.1    1.8e-41  142.1   0.1    1.0  1  AstE_AspA        Succinylglutamate desuccinylase / Aspartoacy
     0.0016   18.3   0.0     0.0033   17.3   0.0    1.6  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens


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 !  142.1   0.1     2e-45   1.8e-41       1     289 [.      90     370 ..      90     372 .. 0.90

  Alignments for each domain:
  == domain 1  score: 142.1 bits;  conditional E-value: 2e-45
                                       SS-EEEEEE-SSTT-HHHHHHHHHHHHHHHCCCESCCEEEEEESSHHHHHCTSSSSS....TT-S-CTTTTTCCCCC CS
                         AstE_AspA   1 sgpkvlisAGvHGnElaGvellrqllkqleeadilgeitlvplaNppAiaagsRyip....idredLNRaFpgrslg 73 
                                       +gp+v+i+A+ HG El+G+++lr+l  +l  a i+g+++++p++N +A+ + s   p    + + +LNR++pg+++g
  gi|344210139|ref|YP_004786315.1|  90 PGPTVYIQAAQHGIELNGPAALRRLHDRLTDAAIAGTVLVIPVVNQLAFDHRSYMTPgeydVMNPNLNRVWPGDESG 166
                                       79***************************************************888888888899************ PP

                                       SSTCHHHHHHHHHHHHHHHCHCTCCCGCEEEEEEEESSTBCCSSEEEE---SSHHHHHHHHHHTTTSEEEEEESS-- CS
                         AstE_AspA  74 rsldealrateaerladalfaaalpeadivlDLHtgtrglkhllfaeadiaeaqlqslallkalglpavllldekes 150
                                                +  e+ a +l+ ++ + ad ++DLHtgt+ +  l +++++  ++ +   +l++a+g+ + +  de+e+
  gi|344210139|ref|YP_004786315.1| 167 ---------SLQEQFAARLW-ELVKDADAAVDLHTGTADM--LEHVRCRAGDPAA--ERLAEAFGTSYRI-TDESED 228
                                       .........***********.6669************988..7888888877777..899**********.666666 PP

                                       S......SHHHHHHHHCTSEEEEEEEES.TTTTCCHHCCHHHHHHHHHHHHCTCHTT-SCC.CEEEEEEEEEEGGSC CS
                         AstE_AspA 151 a......gfletaaeelgalaftlElGgagrlgaedisrtakgvlnvlahigvvagqeavepaklyrvlreldeprd 221
                                              g++++aa+ +g++ +t El   +r+ +++++  + g++n+l+++ v+  +  +ep +   +++  ++ ++
  gi|344210139|ref|YP_004786315.1| 229 TgddgsgGTFRAAAAAAGIPVITAELSNSRRIAQDAVAAGVDGIQNLLRERAVLPAE--PEPHA--GQTVLRNDAEP 301
                                       689******************************************************..56444..55555567777 PP

                                       CCSSCSEEEC..CCCSTTTTETCTEEEETTEEEEECTSTEEEEESSSSEEEESCCTSCCTTTTEEEEEEE CS
                         AstE_AspA 222 iraeeaGlve..fkvklgddveagellakalvldslggekvelrapqdgvivfineaalvekgaalvkva 289
                                       + a e+Gl+e  +++ +gd v+age l  ++  +s+ ++++++ a + gvi++  ++  v kg+ l+ +a
  gi|344210139|ref|YP_004786315.1| 302 VTASESGLFEcrPDIAVGDTVDAGERLGAVYEPSSF-EQQQVVSATERGVIFSLARESVVVKGERLAGIA 370
                                       77*******75589*************999999999.55568999999***9999999999999998765 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 !   17.3   0.0   3.7e-07    0.0033      29      81 ..     305     357 ..     269     370 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.7e-07
                                       -SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEEEEEE--E CS
                   ATP-synt_ab_Xtn  29 drekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkvegkvkeiaee 81 
                                       +++  +e +p ++vgd+v +g+ lG v e +++e++ +v+ + +g + ++a+e
  gi|344210139|ref|YP_004786315.1| 305 SESGLFECRPDIAVGDTVDAGERLGAVYEPSSFEQQQVVSATERGVIFSLARE 357
                                       456679999************************************99999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2719.09
//
Query:       gi|344210140|ref|YP_004786316.1|  [L=396]
Description: hypothetical protein HAH_5199 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2820.26
//
Query:       gi|344210141|ref|YP_004786317.1|  [L=286]
Description: 5,10-methylenetetrahydrofolate reductase [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-13   50.7   0.0    3.6e-13   49.5   0.0    1.6  1  MTHFR      Methylenetetrahydrofolate reductase
  ------ inclusion threshold ------
      0.081   13.2   0.0       0.16   12.2   0.0    1.5  1  DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-li
       0.14   11.2   0.0       0.39    9.8   0.0    1.6  2  GcpE       GcpE protein


Domain annotation for each model (and alignments):
>> MTHFR  Methylenetetrahydrofolate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0     6e-17   3.6e-13      67     225 ..      65     215 ..      41     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 6e-17
                                       HHH-S-EEEEEESTTS.-HHHHHHHHHHHHHCT--EEEEE--S--TT-GGC---S----SHHHHHHHHHHHHCGGSE CS
                             MTHFR  67 qelgleailhlTctda.skeeldkalekakelGirnilALrGDppkdedkweekeeefkyaldLvrlireeygdlfd 142
                                       +e+g +++ h+ ++ + ++e+l++++e+ +++Gi +i    GD        ee+ +e++ a  L + + e       
  gi|344210141|ref|YP_004786317.1|  65 AEMGYDVVPHIAARYVeDQEQLEAIAERLEQAGITDIFVPGGD-------REEPAGEYESAHGLLEALAETEYSFEE 134
                                       467789999999987616799*****************99998.......34677889999*******986666678 PP

                                       EEEEE-TT--TT-S-HHHHHHHHHHHHHCT--EEEEEE-S-HHHHHHHHHHHHHCT-SS-EEEEE---SSHHHHHHH CS
                             MTHFR 143 igvaaYPevhpeaksleadlkylkeKvdaGAdfiitQlffdvdkflkfveqvreagidipiipgimpiksykslkrl 219
                                       +g+ +YPe+h   ++ e+  + + +K +  A +i+tQl +d+++ +++ve++r++gi++p+  gi  +++y+ l ++
  gi|344210141|ref|YP_004786317.1| 135 VGITGYPEGHDFIDD-ETLAESMAQK-EPYATYIVTQLCYDPETVVEWVEDIRARGIELPVEVGIPGVMNYQRLMQI 209
                                       **********86655.5566677777.778*******************************9999999999999998 PP

                                       HHHHT- CS
                             MTHFR 220 aklskv 225
                                        + ++v
  gi|344210141|ref|YP_004786317.1| 210 SQKVGV 215
                                       876665 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 ?   12.2   0.0   2.7e-05      0.16      20      90 ..      28     100 ..      10     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
                         DUF1611_N  20 vssleea..laagaevlviGiapeggklpeswreavkeAleaGldvvsGlHe.rLsddpelaalakk.kgvkiiD 90 
                                       ++s++e+  + ++  ++ i++ p+ g    + +e+ +eA e+G+dvv      +++d+++l+a+a++ +++ i D
  gi|344210141|ref|YP_004786317.1|  28 FESFDEEitHLPDNATIAITTSPQLGIE--KTVEKTEEAAEMGYDVVPHIAArYVEDQEQLEAIAERlEQAGITD 100
                                       5666666555566667777777777765..999****************9999************9944455665 PP

>> GcpE  GcpE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   6.5e-05      0.39      23      74 ..      47      99 ..      39     104 .. 0.88
   2 ?   -2.1   0.0      0.25   1.5e+03      28      68 ..     172     213 ..     165     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 6.5e-05
                                      --S-TT-HHHHHHHHHHHHHCT-SEE.EEEE-SHHHHHHHHHHHHHHHHTT-S CS
                              GcpE 23 tntdtadveatvkqikrlaeaGaelv.Rvtvqdeeeaealkeikeklkkkglk 74
                                      t++    +e+tv+++++ ae+G ++v  ++++ +e+ e+l++i e+l+++g++
  gi|344210141|ref|YP_004786317.1| 47 TTSPQLGIEKTVEKTEEAAEMGYDVVpHIAARYVEDQEQLEAIAERLEQAGIT 99
                                      66677789******************679******************888765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.25
                                       T-HHHHHHHHHHHHHCT-SE.EEEEE-SHHHHHHHHHHHHHH CS
                              GcpE  28 adveatvkqikrlaeaGael.vRvtvqdeeeaealkeikekl 68 
                                        d e++v+ ++++ + G+el v v ++++ + + l +i++k+
  gi|344210141|ref|YP_004786317.1| 172 YDPETVVEWVEDIRARGIELpVEVGIPGVMNYQRLMQISQKV 213
                                       577888999999999999998999999999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1909.05
//
Query:       gi|344210142|ref|YP_004786318.1|  [L=458]
Description: aminomethyltransferase [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-47  160.6   0.0    5.7e-47  160.2   0.0    1.1  1  GCV_T     Aminomethyltransferase folate-binding domain
    0.00014   21.7   0.0    0.00034   20.5   0.0    1.8  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 !  160.2   0.0   6.4e-51   5.7e-47      25     256 ..      62     299 ..      47     300 .. 0.92

  Alignments for each domain:
  == domain 1  score: 160.2 bits;  conditional E-value: 6.4e-51
                             GCV_T  25 a............sesikaehlavreaaglfDvShmgkievsGpdaaalLqrlltndisklkpgkatytlllnedGg 89 
                                       +            ++++++e+ a  +++ l Dv    +i+v+Gpda+al ++++t+d++++++ +++y +l+nedGg
  gi|344210142|ref|YP_004786318.1|  62 NrlyhprgliepeDGGVMKEYDALTNTVTLWDVAVERQIRVKGPDAEALTNYVVTRDVTGMDAMDGKYVILCNEDGG 138
                                       33555666666667899************************************************************ PP

                             GCV_T  90 vidDlivarldedefllvvnaankekdlawlekaaekkdldvevedvteelallalqGPkarevlskllgadlselk 166
                                       v++D ++ r +edef++ ++     ++++wl+  +  +d+dve+++   ++a +++qGP+a +v+ +++g+++++++
  gi|344210142|ref|YP_004786318.1| 139 VLNDPVLLRPEEDEFWFSISD---STLMQWLQGVNVDNDFDVEIDE--IDVAPMQIQGPRALDVMVDVVGDKVKDVP 210
                                       ******************997...5679*****9998899999888..779************************** PP

                             GCV_T 167 ffsfaevelaggkkvlvsRtgytGedGfeiyipa..eeaeelweaLleagkeegvkpaGlgArdtlRlEaglrlygh 241
                                       ++ +++ e++ g++vl+s tg++Ge+Gfe+y+++  e+ae++w+ ++e++k+++ +++  g  +  R+ ag+  +g+
  gi|344210142|ref|YP_004786318.1| 211 YYGLMDAEIN-GCDVLISQTGFSGEKGFEVYVKDamENAEQVWDPVMESVKDHDGRQIAPG--HHRRIAAGIMSWGQ 284
                                       *********9.*********************98789********************9888..567*********** PP

                             GCV_T 242 dldeettPleaglgw 256
                                       dld+et+P++++lg+
  gi|344210142|ref|YP_004786318.1| 285 DLDHETSPFQVNLGY 299
                                       ************985 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 !   20.5   0.0   3.8e-08   0.00034       2      55 ..     332     389 ..     331     432 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.8e-08
                           GCV_T_C   2 rlvgleld.dgapllrggepil.r.....dgevvGhvTSgaysptlgksialAyvkaelak 55 
                                       +l+gl++  ++   +r  +p +        ge++G++TS  + p l+ +i++++v+ae  +
  gi|344210142|ref|YP_004786318.1| 332 KLIGLKIAgEP---IRDYAPDFwLisdpdTGEECGYLTSPWWNPDLETNIGMGFVPAEKIQ 389
                                       57777775444...44444433212335589*************************88655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3194.32
//
Query:       gi|344210143|ref|YP_004786319.1|  [L=165]
Description: dihydrofolate reductase [Haloarcula hispanica ATCC 33960]
Scores for 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-50  169.1   0.0    7.1e-50  168.8   0.0    1.0  1  DHFR_1    Dihydrofolate reductase


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 !  168.8   0.0   3.9e-54   7.1e-50       1     145 [.       2     150 ..       2     160 .. 0.92

  Alignments for each domain:
  == domain 1  score: 168.8 bits;  conditional E-value: 3.9e-54
                                       EEEEEEEEETT-EEEBTTB-SS--HHHHHHHHHHHTTCEEEEEHHHHHCC-....S--TTCEEEEE-S-TT---TTE CS
                            DHFR_1   1 kislivAvaengvIGkdnklpwhlpeDlkrFkklTtgkpvimGrkTfeslg...krpLpnrkniVltrnedlkvegv 74 
                                       k+sli+Ava+ngvIG+ +++pw++peDl +Fk++T+g+pvimGr+Tfes++     pLp+r niVlt+++   ++ v
  gi|344210143|ref|YP_004786319.1|   2 KLSLIAAVATNGVIGAGGDIPWQYPEDLIHFKQTTIGHPVIMGRRTFESIRrdlDGPLPERLNIVLTTTPRHLPDSV 78 
                                       589***********************************************966667***************98899* PP

                                       EEESSHHHHCCCCTTS..SEEEEEE-HHHHHHCGGG-SEEEEEEESS----SEE-----CCCEEEEEEEEE- CS
                            DHFR_1  75 evvssleealalakee.keevfviGGaeiYkqalpladklylTeidaefegdtffpeideeewelvereehe 145
                                       + v+s+++al  a++  +++ +viGGa++Y+q+lp ad+l+lTe  a+f+gdt+fp++d++ w+++er++h+
  gi|344210143|ref|YP_004786319.1|  79 TAVTSTTAALTEAANSgASTTYVIGGATVYEQFLPKADELILTELTATFDGDTVFPTVDWSCWSETERTTHS 150
                                       *999999999855444499*************************************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1182.09
//
Query:       gi|344210144|ref|YP_004786320.1|  [L=91]
Description: hypothetical protein HAH_5203 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   16.3   1.9     0.0033   16.2   1.9    1.0  1  TctA             Tripartite tricarboxylate transporter TctA f
  ------ inclusion threshold ------
       0.18   11.8   4.0       0.22   11.5   4.0    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


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 !   16.2   1.9   3.7e-07    0.0033      86     144 ..      11      72 ..       1      79 [. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.7e-07
                              TctA  86 rageAlrlaaigSfiGglvsvllll...llapllakvalkfgpaeyfalillglvliailse 144
                                        a++A rl +i+S++Ggl ++  l    +l+p++a  al    + y++ +  +l++ + + +
  gi|344210144|ref|YP_004786320.1|  11 AAAQAFRLGIIASAVGGLAGIATLYwldVLTPVFAGYALVLLFPVYLVFAATALSVWLGYNK 72 
                                       5899**************99998873346799999999999999999999999998877655 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 ?   11.5   4.0   2.5e-05      0.22      30      90 ..      12      72 ..       9      85 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.5e-05
                   Phage_holin_3_6 30 akragsgagllgaagvlallalllllval..alalaalwlaalivaavllvla..gvlalvglkk 90
                                      a++a+++++++ a g la +a l++l  l  ++a      a ++++ v+lv a  ++ +++g++k
  gi|344210144|ref|YP_004786320.1| 12 AAQAFRLGIIASAVGGLAGIATLYWLDVLtpVFAG----YALVLLFPVYLVFAatALSVWLGYNK 72
                                      67788888888888888888888888888565555....33344666666666225556666653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 640.05
//
Query:       gi|344210145|ref|YP_004786321.1|  [L=217]
Description: putative transcriptional regulator [Haloarcula hispanica ATCC 33960]
Scores for 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   60.4   0.0    1.7e-16   59.7   0.0    1.4  1  HTH_10        HTH DNA binding domain
    0.00032   20.6   0.0    0.00044   20.1   0.0    1.2  1  BAT           GAF and HTH_10 associated domain
     0.0053   16.2   0.0      0.012   15.1   0.0    1.5  1  Sigma70_r4    Sigma-70, region 4
  ------ inclusion threshold ------
      0.017   14.6   0.0      0.049   13.2   0.0    1.7  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.077   12.7   0.0       0.69    9.6   0.0    2.2  1  Sigma70_r4_2  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 !   59.7   0.0   4.8e-20   1.7e-16       1      52 [.     157     208 ..     157     209 .. 0.98

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 4.8e-20
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LTd q+++l++Aye+GYF +PR+++l+e+A+e+G+s +++s +Lr+ +++li
  gi|344210145|ref|YP_004786321.1| 157 LTDEQRTALTTAYENGYFGEPRDISLNEVADEIGLSSTAMSGRLRRGMRNLI 208
                                       9************************************************998 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 !   20.1   0.0   1.2e-07   0.00044      33     132 ..      33     134 ..       6     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.2e-07
                               BAT  33 lvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddg..tlleltvsgpslastlaehGgtvrsaeaed 107
                                          ++ g+++  f ++  d +++++++++ ++v+++++v+ +d++    +e t ++  + s++++ +g +   e+ +
  gi|344210145|ref|YP_004786321.1|  33 QGNTDPGSTVFPFLIEYRDRDRLEEMLDADPTVQSYELVDWTDQTgiYYIEHTPETKLISSVVTDVNGFLVHTETKG 109
                                       4455668888889999999*************************95556677777888888**************** PP

                               BAT 108 grarlvvevPpgadvRsvvealeer 132
                                        ++ +++ +P+++++ ++ e+ +e+
  gi|344210145|ref|YP_004786321.1| 110 NGWLVRLLLPDREALNTIWEYANEN 134
                                       ***************9999988776 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.3e-06     0.012       5      48 ..     157     207 ..     156     208 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-06
                                       S-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   5 Lpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       L++++r+ l+  +        ++ +l E++++ g+S  + + +++r++r+L
  gi|344210145|ref|YP_004786321.1| 157 LTDEQRTALTTAYengyfgePRDISLNEVADEIGLSSTAMSGRLRRGMRNL 207
                                       9***************99877889************************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 ?   13.2   0.0   1.4e-05     0.049      16      40 ..     177     202 ..     175     202 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                            HTH_24  16 pr.isqreLAerlglSpstvnrrlkr 40 
                                       pr is +e+A+++glS+++ + rl+r
  gi|344210145|ref|YP_004786321.1| 177 PRdISLNEVADEIGLSSTAMSGRLRR 202
                                       666*****************999997 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 ?    9.6   0.0   0.00019      0.69      14      54 .]     160     207 ..     156     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHTS--.......-HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  14 rqreifllrylegl.......sykEIAellgisegtVksrlsRArkkL 54 
                                       +qr++++  y++g+       s  E+A ++g+s++++  rl+R+++ L
  gi|344210145|ref|YP_004786321.1| 160 EQRTALTTAYENGYfgeprdiSLNEVADEIGLSSTAMSGRLRRGMRNL 207
                                       555555555555554444444788********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1561.80
//
Query:       gi|344210146|ref|YP_004786322.1|  [L=55]
Description: hypothetical protein HAH_5205 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       155  (0.00864521); expected 358.6 (0.02)
Passed bias filter:                      147  (0.00819901); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 379.24
//
Query:       gi|344210147|ref|YP_004786323.1|  [L=66]
Description: hypothetical protein HAH_5206 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   0.1     0.0012   18.6   0.1    1.1  1  MTH865    MTH865-like family
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.14   12.0   0.0    1.0  1  PA14      PA14 domain


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 !   18.6   0.1   1.3e-07    0.0012      19      69 ..      15      65 ..      14      66 .] 0.95

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-07
                                      HHHHHHHH-TTSS-----BTTB---TTTTGGGS-GGGSB-SHHHHHHHHHH CS
                            MTH865 19 speeLlaalPkGaettceagdvevtagelgkklkdsdFPyksaedladdiv 69
                                      + e L++  P  ++ +  ag+ +++a  +++ +++ d P + +e++ad+++
  gi|344210147|ref|YP_004786323.1| 15 NDETLAPSQPREPSKNPVAGTSSLSAAQAQAVADEYDVPVEAVEAVADKLT 65
                                      5688999******************************************97 PP

>> PA14  PA14 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.5e-05      0.14      70     125 ..       8      63 ..       3      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.5e-05
                                       CCEEEEETTCCCEETT-TTS--TT----S-EEEEEEE-TT-EEEEEEEEEESSSSC CS
                              PA14  70 dgvrlsidgelvidnngqqekksnadasteesatlyltaGkkYpirieyfhagtdg 125
                                       d v lsi++e++ +  + + +k   ++++++sa      + +Y++ +e ++a  d+
  gi|344210147|ref|YP_004786323.1|   8 DAVSLSINDETLAPSQPREPSKNPVAGTSSLSAAQAQAVADEYDVPVEAVEAVADK 63 
                                       8999*******************************************999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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 0.28s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 454.46
//
Query:       gi|344210148|ref|YP_004786324.1|  [L=286]
Description: nitrilase [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-38  132.0   0.0    2.8e-38  131.7   0.0    1.1  1  CN_hydrolase  Carbon-nitrogen hydrolase


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 !  131.7   0.0   1.6e-42   2.8e-38       1     250 [.       7     285 ..       7     286 .] 0.90

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 1.6e-42
                                       EEEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBS.............SSHHHHHHHHB....... CS
                      CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgy.............keeahfleaAe....... 57 
                                       ++A++Q ++++ d+e++l+k+ ++i++A r gad++v+PE+  +gy             +                 
  gi|344210148|ref|YP_004786324.1|   7 TLAAAQVEPVYHDKEGTLDKTCRYIEQAGRDGADIVVFPETYFPGYpywrgsvsisrwtDLM-------Vdlqknsl 76 
                                       58*******99***********************************8888886665555222.......14445555 PP

                                       HSSSHHHHHHHHHHHHHTEEEEEEEEEEEC..CTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTS CS
                      CN_hydrolase  58 aglgetlallaalarkngiavviglierel..tngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelf 132
                                        ++ e ++ l ++ ++ + ++v+g+ e  +   + +l  yn+ +++d +g+l+g++rKl+        pt+ er ++
  gi|344210148|ref|YP_004786324.1|  77 HVDDEAIEVLGEAVAEADLTLVLGTNEVSDrqGSETL--YNSLFYFDSTGELMGRHRKLM--------PTHEERAIW 143
                                       8999********************9999995455555..*********************........9******** PP

                                       CS-SS..S-EEEETTEEEEEEEGGGGGSHHHHHHHHHTT-SEEEE.............BH.GCCCTCHHHHHHHHHH CS
                      CN_hydrolase 133 epgdg..ipvfdtpvgkiGaaiCyeigfpellralalkgaeilvn.............lserapvpksmgppqwell 194
                                       ++gd   ++ ++t+vg +G +iCye+++ +++ al ++g+ei+ +             ++ ra++ ++        +
  gi|344210148|ref|YP_004786324.1| 144 GRGDPssLATYETDVGWLGGLICYENHMTLSKAALTAMGEEIHAAvwpgfweqhghpgDKTRAETSEAVDTCDIYPA 220
                                       ****99999********************************************99998667899999999999999* PP

                                       HHHHHHHHTSEEEEEEBEEE..........HCETTEEEE--EEEE-TTS-EEEECCSSSTEEEEEE CS
                      CN_hydrolase 195 graralengcfviaanqvgg..........yeqlilwpvghSaiidpdGrilaglgeeeegvliae 250
                                       +r +a+e++ fv aa+++ +           e +  +  g+S++i+p G++ ag+   eeg+l+ae
  gi|344210148|ref|YP_004786324.1| 221 MREYAFETQSFV-AACSAYMsdavpdgfseDELGFNVAAGGSMLINPAGIVKAGPLVGEEGLLTAE 285
                                       ***********5.55555566*******99999999****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1724.89
//
Query:       gi|344210149|ref|YP_004786325.1|  [L=412]
Description: sugar transporter [Haloarcula hispanica ATCC 33960]
Scores for complete 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-45  154.8  64.5    1.9e-36  125.8  41.2    2.1  2  MFS_1       Major Facilitator Superfamily
    0.00011   21.3  18.3      0.013   14.4   5.0    2.3  2  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
       0.84    8.4  28.6      0.023   13.6   9.0    2.5  2  Sugar_tr    Sugar (and other) 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 !  125.8  41.2   3.1e-40   1.9e-36       9     338 ..      39     358 ..      28     359 .. 0.88
   2 !   42.8  15.4   5.1e-15   3.1e-11      53     173 ..     285     407 ..     284     412 .] 0.85

  Alignments for each domain:
  == domain 1  score: 125.8 bits;  conditional E-value: 3.1e-40
                             MFS_1   9 alarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa... 82 
                                        +a+ i+ ++++++++e+l++ p+++gll+++ + +a+v slp+G++ dr  +r  + l++ +++++++++++a   
  gi|344210149|ref|YP_004786325.1|  39 LAAYEIVPASVTPLIQESLQVGPTAAGLLVGVMFGTAVVVSLPVGAVLDRTDSRTAMALAVGTLVIAGTWGWLAgrr 115
                                       4445555555556******************************************************9999987787 PP

                             MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilai 159
                                        ++  +l++r+l G+++ +++ ag+ ++++ + +++r+ a+g+++a+  +G++lg + g+l+a+ +gW+avf+++ +
  gi|344210149|ref|YP_004786325.1| 116 GQYQSILASRALGGAAYVIVWNAGIDMVSRAVDGSNRATAVGIFTASGPVGFALGQGTGPLIAQRFGWPAVFLAFIG 192
                                       66779************************************************************************ PP

                             MFS_1 160 vsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqe 236
                                        +l +  l  ++++   + ++ +++          +l + ++a+l+++ +w++ +  +l+ + + ++ ++  +yl +
  gi|344210149|ref|YP_004786325.1| 193 PALAG--L--AVFWPASRGHGGSRGDAP-------SLQE-FGAVLRSRNVWLVGVLGFLGYALYLFVNSWGSSYLTQ 257
                                       ****9..6..788888888888877666.......7888.********998444444444457777*********** PP

                             MFS_1 237 vlglsglllaglllallalvgailallagrlsdr.lgrrrrlllallllllaalglallavtssavllllvlvliGf 312
                                        l++s l  +gl++a++ +vg+++++ +g +sdr ++ rrr ++  +++l+a l+l ++ +  s +ll++vl+liGf
  gi|344210149|ref|YP_004786325.1| 258 GLDFS-LAVSGLVVAVFPAVGVVSRISGGLISDRvFNGRRRPVVLSSFGLAAPLLLGFTQFR-SLPLLVAVLLLIGF 332
                                       *****.****************************6777777777777777777777777777.88888889****** PP

                             MFS_1 313 glgfvfpsllalasdlappeeagtas 338
                                       ++ ++ +++++++ +l+ p  a+ta+
  gi|344210149|ref|YP_004786325.1| 333 AVQLTLGLSFTYVRELVDPPVAATAV 358
                                       *****************999999886 PP

  == domain 2  score: 42.8 bits;  conditional E-value: 5.1e-15
                             MFS_1  53 Grlsdrf..Grrrvlllglllfalglllll...fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraig 124
                                       G +sdr+  Grrr ++l+ +++a+  lll    f  sl+ll+++ +l G++  + + ++ +++++++ ++  + a++
  gi|344210149|ref|YP_004786325.1| 285 GLISDRVfnGRRRPVVLSSFGLAAP-LLLGftqF-RSLPLLVAVLLLIGFAVQLTLGLSFTYVRELVDPPVAATAVA 359
                                       899***6699***777777777777.44441355.8899************************************** PP

                             MFS_1 125 llsagfslGailgpllggllasslgWravfyilaivsllafvlfllllp 173
                                       + ++   +Ga ++p++gg+++ s+g++ +f++++ v++ ++++ ++  p
  gi|344210149|ref|YP_004786325.1| 360 FQTSIGLAGAFVAPIAGGAVVNSVGFEPAFLLAGTVAVAGIIV-AWQAP 407
                                       ***************************************9883.33333 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 !   14.4   5.0   2.1e-06     0.013     261     376 ..      67     183 ..      56     192 .. 0.73
   2 !   11.7   6.9   1.5e-05     0.087     209     380 ..     212     386 ..     179     391 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.1e-06
                        MFS_1_like 261 llGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaii.enawlvlpievLhgisfgllwaaave 336
                                       l+G++    vv ++p+  +  +   ++     l ++ l+++ ++ ++a    +   +l   +L g+++ ++w a+++
  gi|344210149|ref|YP_004786325.1|  67 LVGVMFGTAVVVSLPVGAVLDRTDSRTA--MALAVGTLVIAGTWGWLAGRrGQYQSILASRALGGAAYVIVWNAGID 141
                                       5555555555555555444333333322..2366788888999999999878899999******************* PP

                        MFS_1_like 337 yvskiapksleatgqgllsg...lyfglGralGsliGGllwdl 376
                                        vs+++  s +at  g++++   + f lG++ G li+ + +++
  gi|344210149|ref|YP_004786325.1| 142 MVSRAVDGSNRATAVGIFTAsgpVGFALGQGTGPLIA-QRFGW 183
                                       ******************9744467888888888776.44444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.5e-05
                        MFS_1_like 209 lkvtkslqvllnilknpeviifllvalilgmswgiienFlflYL.kelgasntllGslva....lgvvaeiplfffa 280
                                        + + slq++ ++l+ ++v+++ +  ++  +++ +++++ + YL + l++s  + G +va    +gvv+ i   +++
  gi|344210149|ref|YP_004786325.1| 212 RGDAPSLQEFGAVLRSRNVWLVGVLGFLGYALYLFVNSWGSSYLtQGLDFSLAVSGLVVAvfpaVGVVSRISGGLIS 288
                                       44455679999********999999999999*************888998888888777611115667777666666 PP

                        MFS_1_like 281 eklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsgl 357
                                        ++++    + +++ ++ + +  +l+   ++++ l++ + +L g+++ l+ +   +yv++++ + ++at  ++ +++
  gi|344210149|ref|YP_004786325.1| 289 DRVFNGR-RRPVVLSSFGLAAPLLLGFTQFRSLPLLVAVLLLIGFAVQLTLGLSFTYVRELVDPPVAATAVAFQTSI 364
                                       6666532.4568888999999999999999******************************************99998 PP

                        MFS_1_like 358 yfglGralGsliGGllwdlksai 380
                                          +G ++  ++GG++ +  +  
  gi|344210149|ref|YP_004786325.1| 365 GL-AGAFVAPIAGGAVVNSVGFE 386
                                       54.58899999999987766655 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  11.5     0.042   2.5e+02      36     194 ..      47     205 ..      27     208 .. 0.77
   2 ?   13.6   9.0   3.9e-06     0.023      44     193 ..     262     408 ..     224     411 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.042
                                       -SHHHHHH...HHHHHHHTHHHHHHHH.....HHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGG CS
                          Sugar_tr  36 ksksskeessvlsglivsiflvGaiiG.....slfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevliv 107
                                        s+++  + s+++g +++ +lvG ++G     sl +g + dr + + +++ a+  +vi++    +a  + +++ +++
  gi|344210149|ref|YP_004786325.1|  47 ASVTPLIQESLQVGPTAAGLLVGVMFGtavvvSLPVGAVLDRTDSRTAMALAVGTLVIAGTWGWLAGRRGQYQSILA 123
                                       555555556666666777777777776333336778999**********997777777777777777789******* PP

                                       GHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHH CS
                          Sugar_tr 108 gRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpalll 184
                                       +R l G +  ++ +     +s     + R + v+++  +  +G+ +++++g  +++  +   w+  +   + pa  l
  gi|344210149|ref|YP_004786325.1| 124 SRALGGAAYVIVWNAGIDMVSRAVDGSNRATAVGIFTASGPVGFALGQGTGPLIAQRFG---WPAVFLAFIGPA--L 195
                                       ******99999999998999999999999999999999999999999999999888777...887777666666..7 PP

                                       HHHGGGS--- CS
                          Sugar_tr 185 lilllflPES 194
                                       + l +f+P S
  gi|344210149|ref|YP_004786325.1| 196 AGLAVFWPAS 205
                                       7777888876 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.9e-06
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHT..THHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHH CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrf..GRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGl 118
                                       s   sgl+v++f ++++++ + +gl++dr+  GR+   + +++ + +  +l ++++  +s+ +l++  +l+G++v l
  gi|344210149|ref|YP_004786325.1| 262 SLAVSGLVVAVFPAVGVVSRISGGLISDRVfnGRRRPVVLSSFGLAA-PLLLGFTQF-RSLPLLVAVLLLIGFAVQL 336
                                       66789***********************9777*****9999988765.566666664.5****************** PP

                                       HHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS-- CS
                          Sugar_tr 119 asvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPE 193
                                       + +l+ +y+ E+  + ++ + v ++ +   +G +va i g ++ ++ +   +   + l+   a++ +i+ + +PE
  gi|344210149|ref|YP_004786325.1| 337 TLGLSFTYVRELVDPPVAATAVAFQTSIGLAGAFVAPIAGGAVVNSVG---FEPAFLLAGTVAVAGIIVAWQAPE 408
                                       ***********************999999*********9999877766...99999999999999**99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 2527.90
//
Query:       gi|344210150|ref|YP_004786326.1|  [L=64]
Description: hypothetical protein HAH_5209, partial [Haloarcula hispanica ATCC 33960]
Scores for 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-12   44.9   0.0    5.9e-12   44.8   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
       0.11   12.9   0.0       0.13   12.6   0.0    1.1  1  PE        PE 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 !   44.8   0.0   6.5e-16   5.9e-12     251     302 ..       2      53 ..       1      61 [. 0.94

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 6.5e-16
                                       HHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TT CS
                            Aldedh 251 dkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpl 302
                                       + av+a+ +g+++++G++C a sr++v+e+i+defv++l  +a+++++gdp 
  gi|344210150|ref|YP_004786326.1|   2 ETAVDAATAGVYYSTGETCDALSRAIVHEDIHDEFVDRLMTRAESFTLGDPA 53 
                                       789***********************************************94 PP

>> PE  PE 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      0.13      47      91 ..       5      51 ..       3      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHS-- CS
                                PE 47 VSaaiAalfsahaqeyqalsaqaaa..fheqfvqalaaaagsYaaaE 91
                                      V aa+A +  + +++++als+  ++   h++fv  l + a+s++  +
  gi|344210150|ref|YP_004786326.1|  5 VDAATAGVYYSTGETCDALSRAIVHedIHDEFVDRLMTRAESFTLGD 51
                                      66899****************9876347**************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        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 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 412.91
//
Query:       gi|344210151|ref|YP_004786327.1|  [L=260]
Description: transcription regulator [Haloarcula hispanica ATCC 33960]
Scores for complete 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  111.5   0.0    1.6e-31  108.8   0.0    2.0  2  IclR            Bacterial transcriptional regulator
    8.7e-10   38.3   0.1    5.8e-09   35.6   0.0    2.4  3  HTH_IclR        IclR helix-turn-helix domain
    3.6e-05   23.6   0.4    0.00011   22.0   0.0    2.0  2  MarR_2          MarR family
    7.4e-05   22.5   0.0    0.00026   20.8   0.0    2.0  2  HTH_5           Bacterial regulatory protein, arsR family
    0.00015   21.6   0.0    0.00043   20.1   0.0    1.8  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00019   21.3   0.0    0.00036   20.4   0.0    1.4  1  MarR            MarR family
     0.0004   20.4   0.0     0.0012   18.9   0.0    1.8  1  HTH_20          Helix-turn-helix domain
    0.00063   19.2   0.0     0.0016   17.9   0.0    1.7  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0094   16.3   0.0      0.021   15.2   0.0    1.6  1  Rrf2            Transcriptional regulator
  ------ inclusion threshold ------
      0.037   14.2   0.0       0.12   12.5   0.0    1.8  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.064   13.3   0.0       0.15   12.2   0.0    1.6  1  FeoC            FeoC like transcriptional regulator
      0.085   12.7   0.0       0.18   11.6   0.0    1.5  1  DUF742          Protein of unknown function (DUF742)
       0.13   11.9   0.0       0.24   11.1   0.0    1.4  1  Diacid_rec      Putative sugar diacid recognition


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 ?    0.1   0.0      0.47   6.5e+02       9      23 ..     109     123 ..     106     124 .. 0.89
   2 !  108.8   0.0   1.2e-34   1.6e-31       8     127 ..     129     247 ..     126     249 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.47
                                       TT-EEEGGGSHHHHH CS
                              IclR   9 iGtrlplyataiGKa 23 
                                        G+r+ ly ++ GKa
  gi|344210151|ref|YP_004786327.1| 109 NGQRVILYRSSGGKA 123
                                       59************8 PP

  == domain 2  score: 108.8 bits;  conditional E-value: 1.2e-34
                                       STT-EEEGGGSHHHHHHHHTS-HHHHHHHHHHHT---SSTTS--SHHHHHHHHHHHHHHTSEEEESSSSTTEEEEEE CS
                              IclR   8 aiGtrlplyataiGKalLaaldeeeleallerlelkrlterTitdpeeLleeLakvReqGyavdreEeeegvrciAa 84 
                                        iG++ +++ t++GK++La+l+ e++++++  ++l + t++T+ ++ +L+++L++vR+qGya+d+eE+  gvr +A+
  gi|344210151|ref|YP_004786327.1| 129 PIGNHTEMHWTSLGKVILAHLPVEKRNEIVADHGLPKGTDNTLSSRSDLEAALKRVRDQGYAIDDEEHLRGVRGVAV 205
                                       59*************************************************************************** PP

                                       EEE-TTSSEEEEEEEEEETTTSHHHHHHHHHHHHHHHHHHHHH CS
                              IclR  85 pifdasgevvaAvsvsgptarlteeelkeellalvreaArkis 127
                                       pif++++ev++ + ++gp+ r+t +++++ ll+++r + ++i+
  gi|344210151|ref|YP_004786327.1| 206 PIFNDEQEVMVSLGITGPRDRFTSRYMAN-LLEILRYTKNEIE 247
                                       *****************************.*********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 !   35.6   0.0   4.2e-12   5.8e-09       2      50 ..      12      59 ..      11      61 .. 0.92
   2 ?   -2.3   0.0       2.8   3.9e+03      20      29 ..      90      99 ..      87     100 .. 0.85
   3 ?   -1.4   0.0       1.5   2.1e+03      22      34 ..     155     167 ..     146     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 4.2e-12
                                      HHHHHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  2 ldRalaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      ++ +l+iL al+++ + ++ls+lA ++++p Stv+ +L+tLv++ yv +
  gi|344210151|ref|YP_004786327.1| 12 VETTLDILAALEKREP-VGLSDLASHLDIPTSTVFIHLNTLVQRDYVVK 59
                                      67789******99988.8*****************************87 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.8
                                      BHHHHHHHHT CS
                          HTH_IclR 20 tlselArrtg 29
                                      ++ el+r+tg
  gi|344210151|ref|YP_004786327.1| 90 KVEELSRETG 99
                                      5789****98 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.5
                                       HHHHHHHTS-HHH CS
                          HTH_IclR  22 selArrtglpkSt 34 
                                        e+ +  glpk t
  gi|344210151|ref|YP_004786327.1| 155 NEIVADHGLPKGT 167
                                       5899999***987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0     8e-08   0.00011       7      56 ..      15      62 ..      13      66 .. 0.93
   2 ?   -2.2   0.1       2.8   3.9e+03      36      61 ..     175     198 ..     172     199 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8e-08
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                       +++LaaL  r++  +  ++la +l+++ s+v  +l+ Lv++ +v++++g
  gi|344210151|ref|YP_004786327.1| 15 TLDILAALEKREP--VGLSDLASHLDIPTSTVFIHLNTLVQRDYVVKESG 62
                                      679**********..*******************************9987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2  36 savsrilkrLvaaGLverrpgpeDkR 61 
                                       s +  +lkr  ++G+    +++e++R
  gi|344210151|ref|YP_004786327.1| 175 SDLEAALKRVRDQGYAI--DDEEHLR 198
                                       55666788888888886..5566777 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 !   20.8   0.0   1.9e-07   0.00026       3      45 ..      14      57 ..      13      59 .. 0.92
   2 ?   -3.3   0.0       6.4   8.8e+03      17      26 ..      90      99 ..      89      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.9e-07
                                      HHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  3 tRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      t l+IL +L++ ++   ++la +l+++ stv  HL+ L + ++V
  gi|344210151|ref|YP_004786327.1| 14 TTLDILAALEKrEPVGLSDLASHLDIPTSTVFIHLNTLVQRDYV 57
                                      5589*******777*************************99988 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.4
                                      EHHHHHHHHT CS
                             HTH_5 17 cvcelaeelg 26
                                      +v el++e+g
  gi|344210151|ref|YP_004786327.1| 90 KVEELSRETG 99
                                      6889999986 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   3.1e-07   0.00043      13      60 ..      18      65 ..      12      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.1e-07
                                      HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                      + +aL k++p   +++a++l++p s+v   L+ L+++++V +e g+++
  gi|344210151|ref|YP_004786327.1| 18 ILAALEKREPVGLSDLASHLDIPTSTVFIHLNTLVQRDYVVKESGQYR 65
                                      6778889************************************99965 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.6e-07   0.00036       4      49 ..      14      59 ..      13      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.6e-07
                                      HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      t ++iL+ l+ ++p  +s+La++l + +stv   l +L++++++ +
  gi|344210151|ref|YP_004786327.1| 14 TTLDILAALEKREPVGLSDLASHLDIPTSTVFIHLNTLVQRDYVVK 59
                                      6689**************************************9966 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   8.5e-07    0.0012      10      55 ..      13      58 ..       7      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 8.5e-07
                                      HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 10 PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      ++ ++il+aL  +e++ +s+la  ld++ +t+  HL++L++ ++v 
  gi|344210151|ref|YP_004786327.1| 13 ETTLDILAALEKREPVGLSDLASHLDIPTSTVFIHLNTLVQRDYVV 58
                                      6789*************************************99975 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   1.2e-06    0.0016       3      47 ..      13      57 ..      13      58 .. 0.97

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.2e-06
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      et+++IL +L+k      ++LA +l+++ stv  +l+ L++  ++
  gi|344210151|ref|YP_004786327.1| 13 ETTLDILAALEKREPVGLSDLASHLDIPTSTVFIHLNTLVQRDYV 57
                                      689***************************************998 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.5e-05     0.021      12      61 ..      14      63 ..       3      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                              Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                      ++l +La+ e++epv ++++a++ +i+ s +   l++L + ++v  + G+
  gi|344210151|ref|YP_004786327.1| 14 TTLDILAALEKREPVGLSDLASHLDIPTSTVFIHLNTLVQRDYVVKESGQ 63
                                      34445799999999******************************999886 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 ?   12.5   0.0     9e-05      0.12      13      54 ..      18      59 ..      13      63 .. 0.92
   2 ?   -2.2   0.0       3.6     5e+03      43      52 ..     181     190 ..     178     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9e-05
                                      HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                    Fe_dep_repress 13 IYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyvey 54
                                      I+ + e++++v+ +dla+ L++  s+V   l+ L +  yv+ 
  gi|344210151|ref|YP_004786327.1| 18 ILAALEKREPVGLSDLASHLDIPTSTVFIHLNTLVQRDYVVK 59
                                      788999*****************************9999975 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.6
                                       HHHHHHTTSE CS
                    Fe_dep_repress  43 lkkLekdGyv 52 
                                       lk+ +++Gy 
  gi|344210151|ref|YP_004786327.1| 181 LKRVRDQGYA 190
                                       89999***96 PP

>> FeoC  FeoC like transcriptional regulator
   #    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       5      41 ..      18      54 ..      15      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                              FeoC  5 lkeyleergrvslkeLsrhfkaspealeamLeqwvrk 41
                                      + ++le+r+ v l++L+ h+++ ++++   L+++v++
  gi|344210151|ref|YP_004786327.1| 18 ILAALEKREPVGLSDLASHLDIPTSTVFIHLNTLVQR 54
                                      66899********************998777777765 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00013      0.18      47      91 ..      17      63 ..       2      70 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                            DUF742 47 ailrLcre..plsVaelaAelklPvgvvrvLlsdLldaglltvrapv 91
                                      +il+  ++  p    +la +l++P ++v + l  L++ ++++ +  +
  gi|344210151|ref|YP_004786327.1| 17 DILAALEKrePVGLSDLASHLDIPTSTVFIHLNTLVQRDYVVKESGQ 63
                                      555544442466779************************99877655 PP

>> Diacid_rec  Putative sugar diacid recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00017      0.24      61      96 ..     192     227 ..     178     249 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                        Diacid_rec  61 eeakklkgvkpGinlpivfn.gevvGviGitGepeev 96 
                                       +++++l+gv+ G+ +pi+ + +ev+  +GitG+ ++ 
  gi|344210151|ref|YP_004786327.1| 192 DDEEHLRGVR-GVAVPIFNDeQEVMVSLGITGPRDRF 227
                                       4555677875.*******761567888*****99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1722.31
//
Query:       gi|344210152|ref|YP_004786328.1|  [L=375]
Description: multiple sugar ABC transporter ATP-binding protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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  112.0   0.0    5.1e-32  111.3   0.0    1.4  1  ABC_tran         ABC transporter
    2.5e-10   40.4   0.1      9e-10   38.6   0.1    2.0  1  TOBE_2           TOBE domain
      3e-09   37.6   0.2    2.3e-08   34.7   0.0    2.7  1  OB_MalK          MalK OB fold domain
      1e-06   28.8   0.0      0.051   13.4   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.8e-05   25.0   0.1    0.00031   21.0   0.0    2.6  2  TOBE             TOBE domain
    2.7e-05   23.7   0.7    0.00012   21.6   0.7    1.9  1  SMC_N            RecF/RecN/SMC N terminal domain
     0.0013   19.1   0.3     0.0029   18.0   0.3    1.7  1  AAA_16           AAA ATPase domain
     0.0015   18.8   0.2     0.0038   17.5   0.2    1.8  1  AAA_22           AAA domain
     0.0018   18.2   0.1     0.0044   17.0   0.1    1.6  1  RsgA_GTPase      RsgA GTPase
     0.0029   17.6   0.0     0.0041   17.1   0.0    1.4  1  Rad17            Rad17 P-loop domain
  ------ inclusion threshold ------
      0.011   16.0   0.4       0.12   12.6   0.0    2.5  2  AAA_28           AAA domain
      0.017   14.7   0.0       0.73    9.4   0.0    2.4  2  AAA_25           AAA domain
      0.025   15.1   3.2       0.21   12.2   0.1    3.5  4  CysA_C_terminal  CysA C-terminal regulatory domain
      0.032   14.7   0.8       0.18   12.2   0.8    2.2  1  AAA              ATPase family associated with various cellul
      0.032   13.9   0.1      0.067   12.9   0.1    1.4  1  AAA_30           AAA domain
      0.067   13.7   0.0       0.19   12.3   0.0    1.8  1  AAA_18           AAA domain
      0.079   12.2   0.1       0.35   10.1   0.0    1.9  2  Zeta_toxin       Zeta toxin
      0.083   12.3   0.5       0.79    9.1   0.0    2.2  2  PhoH             PhoH-like protein
      0.089   12.9   0.7       0.18   11.9   0.7    1.7  1  AAA_33           AAA domain
      0.093   12.6   0.6       0.51   10.2   0.0    2.2  2  NTPase_1         NTPase
      0.094   12.5   0.0       0.21   11.4   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
       0.11   12.3   0.0       0.22   11.4   0.0    1.4  1  ATPase_2         ATPase domain predominantly from Archaea
       0.12   12.9   0.4       0.37   11.3   0.0    1.9  2  AAA_23           AAA domain
       0.15   11.6   0.0        0.3   10.7   0.0    1.4  1  AAA_27           AAA domain
       0.19   11.4   0.0        0.8    9.3   0.0    1.8  2  AAA_15           AAA ATPase domain
        0.2   12.1   0.0       0.69   10.3   0.0    1.9  1  RNA_helicase     RNA helicase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   0.0   7.4e-35   5.1e-32       2     136 ..      31     172 ..      30     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 7.4e-35
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +++sl ++ ge v++vG++G+GKSt l+++agl++ t Gei + g+ +++   +  +++i++++q   l p++tvr+
  gi|344210152|ref|YP_004786328.1|  31 EDLSLAVEDGEFVVVVGPSGCGKSTTLRMIAGLETVTDGEIAIGGDVVND--VRPQDRNIAMVFQSYALYPHMTVRD 105
                                       689****************************************9999999..99999******************** PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             + ++++++a++ l++++l d+      ++LSgGq+qrval ra++++p+++l+DEp 
  gi|344210152|ref|YP_004786328.1| 106 NmsfglrlsgeyddQIEQRVTEAAELLEISDLMDDLP----KQLSGGQQQRVALGRAIVRDPEVFLMDEPL 172
                                       **********766666666888888888888777776....*****************************7 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.1   1.3e-12     9e-10       1      76 []     286     357 ..     286     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1.3e-12
                            TOBE_2   1 laiRPEklrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                       l++RPE+     ++++  +  +V+ ve +Gs+  +++e+a+g++ vv++ +++   +++ Gd+++l+++++d++++
  gi|344210152|ref|YP_004786328.1| 286 LGVRPEDFVA--EDAGSYIDTVVDVVEPMGSDNFLYLETADGSKEVVARVDSEY--RPERGDEIALGFHTEDMHLF 357
                                       79********..34457************************9987776666664..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 !   34.7   0.0   3.3e-11   2.3e-08       1      53 []     246     293 ..     246     293 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 3.3e-11
                           OB_MalK   1 GSPaMNflpatveedg..vlvegggvtlplpeeqklalklyagkevilGiRPEhi 53 
                                       GSP+MNf+++ v+++g  ++v   gv+++l+ +           e +lG+RPE++
  gi|344210152|ref|YP_004786328.1| 246 GSPSMNFFEVSVTNSGgrTAVHSAGVEFTLNVDI-------PDGEYTLGVRPEDF 293
                                       9*************99998888888888887777.......889*********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 !   13.4   0.0   7.4e-05     0.051       1      25 [.      42      66 ..      42     112 .. 0.71
   2 !   13.3   0.0   7.7e-05     0.053     235     298 ..     143     204 ..     108     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.4e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl 25
                                      + v++Gp g+GKS+ L+ + +l  +
  gi|344210152|ref|YP_004786328.1| 42 FVVVVGPSGCGKSTTLRMIAGLETV 66
                                      689****************999443 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 7.7e-05
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHS 298
                                        +lS G+++  al  a+ r++    ++l DEp ++L+ kl +   + + ++ ++ ++  i +TH+
  gi|344210152|ref|YP_004786328.1| 143 KQLSGGQQQRVALGRAIVRDP---EVFLMDEPLSNLDAKLRTQMRTEIqRIQEELDVTTIYVTHD 204
                                       357999999999999999999...9********************99976666699********8 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.99   6.9e+02      13      32 ..     265     285 ..     264     289 .. 0.84
   2 !   21.0   0.0   4.4e-07   0.00031      10      64 .]     305     356 ..     298     356 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.99
                              TOBE  13 vveplgseveVrvdlggga.t 32 
                                       +v  +g+e +++vd+++g+ t
  gi|344210152|ref|YP_004786328.1| 265 AVHSAGVEFTLNVDIPDGEyT 285
                                       788899***********9855 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 4.4e-07
                              TOBE  10 tVvvveplgseveVrvdlggga.tLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                        V+vvep gs+ ++++++++g  +++Arv+ + ++e    +G+e+ + +  +++hl
  gi|344210152|ref|YP_004786328.1| 305 VVDVVEPMGSDNFLYLETADGSkEVVARVDSEYRPE----RGDEIALGFHTEDMHL 356
                                       79**********************************....*******999999986 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 !   21.6   0.7   1.8e-07   0.00012      25     212 ..      41     216 ..      31     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.8e-07
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisr 101
                                       +f ++vGp G+GKs  l  i    G ++ +    +   d+++   + +  + a v   +    + ++ ++ ++ ++ 
  gi|344210152|ref|YP_004786328.1|  41 EFVVVVGPSGCGKSTTLRMI---AGLETVTDGEIAIGGDVVND-VRPQDRNIAMVFQSYALYPHMTVRDNMSFGLRL 113
                                       799***********999888...798899888999999***98.777777888887777777777566665566555 PP

                                       EEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 102 rvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                       + + +++    i+++  + +e+ e+   ++  +++LSgG+++ val    Ai  v+   ++l+De  ++LD+k +++
  gi|344210152|ref|YP_004786328.1| 114 SGEYDDQ----IEQRVTEAAELLEISDLMDDLPKQLSGGQQQRVALG--RAI--VRDPEVFLMDEPLSNLDAKLRTQ 182
                                       5555555....55555555555555555555689*******977664..455..45556899*************** PP

                                       HHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 179 vaellkeksknaQfivislreemlekadklvgvt 212
                                       + + +++ +++  +  i ++++++e +    ++ 
  gi|344210152|ref|YP_004786328.1| 183 MRTEIQRIQEELDVTTIYVTHDQTEAMTMADRIV 216
                                       **99999999987777766666666665554444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   4.3e-06    0.0029      20      45 ..      38      61 ..      28     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.3e-06
                            AAA_16 20 rsgrpelvllsGesGvGKsslvrell 45
                                       +g  e v+++G+sG+GKs+ +r+++
  gi|344210152|ref|YP_004786328.1| 38 EDG--EFVVVVGPSGCGKSTTLRMIA 61
                                      344..89****************987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2   5.5e-06    0.0038       4      27 ..      39      62 ..      37     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.5e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlle 27
                                      +  ++vv+G+sG+GK+t+lr+++ 
  gi|344210152|ref|YP_004786328.1| 39 DGEFVVVVGPSGCGKSTTLRMIAG 62
                                      56799***************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   0.1   6.3e-06    0.0044      88     129 ..      28      70 ..      12      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.3e-06
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelelktge 129
                                        ++e+l+ +++d +++v+vG+SG GKSt + ++++ +++  ge
  gi|344210152|ref|YP_004786328.1|  28 LAVEDLSLAVEDgEFVVVVGPSGCGKSTTLRMIAGLETVTDGE 70 
                                       56788888888889*****************999876666555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     6e-06    0.0041      44      67 ..      39      62 ..      16     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6e-06
                             Rad17 44 kkriLLisGPsGCgkstvvkvLsk 67
                                        + +++ GPsGCgkst++++++ 
  gi|344210152|ref|YP_004786328.1| 39 DGEFVVVVGPSGCGKSTTLRMIAG 62
                                      4557899*************9875 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   0.00017      0.12       2      26 ..      43      67 ..      42      94 .. 0.84
   2 ?    0.8   0.0      0.74   5.1e+02      84     129 ..     315     365 ..     303     375 .] 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                            AAA_28  2 ivitGgestGKTtlleaLaargypv 26
                                      +v++G++++GK+t+l+ +a  ++++
  gi|344210152|ref|YP_004786328.1| 43 VVVVGPSGCGKSTTLRMIAGLETVT 67
                                      89**************999655544 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.74
                            AAA_28  84 dtlaYarayggeaeae..leaaar...ekrydlvfllppapeidddgeRre 129
                                       d++ Y+++ +g +e    ++++ r    ++++l f+++ +  + +dgeR e
  gi|344210152|ref|YP_004786328.1| 315 DNFLYLETADGSKEVVarVDSEYRperGDEIALGFHTEDMHLFGPDGERVE 365
                                       67788888877733322266655522144477889999999889****987 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    0.0011      0.73      31      50 ..      38      57 ..      33      92 .. 0.85
   2 ?    2.8   0.0      0.11        73     149     188 ..     162     203 ..     149     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                            AAA_25 31 pagelallaGapgtGKttla 50
                                        ge+++++G++g+GK+t +
  gi|344210152|ref|YP_004786328.1| 38 EDGEFVVVVGPSGCGKSTTL 57
                                      5799*************976 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.11
                            AAA_25 149 Dplsralgg..densnsdvgalvealeriarrtgaavllvhH 188
                                       Dp  ++++   ++ +++  +++ + ++ri+++++++++ v H
  gi|344210152|ref|YP_004786328.1| 162 DPEVFLMDEplSNLDAKLRTQMRTEIQRIQEELDVTTIYVTH 203
                                       5555555555333444445999*******************9 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 ?   -1.6   0.0       6.3   4.3e+03       9      22 ..      25      38 ..      22      46 .. 0.65
   2 ?    1.1   0.1      0.89   6.1e+02       6      19 ..      65      78 ..      65      87 .. 0.80
   3 ?   -2.1   0.0       9.1   6.3e+03      13      35 ..     133     156 ..     131     156 .. 0.75
   4 ?   12.2   0.1    0.0003      0.21       1      41 [.     251     293 ..     251     295 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6.3
                   CysA_C_terminal  9 dGklriGglalpvP 22
                                      d  l + +l+l+v+
  gi|344210152|ref|YP_004786328.1| 25 DNVLAVEDLSLAVE 38
                                      56677778888877 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.89
                   CysA_C_terminal  6 rvedGklriGglal 19
                                      +v dG + iGg  +
  gi|344210152|ref|YP_004786328.1| 65 TVTDGEIAIGGDVV 78
                                      6999*****99655 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 9.1
                   CysA_C_terminal  13 riGglalpvP.elagadgqevvay 35 
                                       +i +l  ++P +l g ++q+v ++
  gi|344210152|ref|YP_004786328.1| 133 EISDLMDDLPkQLSGGQQQRVALG 156
                                       566666688988889999998776 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.0003
                   CysA_C_terminal   1 NlFhGrve..dGk..lriGglalpvPelagadgqevvayVRPhDl 41 
                                       N+F+  v   +G+  ++ +g+++ +    +  ++e +++VRP+D+
  gi|344210152|ref|YP_004786328.1| 251 NFFEVSVTnsGGRtaVHSAGVEFTLN--VDIPDGEYTLGVRPEDF 293
                                       88888884425556677788888888..778999**********7 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 ?   12.2   0.8   0.00027      0.18       1      25 [.      43      67 ..      43     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00027
                                      EEEESSTTSSHHHHHHHHHHHHTHE CS
                               AAA  1 vllyGppGtGKTllakavakelgve 25
                                      v+++Gp G+GK+++ + +a    v+
  gi|344210152|ref|YP_004786328.1| 43 VVVVGPSGCGKSTTLRMIAGLETVT 67
                                      6799**************9865444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   9.7e-05     0.067      15      43 ..      38      65 ..      31      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.7e-05
                            AAA_30 15 tsgdrvavltGpAGtGKttalkalreawe 43
                                      ++g  ++v++Gp G GK+t+l+ ++ + +
  gi|344210152|ref|YP_004786328.1| 38 EDG-EFVVVVGPSGCGKSTTLRMIAGLET 65
                                      444.599***************9987655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00027      0.19       1      43 [.      43      93 ..      43     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00027
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf........gvnlrdvakenglllevdp 43
                                      +++ G++G+GK+t  + ++ ++ +        g++++dv ++++   +v++
  gi|344210152|ref|YP_004786328.1| 43 VVVVGPSGCGKSTTLRMIAGLETVtdgeiaigGDVVNDVRPQDRNIAMVFQ 93
                                      789***************888744677777777777777666666555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00051      0.35      18      60 ..      42      84 ..      26     102 .. 0.84
   2 ?   -0.9   0.0       1.2   8.2e+02      34      59 ..     203     228 ..     178     242 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00051
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60
                                       ++++G +G+GKs+++++++   + +++ + + +D +    P+
  gi|344210152|ref|YP_004786328.1| 42 FVVVVGPSGCGKSTTLRMIAGLETVTDGEIAIGGDVVNDVRPQ 84
                                      6899***************987778888888888887776665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.2
                        Zeta_toxin  34 ellkdelerqgnvvrldpDdlRelhP 59 
                                       ++ ++++++++++v l++ +l++  P
  gi|344210152|ref|YP_004786328.1| 203 HDQTEAMTMADRIVILNQGELQQVAP 228
                                       34445555666666666666666665 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    0.0011      0.79      15      49 ..      36      71 ..      29      73 .. 0.84
   2 ?    0.9   0.1      0.39   2.7e+02      51     108 ..     157     218 ..     143     223 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                                      HHHH-SEEEEE--TTSST.THHHHHHHHHHHHTTS- CS
                              PhoH 15 alkkndivfaiGpaGtGK.tylavalavealkkkkv 49
                                      a+++ ++v+++Gp+G+GK t l + +++e ++++++
  gi|344210152|ref|YP_004786328.1| 36 AVEDGEFVVVVGPSGCGKsTTLRMIAGLETVTDGEI 71
                                      5667889***********668999999999998876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.39
                                       EEEEEE-S--T.T----SS---------TTTHHHHHHHTTTS...-TTCHHHHHHTTSEEEE CS
                              PhoH  51 riiltrpavea.geelGflpgdleekvdpylrplydaLkdll...gaekvekllekgkieva 108
                                       r i+  p v   +e l  l+ +l+++++  ++ + ++L+ ++    ++++e ++ +++i ++
  gi|344210152|ref|YP_004786328.1| 157 RAIVRDPEVFLmDEPLSNLDAKLRTQMRTEIQRIQEELDVTTiyvTHDQTEAMTMADRIVIL 218
                                       44444455532599999999999999999999999999865444478888888888888775 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7   0.00026      0.18       2      20 ..      43      61 ..      42     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00026
                            AAA_33  2 vllvGlpGsGKstlaerll 20
                                      v++vG++G+GKst ++ ++
  gi|344210152|ref|YP_004786328.1| 43 VVVVGPSGCGKSTTLRMIA 61
                                      899**********999876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00073      0.51       2      46 ..      43      89 ..      42      97 .. 0.86
   2 ?   -0.3   0.1       1.2   8.6e+02      96     152 ..     163     223 ..     149     232 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00073
                                      EEEE--TTSSHHHHHHHHH..HHH...GGGEEEEEEEEE-------E CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvl..ellkssgvkvgGfyteevreggrrig 46
                                      v++ Gp+G GK+T ++ ++  e++ + ++ +gG ++++vr ++r i+
  gi|344210152|ref|YP_004786328.1| 43 VVVVGPSGCGKSTTLRMIAglETVTDGEIAIGGDVVNDVRPQDRNIA 89
                                      6899************996447899999************8888765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                                       H-EEEE--.-STTGGG-H.HHHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT-TT-EE CS
                          NTPase_1  96 adviviDE.iGkmElksk.kfkeaveevLk.sekpvlavihrrk.dlalveeirerkdvkv 152
                                       ++v+++DE   ++  k + +++++++++ +  ++  + v h ++    + ++i   +++++
  gi|344210152|ref|YP_004786328.1| 163 PEVFLMDEpLSNLDAKLRtQMRTEIQRIQEeLDVTTIYVTHDQTeAMTMADRIVILNQGEL 223
                                       5555555533444444331345555555555555556666665555555566655555555 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 ?   11.4   0.0    0.0003      0.21      20      39 ..      38      57 ..      25      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0003
                            AAA_29 20 dlkg.atlltGpsGsGKSTll 39
                                      + +g +++++GpsG GKST l
  gi|344210152|ref|YP_004786328.1| 38 E-DGeFVVVVGPSGCGKSTTL 57
                                      4.345899***********76 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   0.00032      0.22      18      41 ..      38      61 ..      28      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                          ATPase_2 18 epneiyfiYGpegsGKtaLlkeii 41
                                      e  e++++ Gp g+GK++ l+ i+
  gi|344210152|ref|YP_004786328.1| 38 EDGEFVVVVGPSGCGKSTTLRMIA 61
                                      567899*************99886 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00054      0.37      19      39 ..      40      60 ..      14      67 .. 0.80
   2 ?   -1.8   0.6       5.2   3.6e+03     173     173 ..     156     156 ..     111     207 .. 0.44

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00054
                            AAA_23 19 kgltlItGpNGaGKTTildAi 39
                                        +++++Gp G+GK+T l+ i
  gi|344210152|ref|YP_004786328.1| 40 GEFVVVVGPSGCGKSTTLRMI 60
                                      457899***********9987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.2
                            AAA_23 173 e 173
                                        
  gi|344210152|ref|YP_004786328.1| 156 G 156
                                       0 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   0.00043       0.3      18      47 ..      32      61 ..      28      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00043
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAis 47
                                       l++  e+ ++ +++Gp   GKst+lr i 
  gi|344210152|ref|YP_004786328.1| 32 DLSLAVEDGEFVVVVGPSGCGKSTTLRMIA 61
                                      4666777999****************9886 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0012       0.8      22      44 ..      38      61 ..      28     100 .. 0.84
   2 ?   -0.6   0.0       1.2   8.3e+02     323     365 ..     162     204 ..     143     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                            AAA_15 22 see.ltvliGkNnsGKSsileald 44
                                      ++  + v++G+ ++GKS+ l+++ 
  gi|344210152|ref|YP_004786328.1| 38 EDGeFVVVVGPSGCGKSTTLRMIA 61
                                      444599***************995 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       ++ ++l++EP  +L  ++ +++   ++++ ++ +  +i+ TH 
  gi|344210152|ref|YP_004786328.1| 162 DPEVFLMDEPLSNLDAKLRTQMRTEIQRIQEELDVTTIYVTHD 204
                                       6788999999999999999999999999999999999999996 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0     0.001      0.69       1      18 [.      43      60 ..      43      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.001
                      RNA_helicase  1 iwlyGpsgeGKStlakeL 18
                                      ++++Gpsg+GKSt+ + +
  gi|344210152|ref|YP_004786328.1| 43 VVVVGPSGCGKSTTLRMI 60
                                      689**********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); 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: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 2217.90
//
Query:       gi|344210153|ref|YP_004786329.1|  [L=266]
Description: creatinine amidohydrolase [Haloarcula hispanica ATCC 33960]
Scores for 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-62  208.7   0.4      1e-61  208.5   0.4    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 !  208.5   0.4   5.6e-66     1e-61       3     240 ..      16     257 ..      14     258 .. 0.93

  Alignments for each domain:
  == domain 1  score: 208.5 bits;  conditional E-value: 5.6e-66
                      Creatininase   3 ltwpeveea.lkeddvailPvGstEqHGphlplgtDtliaealaervaeklgak.alvlPtlpyGvseehlgfpGTi 77 
                                       +t+ +++ +  + ++v+++PvGs+EqHG hlp+ tDtl++ea+++ + e+l+   ++v+P+++ G s++hl+f GT+
  gi|344210153|ref|YP_004786329.1|  16 MTASQIRGVgEQPGSVLVIPVGSVEQHGNHLPVVTDTLLVEAMVDTAVERLDDVpVVVTPPIWSGFSPHHLSFGGTL 92 
                                       999******99999********************************999996447********************** PP

                      Creatininase  78 slspetliavlrdileslarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaae.a 153
                                       sl+ + l+a l+di+   +++Gf+ +++vngHggns++++ ++++++ ++da           +  +++++ a++  
  gi|344210153|ref|YP_004786329.1|  93 SLEFAHLRATLEDIAHAGIQNGFDAVLFVNGHGGNSSLIDAVVSTVGVDTDAE----------VLGTTYFHLASDrI 159
                                       **************************************************444..........44446777788888 PP

                      Creatininase 154 aeeseeee.gggHAgelEtSlmlalrpelVrmdraedpeeaklakeg..........vstaedaeelspsGvlGdps 219
                                       +e++++e+ g+ H+ge+EtSlmlalrp+lV   +++d+e+ +++             v ++++++e+s sG++G p+
  gi|344210153|ref|YP_004786329.1| 160 EELRTTETgGMAHGGEFETSLMLALRPDLVGDPEVRDGEPMDEHYRWggqdlldggnVAVYRSFDEYSTSGAIGTPK 236
                                       899999999****************************99987766669***************************** PP

                      Creatininase 220 kataekGealleaaveelael 240
                                       +atae Ge++   + +ela+l
  gi|344210153|ref|YP_004786329.1| 237 QATAETGERIRSVIGDELAAL 257
                                       **************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1649.30
//
Query:       gi|344210154|ref|YP_004786330.1|  [L=452]
Description: putative extracellular solute binding protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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  141.9   0.1    6.1e-41  141.4   0.1    1.1  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    6.5e-37  127.9   0.0    9.4e-37  127.3   0.0    1.1  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    1.6e-05   24.4   0.1       0.14   11.6   0.2    2.3  2  SBP_bac_6   Bacterial extracellular solute-binding protein
     0.0026   17.6   0.0     0.0061   16.3   0.0    1.6  1  SBP_bac_11  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.015   15.1   0.1      0.033   14.1   0.1    1.6  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


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 !  141.4   0.1   1.7e-44   6.1e-41       5     312 ..      75     366 ..      69     368 .. 0.92

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 1.7e-44
                                       HHHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHT CS
                         SBP_bac_1   5 tegaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkay 81 
                                       ++   +++   +afe eh +++Ve++sv +++ +q +  ++ +G +p Dv  +  +wi++l+ +++l+pld++++ +
  gi|344210154|ref|YP_004786330.1|  75 KQ--FFEENN-AAFEDEH-DVDVEFTSVTWDNARQTVNNRVDGGEAP-DVSRWPARWIPQLVGKDALEPLDDMMDGE 146
                                       44..555555.66*9976.**************************88.***************************** PP

                                       TECTTCCTEEEEHHHHTHHHHCE.EE...ES.EEEEE.EEEEEEETTTHHCTTGGG....SHBHHHHHHHHHHHHHH CS
                         SBP_bac_1  82 lapgvkdaadklsssvlpkilds.kv...ly.vPlya.argliYNkdlfekagldp....pwtWdelveaakklkek 148
                                        +++           +++++ ++  +   +y vP+ a +  l+YNkd+fe agldp      +W++ ++aa  ++++
  gi|344210154|ref|YP_004786330.1| 147 FGEQ-----------FYDGVAEGtMYngsHYgVPWAAsNKCLYYNKDVFETAGLDPedpsLDSWQDMLDAATQIRDS 212
                                       9888...........8888999767789********77*******************98889*************** PP

                                       CTCTHCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT.HHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHH CS
                         SBP_bac_1 149 gkkpiggarggsasgtayyfalalakslggkvfdkdgg.gldnpegvtaatylvklyavanltkelkgkgaenkdga 224
                                       + + ++    g+++ +++  ++++ +s g++++d++g+  +++ ++v+a+  +++l+    l+++ ++ ++++++ +
  gi|344210154|ref|YP_004786330.1| 213 DASVPALGLAGADAIETGSQYYHYHWSHGADLVDDEGMpVVNSSGAVDALSLYTDLH----LEHNVTQSSPLSSTRQ 285
                                       *********************************************************....7778************ PP

                                       HHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHH CS
                         SBP_bac_1 225 aalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaA 301
                                       + ++lfe+G+ +m i   +        +++  +a+   ++++++g+  +P g+ g ++++  ++lai+++s +++ A
  gi|344210154|ref|YP_004786330.1| 286 DIRQLFENGDLGMVIGHVY-------TGLNITAAKENGDVDFDYGIVQVPRGPEGRYSLFTIDTLAILSQSEHKDLA 355
                                       *************876644.......47777888888888888888888**************************** PP

                                       HHHHHHHTSHH CS
                         SBP_bac_1 302 kkFldfllspe 312
                                       +++++f++ +e
  gi|344210154|ref|YP_004786330.1| 356 RDLIRFYFDEE 366
                                       ******99876 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 !  127.3   0.0   2.6e-40   9.4e-37       4     274 ..      83     390 ..      82     396 .. 0.79

  Alignments for each domain:
  == domain 1  score: 127.3 bits;  conditional E-value: 2.6e-40
                                       HHHHHH-TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGSTTHHH...-HH.HHH CS
                         SBP_bac_8   4 kefekktgvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdldnldd...ltd.ala 76 
                                       ++fe++++v+v+++++ ++ + q++++ +  g+apd+   w+ + ++++l+ +++l++l+d  + +    + d +++
  gi|344210154|ref|YP_004786330.1|  83 AAFEDEHDVDVEFTSVTWDNARQTVNNRVDGGEAPDVS-RWP-ARWIPQLVGKDALEPLDDMMDGEFgeqFYDgVAE 157
                                       58*********************************864.666.68***************76333334565554777 PP

                                       TT--TS.----EEEEEEE-EEEEEHHHHHHS.......---BHHHHHHHHHHH..HHH-......SEG.G---G... CS
                         SBP_bac_8  77 avgydgklygvPyasetpyvliynkdlleka......edpktwdellaaakkl..kgkf......glp.dpasg... 135
                                       + +y+g +ygvP+a+++  +l+ynkd++e a       + ++w+++l+aa ++            gl+ ++a+    
  gi|344210154|ref|YP_004786330.1| 158 GTMYNGSHYGVPWAASN-KCLYYNKDVFETAgldpedPSLDSWQDMLDAATQIrdS--DasvpalGLAgADAIEtgs 231
                                       7799*************.8**********99999977888********88888440..2344544332123322112 PP

                                       GGGGGTHHETTEE---H.......HHH.HHHHHHHHHHH..HTT-EE....-S..--SSTTTTTSBSEEEE...-TT CS
                         SBP_bac_8 136 wlqaallakdgksldddg.....gkdglkealellkklk..dngkty....dtgadavsefanGevaftin...gsw 198
                                        ++ +++  +g++l dd      ++ g ++al l+++l+   n+++     +t+ d+ ++f nG+  ++i+      
  gi|344210154|ref|YP_004786330.1| 232 QYYHYHWS-HGADLVDDEgmpvvNSSGAVDALSLYTDLHleHNVTQSsplsSTRQDIRQLFENGDLGMVIGhvyTGL 307
                                       12335666.8888866666889999999*********99755554437787999****************6663456 PP

                                       HHHHHH-TTT...SEEEE.--..S--..EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S- CS
                         SBP_bac_8 199 diaaaqkagk...klgai.vp..kqg..sfaggkglavpknaknedlaAldFlkwltspenqaalaektgyipvnks 267
                                       +i+aa+++g+   ++g++ vp  ++g  s+  +++la++++++++dl A d+++++ ++e   +++++ g++pv  +
  gi|344210154|ref|YP_004786330.1| 308 NITAAKENGDvdfDYGIVqVPrgPEGrySLFTIDTLAILSQSEHKDL-ARDLIRFYFDEERRFQYSKQKGFLPVVEA 383
                                       78888877755347777777876556779999**************9.**************************999 PP

                                       TTTHHHH CS
                         SBP_bac_8 268 aalspev 274
                                       + +  ++
  gi|344210154|ref|YP_004786330.1| 384 VGERSYF 390
                                       8775444 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 !   11.6   0.2   3.9e-05      0.14      13      82 ..     125     204 ..     116     207 .. 0.83
   2 !   10.4   0.0   8.8e-05      0.31     180     223 ..     341     385 ..     336     403 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.9e-05
                         SBP_bac_6  13 dflekfieeglfqpldpanlpnvnkdfa...eeglkdpdgkyy.pygvgplvlavnkdrlkgrpv....P..ksWaD 79 
                                       +++ +++ ++ ++pld+    ++ ++f    +eg+  +  +y  p++ +  +l++nkd+++   +    P   sW+D
  gi|344210154|ref|YP_004786330.1| 125 RWIPQLVGKDALEPLDDMMDGEFGEQFYdgvAEGTMYNGSHYGvPWAASNKCLYYNKDVFETAGLdpedPslDSWQD 201
                                       78999999********6666666666666666999999777767*****************9999956659999*** PP

                         SBP_bac_6  80 Lld 82 
                                        ld
  gi|344210154|ref|YP_004786330.1| 202 MLD 204
                                       998 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 8.8e-05
                         SBP_bac_6 180 ifmlvkkg.kkkelakafidfllspevqailakaggvfPvvtnpa 223
                                       +++++ ++ ++k+la+++i f +++e + +++k+ g +Pvv++++
  gi|344210154|ref|YP_004786330.1| 341 DTLAILSQsEHKDLARDLIRFYFDEERRFQYSKQKGFLPVVEAVG 385
                                       5566666666*************************999*975544 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 !   16.3   0.0   1.7e-06    0.0061       1     214 [.      66     361 ..      66     368 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.7e-06
                                       .EEEE-SSTHHHHHHHHHHHHHHH---EEEEESSHHHHHHHH....HHH..-SEEEESSH.HHHHHHHHGGGGG... CS
                        SBP_bac_11   1 ltvaaagslaaalrelaaaFeahtgvkvevsaggsgklarqi....adgarpDvwipassawlellaaaglvqa... 70 
                                       lt  ++ ++++ ++e +aaFe +++v+ve++++   ++++++     +g++pDv       w+ +l+ ++++ +   
  gi|344210154|ref|YP_004786330.1|  66 LTMGVGDNIKQFFEENNAAFEDEHDVDVEFTSVTWDNARQTVnnrvDGGEAPDVSRWPA-RWIPQLVGKDALEPldd 141
                                       56678899***********************9999999996655548888****86553.6**************** PP

                                       .......................GG-EEEEEEEEEEEESTT-.......TT---..SHHHHHHSS--EEEE--T-TT CS
                        SBP_bac_11  71 .......................esavplassplviavpkgn.......pkkik..gwadLlkpglklavadPttsp 115
                                                                +vp a s  ++ ++k+        p++++  +w+d+l++ +++  +d +  +
  gi|344210154|ref|YP_004786330.1| 142 mmdgefgeqfydgvaegtmyngsHYGVPWAASNKCLYYNKDVfetagldPEDPSldSWQDMLDAATQIRDSDASVPA 218
                                       **************9999999999999999999999999999999988866443449*******9999999999999 PP

                                       TTHH.HHHHG..........GG--.....................HHHHHHHHHTEEEEESSH...HHHHHHHHTTT CS
                        SBP_bac_11 116 sGlaalalle..........aaga.....................qellkalekkvvklgess...rqlltaveage 158
                                        Gla   ++e           +ga                      +++  le +v+++++ s    ++ + +e+g+
  gi|344210154|ref|YP_004786330.1| 219 LGLAGADAIEtgsqyyhyhwSHGAdlvddegmpvvnssgavdalsLYTDLHLEHNVTQSSPLSstrQDIRQLFENGD 295
                                       99988888884443333333112133333333444443345554433333444444444333333344555566666 PP

                                       -SEEEEE....HHHHH.......HSTTSSEEE.E--TTT--....EEEEEEEE-TT--HHHHHHHHH CS
                        SBP_bac_11 159 adagivy....eseakaa.....engdkleav.ylpeglnl.dpldypaavlkkaakreaAraFlaf 214
                                         ++i+     ++ ++a+     +   +++ v + peg ++  ++d ++a+l+++ ++  Ar++++f
  gi|344210154|ref|YP_004786330.1| 296 LGMVIGHvytgLNITAAKengdvDFDYGIVQVpRGPEGRYSlFTID-TLAILSQSEHKDLARDLIRF 361
                                       6655544223322222221122222223333434455555555555.46677777777777777766 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 ?   14.1   0.1   9.1e-06     0.033       2      24 ..      14      35 ..      13      37 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.1e-06
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                      ++RR++L++ +A++ A a +gc+
  gi|344210154|ref|YP_004786330.1| 14 IDRRQLLQALGAGG-AIAIAGCS 35
                                      89******888888.55567765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 2560.21
//
Query:       gi|344210155|ref|YP_004786331.1|  [L=312]
Description: sugar ABC transporter permease [Haloarcula hispanica ATCC 33960]
Scores for complete 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   74.1  17.1    1.1e-20   74.1  15.9    1.5  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 ?   -2.4   0.0      0.19   3.3e+03      54      63 ..      34      43 ..      11      62 .. 0.55
   2 !   74.1  15.9   6.4e-25   1.1e-20       3     180 ..     103     305 ..     101     307 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.19
                      BPD_transp_1 54 lpviilllls 63
                                       p+++ ll  
  gi|344210155|ref|YP_004786331.1| 34 APAAVFLLAV 43
                                      2222222222 PP

  == domain 2  score: 74.1 bits;  conditional E-value: 6.4e-25
                      BPD_transp_1   3 llGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf.....................vilsilghlilpv 56 
                                       llG+l+a  l+   +++k++r+ + +++++P+ + a+++ ++                       il+    ++l+v
  gi|344210155|ref|YP_004786331.1| 103 LLGLLIAvhLKGDIRGRKFFRTAFLIPWGIPYAISAVVFRWIEhpqfgylnaillklgiieqgiGILGNPSIAWLGV 179
                                       7999***8888899********************999988777999999999999999***999999999999999* PP

                      BPD_transp_1  57 iillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgs 133
                                       +++ ++  +p++ +i+ a+l+s+p++l+eaa ++Ga +w+ fr+++lP+++++++   +l+ ++ +  + ++ ++++
  gi|344210155|ref|YP_004786331.1| 180 VVADIWIGTPFMAIIFLAGLQSIPQELYEAAAIDGAEKWHQFRYITLPQLKSVVLIATLLSTIWTFVSFDVIWTMTG 256
                                       ****************************************************************************9 PP

                      BPD_transp_1 134 wpGlgtllleailgydyseis..nggvlalviavlllnlvadilqrlld 180
                                       +++++++ + +i +y++ + +   g  +a+ ++ +l+++v+ i++  ++
  gi|344210155|ref|YP_004786331.1| 257 GGPISSTATLVIHIYQVGLQNgnLGRGAAYSVIGFLFLFVFAIIYLRIY 305
                                       999***************9999955555555555555555555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); 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:                         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: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1755.24
//
Query:       gi|344210156|ref|YP_004786332.1|  [L=281]
Description: ABC transporter permease [Haloarcula hispanica ATCC 33960]
Scores for 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   58.1  18.5      9e-16   58.1  18.5    1.8  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 ?   -0.2   0.4      0.04   7.2e+02      48      48 ..      74      74 ..      14     100 .. 0.46
   2 !   58.1  18.5     5e-20     9e-16       2     183 ..      94     274 ..      89     276 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.04
                      BPD_transp_1 48 i 48
                                      +
  gi|344210156|ref|YP_004786332.1| 74 W 74
                                      2 PP

  == domain 2  score: 58.1 bits;  conditional E-value: 5e-20
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrs 78 
                                       i++++ +a +  +++++ ++  + v++++ ++vl++ l+  ++ + +l ++ l+vi+ ++ +++p+++++ ++++++
  gi|344210156|ref|YP_004786332.1|  94 IPAAYSCA-RNDFVGKRTFLLAVLVVQMFAPVVLIVGLF-DVITQMGLFNTYLAVIVPAAAFTLPFNVWMLYGYFKT 168
                                       56666666.444455555554455555444444444444.33567788899************************** PP

                      BPD_transp_1  79 lpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG...lgtllleailgydyse 152
                                       +p  l+e ar++Gas  qi+ k+vlP+++p +++++ ++f ++++  +++++++++++   + + +++   + ++++
  gi|344210156|ref|YP_004786332.1| 169 IPVALEESARIDGASQLQILTKIVLPLTKPALVASVTYTFLYAWNRLLFVLTFLTDSAkynIPRGVFSMVGALQTDW 245
                                       *********************************************************99887777777777777777 PP

                      BPD_transp_1 153 isnggvlalviavlllnlvadilqrlldprv 183
                                        +  ++ + vi +++l++++ +l +++   +
  gi|344210156|ref|YP_004786332.1| 246 RM--MLTVSVIGIIPLLILFAFLEEYIVAGM 274
                                       77..888888888999999999888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1770.95
//
Query:       gi|344210157|ref|YP_004786333.1|  [L=383]
Description: hypothetical protein HAH_5216 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   13.1   0.0      0.091   12.5   0.0    1.2  1  DUF5036   Domain of unknown function (DUF5036)


Domain annotation for each model (and alignments):
>> DUF5036  Domain of unknown function (DUF5036)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.1e-06     0.091     105     171 ..     269     334 ..     241     346 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.1e-06
                           DUF5036 105 ykvyvvskivkeekdvGavvkfllvkPeedgLPaygstigtidlssyelgdevelelPkdvellksh 171
                                       +  yv+      e  vGa ++ l+ + + + LPay+st   + +++y   ++v+ ++P  v ll  h
  gi|344210157|ref|YP_004786333.1| 269 LGYYVGAPEPGREWVVGADLQALSNHVDYYCLPAYESTSEAV-IEAYDAVETVVDDVPLHVGLLPGH 334
                                       556666666677889***************************.****************99997666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 2520.65
//
Query:       gi|344210158|ref|YP_004786334.1|  [L=389]
Description: N-acylamino acid racemase [Haloarcula hispanica ATCC 33960]
Scores for 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-49  166.3   0.1      1e-48  165.8   0.1    1.2  1  MR_MLE_C  Enolase C-terminal domain-like
    1.7e-16   60.5   0.0    4.8e-16   59.0   0.0    1.7  2  MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N
  ------ inclusion threshold ------
      0.092   13.3   0.1        1.2    9.6   0.1    2.3  2  DHNA      Dihydroneopterin aldolase


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 !  165.8   0.1   1.7e-52     1e-48       6     218 ..     171     381 ..     166     383 .. 0.92

  Alignments for each domain:
  == domain 1  score: 165.8 bits;  conditional E-value: 1.7e-52
                                       HHHHHHHHT-SEEEEETSSSHHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGGT..ESEEESS CS
                          MR_MLE_C   6 arelvaeqgfravKlkvggddvaedvervravreavgpgddvdlmvDanqawdlatAirvareleeld..llwlEEP 80 
                                       are++++ gf+ +K k g+ d+++dver++a+ ++v  + ++++++D nq+w+l++A+rv+ +le+ +  l+++E+P
  gi|344210158|ref|YP_004786334.1| 171 AREALEA-GFTVLKTKAGR-DWRQDVERIKAMHDEV--DGQLEFRLDPNQGWTLDQAVRVGAMLEDAGiyLQYMEQP 243
                                       6666665.********777.5***************..5569**********************8866569****** PP

                                       SSTTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBS CS
                          MR_MLE_C  81 vppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHs 156
                                       ++  d+ ++la+lr ++ + pia +E+ y  + ++ l+eaga+d+  +d++ +gGi++ r+ aa+ e +gvp+ +H+
  gi|344210158|ref|YP_004786334.1| 244 IRV-DSHRSLARLR-QRlRQPIAPNEDTYISHNLQSLVEAGAMDVGVIDLTPAGGISGIRQQAAILEDAGVPFTHHC 318
                                       **9.78********.55688********************************************************* PP

                                       C.SSHHHHHHHHHHHHTTTTBEEEEEEGGGGHTSGCSBSSSSEEETTEEECTSSSBTSSEB-.H CS
                          MR_MLE_C 157 g.sgglglaaslhlaaaipnllileyfldaelleeelleeplevedGrvtvpdgpGlGveld.e 218
                                         ++g+ +aa lh  + ip++    ++++   +e+++ e p+ev+dG++ +p+gpGlG+ +d +
  gi|344210158|ref|YP_004786334.1| 319 AfDLGIRTAAILHAFTGIPGFSLPPDSTYYG-WEADVIEAPFEVSDGCLPAPEGPGLGISIDvD 381
                                       7358***************999999988876.*****************************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 !   59.0   0.0   8.1e-20   4.8e-16      14     117 .]      25     127 ..      13     127 .. 0.95
   2 ?   -2.8   0.1       1.2   7.2e+03      29      43 ..     287     301 ..     280     306 .. 0.78

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 8.1e-20
                                       CEEEETTEEEEEEEEEEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHHHHCSSCH CS
                          MR_MLE_N  14 rPvqlavttvqkqslvlvkietseGvvGigeatsvggraetikaelddhlapllvgkdaanisdlaqllkravlgnm 90 
                                        P+++  +  +  + vlv++ t+eG+ G+ge+     ++ + +++++d + p++ g+ + +i+ l++ +    +   
  gi|344210158|ref|YP_004786334.1|  25 GPYVTNHGKLHSMERVLVRVDTDEGISGWGEMRVFL-SPAATESIIEDGVGPMIEGQSPFEIERLRRQVFVEYTNVD 100
                                       4888999999999********************999.999******************************99***** PP

                                       HHHHHHHHHHHHHHHHHTTSBHHHHTT CS
                          MR_MLE_N  91 sAkaaidmAlwDlkakalnlpladLlG 117
                                       +  aa+++A wD+ +kal+ p+++LlG
  gi|344210158|ref|YP_004786334.1| 101 MFFAAVETACWDIVGKALDRPVYELLG 127
                                       **************************9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                                       EEEEEEECTTEEEEE CS
                          MR_MLE_N  29 vlvkietseGvvGig 43 
                                        +++++ ++G+ Gi 
  gi|344210158|ref|YP_004786334.1| 287 GVIDLTPAGGISGIR 301
                                       578999999999985 PP

>> DHNA  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.13   7.9e+02      16      37 ..     234     255 ..     223     278 .. 0.83
   2 ?    9.6   0.1   0.00021       1.2       5      25 ..     317     337 ..     315     344 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.13
                                       HHHHHHTT-EESTTTHHHHHHH CS
                              DHNA  16 alyHqfvGtPvseesaesleka 37 
                                        +y q++  P++ +s +sl++ 
  gi|344210158|ref|YP_004786334.1| 234 GIYLQYMEQPIRVDSHRSLARL 255
                                       5899*******99999999875 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00021
                                       HHHHHHHHHHHHHHHHHTT-E CS
                              DHNA   5 rAvFEagiklgalyHqfvGtP 25 
                                       + +F+ gi+ +a+ H f+G+P
  gi|344210158|ref|YP_004786334.1| 317 HCAFDLGIRTAAILHAFTGIP 337
                                       578*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2562.83
//
Query:       gi|344210159|ref|YP_004786335.1|  [L=285]
Description: 3-oxoacyl-ACP reductase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-62  210.1   0.2    3.9e-62  209.9   0.2    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    3.1e-49  167.1   0.3    3.8e-49  166.8   0.3    1.1  1  adh_short        short chain dehydrogenase
    6.4e-12   45.8   0.2    9.7e-12   45.2   0.2    1.4  1  KR               KR domain
    3.6e-05   23.3   0.2     0.0002   20.9   0.2    2.1  2  Epimerase        NAD dependent epimerase/dehydratase family
     0.0016   18.4   0.6     0.0025   17.7   0.4    1.4  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
      0.028   14.8   1.9        0.6   10.5   0.2    2.2  2  EccE             Putative type VII ESX secretion system trans
      0.049   12.7   0.0      0.081   12.0   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
      0.086   12.7   0.3       0.23   11.3   0.0    1.7  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.12   11.5   0.0       0.21   10.7   0.0    1.4  1  Polysacc_synt_2  Polysaccharide biosynthesis 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 !  209.9   0.2     2e-65   3.9e-62       1     234 []      20     264 ..      20     264 .. 0.90

  Alignments for each domain:
  == domain 1  score: 209.9 bits;  conditional E-value: 2e-65
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilv 74 
                                       Ga +gIGr+iA ++ae+G +vv++ +  e+ k+ ++el++ ++ +v  +ecDVtd+++v++lv+++ e+fg + +lv
  gi|344210159|ref|YP_004786335.1|  20 GASRGIGREIAARFAEAGGDVVVCSRTYEDvKAVATELTDTHDGRVvpVECDVTDRAAVQDLVDTTIEEFGDIRVLV 96 
                                       999**************************9899999999999988559***************************** PP

                                       E-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHH CS
                      adh_short_C2  75 nnagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaale 149
                                       nnag a++  + ++ ++++ f+ +ld nl+s fll+k++lp ++++g gsi+++ sv +  ++ + + y+ aK +l 
  gi|344210159|ref|YP_004786335.1|  97 NNAGGADESANLLHRCDEDTFESMLDLNLKSQFLLSKEVLPaMVAAGgGSIIHMGSVNGLFGI-GLSGYSEAKSGLL 172
                                       ********77778889*************************5444447*********986666.6689********* PP

                                       HHHHHHHHHHGGGTEEEEEEEE--BHCTG.GGGSTT......HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGG CS
                      adh_short_C2 150 altrylAvelgpkgiRvNavspgpikTla.asgikg......fdelleelearaplgrlgtpeevaeaalfLasdea 219
                                       al+r++A+++g++giR N++s+  i+T    +++++      + + +e++ +++plgr+gtp+eva+++lfLasd++
  gi|344210159|ref|YP_004786335.1| 173 ALSRNIAAHYGQHGIRSNVISAATIETANrRAEMENteertgETSARERWLDQYPLGRFGTPREVADTTLFLASDLS 249
                                       ***************************7643344442223225569999**************************** PP

                                       TT--SEEEEESTTGG CS
                      adh_short_C2 220 syitGqtlvvDgGlt 234
                                       s++tG++lv DgGlt
  gi|344210159|ref|YP_004786335.1| 250 SFVTGENLVLDGGLT 264
                                       *************97 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.8   0.3   1.9e-52   3.8e-49       3     192 ..      16     207 ..      14     210 .. 0.94

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 1.9e-52
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkl 78 
                                       ++vtGas+GIGr+ia ++a++G +vvv++r+ e++++va+el ++   +++++++Dvtdr++v++lv++ ++++g +
  gi|344210159|ref|YP_004786335.1|  16 AIVTGASRGIGREIAARFAEAGGDVVVCSRTYEDVKAVATELTDThDGRVVPVECDVTDRAAVQDLVDTTIEEFGDI 92 
                                       89*******************************************999***************************** PP

                                       SEEEE---S..S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHH CS
                         adh_short  79 dvLvnNAGi..tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsK 153
                                        vLvnNAG   +  +  ++ +e+++e+++++Nl++ fll+++vlpam+++ +G+I+ ++Sv+g+ + +g++ Ys +K
  gi|344210159|ref|YP_004786335.1|  93 RVLVNNAGGadESANLLHRCDEDTFESMLDLNLKSQFLLSKEVLPAMVAAGGGSIIHMGSVNGLFG-IGLSGYSEAK 168
                                       *********866666667777777***************************************776.799******* PP

                                       HHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                         adh_short 154 aavagltrslakelaptgirvnavaPGlvdTdmakelre 192
                                        ++ +l+r++a  + ++gir n++  + ++T+ ++++ e
  gi|344210159|ref|YP_004786335.1| 169 SGLLALSRNIAAHYGQHGIRSNVISAATIETANRRAEME 207
                                       *******************************99887665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.2   4.9e-15   9.7e-12       4     120 ..      17     132 ..      16     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 4.9e-15
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal.gaevevvaaDvsdkdavealleeikaee 79 
                                       ++tG+  g+G+e+a   ae g   +v++sR+    ed ka  +el+++ + +v  v++Dv+d++av+ l+++  +e+
  gi|344210159|ref|YP_004786335.1|  17 IVTGASRGIGREIAARFAEAGG-DVVVCSRT---YEDVKAVATELTDThDGRVVPVECDVTDRAAVQDLVDTTIEEF 89 
                                       79*****************996.6899****...56778888999886589************************** PP

                                       S---EEEE------..---TTT--HHHHHHHHTTTTHHHHHHH CS
                                KR  80 ppikGvihaAgvlr..dklleemtaedleqvlapKvkGawnLh 120
                                       + i+  ++ Ag ++   +ll +++++++e++l   +k    L 
  gi|344210159|ref|YP_004786335.1|  90 GDIRVLVNNAGGADesANLLHRCDEDTFESMLDLNLKSQFLLS 132
                                       ***********998445789*********99987776666665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.2     1e-07    0.0002       2      62 ..      17      84 ..      16     154 .. 0.88
   2 ?    0.2   0.0      0.21   4.2e+02     161     197 ..     170     203 ..     161     258 .. 0.60

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1e-07
                                      EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHHH CS
                         Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrsalerlfke 62
                                      +VtGa+  iG+ ++ +++e+g +v++ +r  ++ +  + e +         ve+d+tdr+a+++l+++
  gi|344210159|ref|YP_004786335.1| 17 IVTGASRGIGREIAARFAEAGGDVVVCSRTYEDVKAVATELTdthdgrvVPVECDVTDRAAVQDLVDT 84
                                      8**************************999776666555544899**9999************99985 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.21
                                       T-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTS CS
                         Epimerase 161 glnaiilrlfnlyGprngegevsrvipalirkilegk 197
                                       gl a++ ++  +yG +   g +s+vi+a+    ++++
  gi|344210159|ref|YP_004786335.1| 170 GLLALSRNIAAHYGQH---GIRSNVISAATIETANRR 203
                                       5555666666677777...556666665544444433 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 !   17.7   0.4   1.3e-06    0.0025       1      97 [.      20     151 ..      20     160 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-06
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH......CTTTCEEEE--TT-CCHHHHHHT.......T-SEE CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaele......aeeglevvegdvtdvedlaealk.......gadaV 64 
                                       GA+ ++Gr+++++ +++g  +v++  R+ e++++++      ++ ++  ve dvtd +++++ ++       ++ + 
  gi|344210159|ref|YP_004786335.1|  20 GASRGIGREIAARFAEAG-GDVVVCSRTYEDVKAVAteltdtHDGRVVPVECDVTDRAAVQDLVDttieefgDIRVL 95 
                                       9****************6.79*******98887554334454458999************99998777777666666 PP

                                       EES---TCC........HHHH...............HHHHHHHHHHCT--EEEEEE CS
                    NAD_binding_10  65 vsalggggk........deeg...............aknivdaakeagvkRfvlvs 97 
                                       v ++gg ++        de++                k ++ a+ +ag   ++ ++
  gi|344210159|ref|YP_004786335.1|  96 VNNAGGADEsanllhrcDEDTfesmldlnlksqfllSKEVLPAMVAAGGGSIIHMG 151
                                       66666655545554444333366667777777777777777777777766666665 PP

>> EccE  Putative type VII ESX secretion system translocon, EccE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.039        77      39      74 ..      25      62 ..      10      88 .. 0.79
   2 ?   10.5   0.2    0.0003       0.6      32      84 ..     167     222 ..     162     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.039
                              EccE 39 aarRlakaLreqGirarvlea..eeldaalaalavgla 74
                                        r +a++ +e+G +++v++   e+++a+++ l++ ++
  gi|344210159|ref|YP_004786335.1| 25 IGREIAARFAEAGGDVVVCSRtyEDVKAVATELTDTHD 62
                                      56889**************9877888888888777665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0003
                              EccE  32 aaraaaaaarRlakaLreqGirarvleaeeldaalaalavglaaapa...dvreew 84 
                                       a+  + a +r +a++  ++Gir +v +a+ +++a +++  +++ +++   ++re+w
  gi|344210159|ref|YP_004786335.1| 167 AKSGLLALSRNIAAHYGQHGIRSNVISAATIETANRRAEMENTEERTgetSARERW 222
                                       556678999**************************999988855554455555555 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   0.0   4.1e-05     0.081       4      49 ..      17      84 ..      14     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.1e-05
                                      EEESTTSHHHHHHHHHCTTTSEEEEEE-TT......................T--TTSHHHHHHHHHH CS
                     RmlD_sub_bind  4 lvtGanGqlGseLakqlaeeglevlaltre......................eldltdaeavaellke 49
                                      +vtGa+  +G+e+a+++ae+g +v+ ++r+                      e+d+td++av++l++ 
  gi|344210159|ref|YP_004786335.1| 17 IVTGASRGIGREIAARFAEAGGDVVVCSRTyedvkavateltdthdgrvvpvECDVTDRAAVQDLVDT 84
                                      79**************************9999999999999999999999999999999999999876 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 ?   11.3   0.0   0.00011      0.23      10      68 ..      25      83 ..      17      98 .. 0.82
   2 ?   -1.9   0.0       1.3   2.6e+03      12      47 ..     176     211 ..     173     224 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                      CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEE CS
                           3HCDH_N 10 mGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalaris 68
                                      +G++iaa fa+ag +Vv++ ++ e +++++ +++++ +  v   +++  +++a+ + + 
  gi|344210159|ref|YP_004786335.1| 25 IGREIAARFAEAGGDVVVCSRTYEDVKAVATELTDTHDGRVVPVECDVTDRAAVQDLVD 83
                                      8*******************************999988887777777666666666555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                                       HHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHH CS
                           3HCDH_N  12 agiaavfasagleVvlvdiseealekalekieksle 47 
                                       + iaa   ++g++ +++  ++   ++ ++++e++ e
  gi|344210159|ref|YP_004786335.1| 176 RNIAAHYGQHGIRSNVISAATIETANRRAEMENTEE 211
                                       578888888888888877766666666666555433 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00011      0.21       2      74 ..      17      83 ..      16      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                                      EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT CS
                   Polysacc_synt_2  2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekale 74
                                      +vtGa+  iG+e+  ++++     +++ +r+   + ++++el+++++      ++vpv +dv+d++ ++++++
  gi|344210159|ref|YP_004786335.1| 17 IVTGASRGIGREIAARFAEAG-GDVVVCSRTYEDVKAVATELTDTHDG-----RVVPVECDVTDRAAVQDLVD 83
                                      69**************99876.6788999999999******9655554.....557899*********99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1960.75
//
Query:       gi|344210160|ref|YP_004786336.1|  [L=124]
Description: translation initiation inhibitor [Haloarcula hispanica ATCC 33960]
Scores for 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-41  139.2   0.0    6.9e-41  139.0   0.0    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 !  139.0   0.0   3.9e-45   6.9e-41       2     120 ..       7     123 ..       6     124 .] 0.98

  Alignments for each domain:
  == domain 1  score: 139.0 bits;  conditional E-value: 3.9e-45
                                       TTSTTTSSS-BSEEEETTEEEEEEE-SB-TTTSCB.-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEESSGGG CS
                     Ribonuc_L-PSP   2 eaapaaaapYsqavkagnlvyvsGqlpldpetgelvegdveeqtrqalenlkavLaaagaslsdvVkvtvFladied 78 
                                       ++ap++++pYsq++ +g+ +yvsGq p+dp+tge+++g+++eqtr++l+n+ avL+a +asl+dvVk+tvF++d+  
  gi|344210160|ref|YP_004786336.1|   7 DDAPDSIGPYSQGIASGDRIYVSGQGPVDPDTGEVIQGTPAEQTRRTLRNVAAVLDAGDASLDDVVKATVFVKDMRY 83 
                                       689************************************************************************** PP

                                       HHHHHHHHHHHSSSSTS--EEEEEE-SBSGGG-SEEEEEEEE CS
                     Ribonuc_L-PSP  79 faevnevyaeafdelkeaParsaveVaaLpkgakvEIeaiav 120
                                       + evnevy+e+++ ++  ParsaveV +Lp +++vEIe+ia+
  gi|344210160|ref|YP_004786336.1|  84 YDEVNEVYGELMSPPY--PARSAVEVVKLPVDIDVEIEVIAE 123
                                       ***************7..**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 814.34
//
Query:       gi|344210161|ref|YP_004786337.1|  [L=207]
Description: phosphoserine phosphatase [Haloarcula hispanica ATCC 33960]
Scores for complete 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   41.9   0.2    2.1e-10   41.3   0.2    1.2  1  HAD        haloacid dehalogenase-like hydrolase
    3.7e-06   27.4   0.3     0.0004   20.7   0.3    2.2  1  Hydrolase  haloacid dehalogenase-like hydrolase
      4e-05   23.8   0.5     0.0036   17.4   0.5    2.9  1  HAD_2      Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.081   12.4   0.0       0.12   11.8   0.0    1.3  1  UMPH-1     Pyrimidine 5'-nucleotidase (UMPH-1)


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 !   41.3   0.2   4.7e-14   2.1e-10       3     186 ..       2     164 ..       1     165 [. 0.74

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 4.7e-14
                               HAD   3 fDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfvae 79 
                                       fD+DgTL+++  +++ll+ l+++ +    ++++++   ++    +   ++g+  +++a   + + +++ ++ r+v  
  gi|344210161|ref|YP_004786337.1|   2 FDLDGTLTRQRGGFELLHTLYGTTPAA-DTLMERFEAGQI---TFAEWCRGAVDVWRA--NDITRADITRATRAV-- 70 
                                       9*********99999999677765544.556666655555...344445555556654..555566666666666.. PP

                               HAD  80 virpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.rltgelglegkpvrgegkv 155
                                         +pk    ga++ll++ ++  +r+ ++S+g   l+  +  ++ +  v ++ l+++d r++g   + g++ +g    
  gi|344210161|ref|YP_004786337.1|  71 --KPK---AGAVDLLNHLQHTDIRFGILSAGVANLATQFE-QYEPAFVRGNWLRFEDgRISGIDVGVGPDQKG---- 137
                                       ..666...5*******7778888****************9.88888889998888888888888888888888.... PP

                               HAD 156 aalrewlaaegegidleevvayGDspsDlpl 186
                                         lre +  + ++    ++ ++GDs++D ++
  gi|344210161|ref|YP_004786337.1| 138 ELLRE-IRIKQNPS---SITYIGDSHTDTEA 164
                                       99999.44444443...499********986 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.3   8.9e-08    0.0004      72     210 .]      48     169 ..       1     169 [. 0.60

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 8.9e-08
                                       THHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHH.HTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  72 gkpewltaldippdlgaaigsaqsqgrtvallqaralavftia.dplkvkpeaaeavasLkaagievvlltgdnpet 147
                                       g ++ ++a+                        +  +a++t a    k+k +a++++++L+   i+ ++l+ +  + 
  gi|344210161|ref|YP_004786337.1|  48 GAVDVWRAN------------------------DITRADITRAtRAVKPKAGAVDLLNHLQHTDIRFGILSAGVANL 100
                                       333333333........................3334444444355569999*******************887765 PP

                                       HHHHHHHTT........GGGESEEEEHHCES....STTTSHHHHHHHHHHHT..STGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxx........xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 148 aeraanqlG........ddyfdaviasdiet....vakpspegkvaaireLq..gkpeevamVGDgvnDaaalaaAg 210
                                       a    +q+          ++ d+              ++ p++k +++re++   +p+ +  +GD+ +D +a+ +A+
  gi|344210161|ref|YP_004786337.1| 101 AT-QFEQYEpafvrgnwLRFEDG-------RisgiDVGVGPDQKGELLREIRikQNPSSITYIGDSHTDTEAFVEAD 169
                                       55.34444433443232222233.......2444566689***********94455*****************9997 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.5   8.1e-07    0.0036      71     174 ..      64     171 ..       1     174 [. 0.71

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.1e-07
                             HAD_2  71 eekkkkevkpydgvkelLeeLkeagyklgivTsksreaveek......leqlgiesyFdvivtsedvekkKPdpevi 141
                                       ++  +  vkp  g+ +lL+ L++ +++ gi + + ++ ++++      + + ++ ++ d  +++ dv+   Pd++  
  gi|344210161|ref|YP_004786337.1|  64 TRATR-AVKPKAGAVDLLNHLQHTDIRFGILSAGVANLATQFeqyepaFVRGNWLRFEDGRISGIDVGVG-PDQKGE 138
                                       33444.89************************99665444331111114456788899999*******99.888876 PP

                             HAD_2 142 ekaleklklkkeeviyvGDsptDieaakkagik 174
                                       +    + k +++++ y+GDs+tD ea  +a + 
  gi|344210161|ref|YP_004786337.1| 139 LLREIRIKQNPSSITYIGDSHTDTEAFVEADTA 171
                                       666667788999************998777665 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 ?   11.8   0.0   2.7e-05      0.12      60     122 ..      43     103 ..      25     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.7e-05
                            UMPH-1  60 veWwskshaLlieqklkkeeiaevvkeskialrdgveelfekleklnvPvlifsaGlgdvlee 122
                                        eW   + ++   + +++ +i+   + +k   + g+ +l+++l+++++ + i saG++++  +
  gi|344210161|ref|YP_004786337.1|  43 AEWCRGAVDVWRANDITRADITRATRAVK--PKAGAVDLLNHLQHTDIRFGILSAGVANLATQ 103
                                       68999999999999999999999888766..589***********************997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1434.20
//
Query:       gi|344210162|ref|YP_004786338.1|  [L=310]
Description: DMT(drug/metabolite transporter) superfamily permease [Haloarcula hispanica ATCC 33960]
Scores for 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-33  113.7  34.7    1.8e-16   60.6  19.6    2.0  2  EamA       EamA-like transporter family
  ------ inclusion threshold ------
      0.012   15.6   1.0      0.012   15.6   1.0    4.0  5  RseC_MucC  Positive regulator of sigma(E), RseC/MucC


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 !   59.2   7.1   5.1e-20   4.5e-16       7     135 ..      10     139 ..       6     140 .. 0.95
   2 !   60.6  19.6     2e-20   1.8e-16       2     133 ..     152     286 ..     151     288 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 5.1e-20
                              EamA   7 allaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllff 83 
                                       +ll a +w+++f++++++l++++p+ +++ rf ia++ll++ ++++++  +  ++ d+ ++++ g+l + + ++++f
  gi|344210162|ref|YP_004786338.1|  10 FLLLAAIWGTAFMATDVGLADLPPVPFAAARFDIASVLLFAALAVTGSLERPQTRDDYVYVVVGGALMIGVHHVFLF 86 
                                       4677779******************************************98888888******************** PP

                              EamA  84 yalkktsasnaslitslePvftlilsvlll.gekltlkqllgivlillGvlli 135
                                       +++++++ ++a++++ l+Pv+t  l  l     ++t  + +g+vl+++Gv++i
  gi|344210162|ref|YP_004786338.1|  87 TGQQYVTGAVAAVLLGLVPVVTPALTKLASsDDTFTANTGVGVVLGFVGVIVI 139
                                       ***************************999899******************98 PP

  == domain 2  score: 60.6 bits;  conditional E-value: 2e-20
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagill.liiallkegkl..aklslkdwllllllgllgt 75 
                                       +gi l++++al +ai +v++  ++ ++s l++ ++ + i++++l + +++l ++++  a+++l+++++ll+l+++++
  gi|344210162|ref|YP_004786338.1| 152 IGIALVFASALAFAIPAVVTHDTSPSMSFLATQAWLMAIGAVVLhVTVLALPGQSFadASWTLSAFAALLYLAVVAG 228
                                       79******************************************64445555555589******************* PP

                              EamA  76 vlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvl 133
                                       + +fll+f +l  +++ + s+i +++P+f+++ ++l+l +++tl ++ g+++il+G +
  gi|344210162|ref|YP_004786338.1| 229 IGGFLLYFRLLDQLGPIEMSFIEYVIPLFAALAGWLVLDQQVTLATVGGFACILMGFI 286
                                       *******************************************************975 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 ?   -1.0   0.3      0.18   1.6e+03      82     107 ..      80     104 ..      66     124 .. 0.49
   2 ?   -0.9   0.5      0.17   1.5e+03      77      77 ..     108     108 ..      78     143 .. 0.47
   3 ?    1.3   2.4     0.035   3.2e+02      63     107 ..     156     199 ..     152     206 .. 0.82
   4 ?   -0.9   0.4      0.16   1.5e+03      93     108 ..     221     236 ..     196     244 .. 0.52
   5 ?   15.6   1.0   1.3e-06     0.012      65     126 ..     246     303 ..     239     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.18
                         RseC_MucC  82 allgsallgssellaalgallglvlg 107
                                       +  + ++ ++++ ++ ++a ++l l 
  gi|344210162|ref|YP_004786338.1|  80 VHHVFLF-TGQQYVTGAVAAVLLGLV 104
                                       3333333.233333333333333333 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.17
                         RseC_MucC  77 l 77 
                                       +
  gi|344210162|ref|YP_004786338.1| 108 T 108
                                       2 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.035
                         RseC_MucC  63 llkaallvYllPllllilgallgsallgssellaalgallglvlg 107
                                       l+ a++l++++P ++   +   +s+l +++ +l a+ga+++ v  
  gi|344210162|ref|YP_004786338.1| 156 LVFASALAFAIPAVVTHDTSPSMSFL-ATQAWLMAIGAVVLHVTV 199
                                       78899***********9999999999.578888888887766554 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.16
                         RseC_MucC  93 ellaalgallglvlgf 108
                                         la+++++ g++l+f
  gi|344210162|ref|YP_004786338.1| 221 LYLAVVAGIGGFLLYF 236
                                       2334444444444444 PP

  == domain 5  score: 15.6 bits;  conditional E-value: 1.3e-06
                         RseC_MucC  65 kaallvYllPllllilgallgsallgssellaalgallglvlgflivrllskrlkkkskfqp 126
                                       + +++ Y++Pl++ ++g l+ ++ +    +la +g+++++++gf+ +++ + r++ ++ ++p
  gi|344210162|ref|YP_004786338.1| 246 EMSFIEYVIPLFAALAGWLVLDQQV----TLATVGGFACILMGFIAAKWATLRAELRRVVEP 303
                                       678999***********99999885....9999***************99988777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2110.97
//
Query:       gi|344210163|ref|YP_004786339.1|  [L=434]
Description: proton/sodium-glutamate symport protein [Haloarcula hispanica ATCC 33960]
Scores for 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-113  377.7  37.4   7.2e-113  377.5  37.4    1.0  1  SDF       Sodium:dicarboxylate symporter family


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 !  377.5  37.4    4e-117  7.2e-113       1     390 []      17     408 ..      17     408 .. 0.98

  Alignments for each domain:
  == domain 1  score: 377.5 bits;  conditional E-value: 4e-117
                               SDF   1 LllqiliglvlGlviGllelvkelaalisplgdlfinllkmlivPlvfasiisgiaslgdakklgklglktllyfll 77 
                                       L+++i+++++lG+ +G+   ++e +a+++p+gdlf++ll+ml++P++++++ +gi +l+ ++klg++g+ t++++ l
  gi|344210163|ref|YP_004786339.1|  17 LIWRIFVAFILGAGAGI--AFGEQMAVVRPVGDLFLRLLNMLVIPIIVFTLLTGIRQLS-PAKLGRIGGATVGLYAL 90 
                                       799**************..***************************************6.***************** PP

                               SDF  78 ttliAaiiglilalllkpgselaleassakeaekketdslldlilslipsnifealaegnvlavivfailfGialaa 154
                                       tt++A iigl++a++l+pg   +  +    ea++k+ +slld++l+++p+n+++alaegn+la ++f i+fGial+ 
  gi|344210163|ref|YP_004786339.1|  91 TTTLAGIIGLAVANVLQPG---RGLEFGGGEAQSKAPPSLLDVVLGIVPNNPVAALAEGNLLATVFFVIVFGIALTY 164
                                       *******************...888888999999999**************************************** PP

                               SDF 155 lgekg.......epllkffeslnevvmkvvkivmklaPigvfaliaslvaskglgalsslakflltvylglaihlli 224
                                       ++ ++       +++++ fe  +e+++ +v+ v+++  +gvfal+as ++++g+g +ssl+ ++l+v+++++ih+ +
  gi|344210163|ref|YP_004786339.1| 165 VRSQQdaladsvDSVFEAFEVGAEAMFVIVRGVLEFGVLGVFALMASGIGTEGIGLFSSLGELVLAVTIAIVIHIGF 241
                                       *999999**99999*************************************************************99 PP

                               SDF 225 vlpllll.vltkknplkflkkilpalltAfsTaSSaAtLPvtlecaeknlgvsesiasfvlPlGatinmdGtalyea 300
                                        +++ll+ v++ ++p++fl+++ +a++tAf+T+SS++tLPvt+++a + l++ e+++sf+lP+Gat nmdG+a+ +a
  gi|344210163|ref|YP_004786339.1| 242 TYLVLLMgVVADVSPIAFLSGAKDAMVTAFATRSSSGTLPVTMRNADEDLQIAERVYSFTLPVGATANMDGAAIRQA 318
                                       998665438999***************************************************************** PP

                               SDF 301 vaaifiaqlfgvelslgqllllvlvatlasiGaagvPgaglvalllvlsalglpvegialilaidrllDmfrTavNv 377
                                       v+++f+a+++g +l l++++ +++va+l+siG+agvPgag+v+l+++l+++glp+e++++++++d++l +++T+ Nv
  gi|344210163|ref|YP_004786339.1| 319 VTVMFAANVVGQPLVLTEQVFVLIVAVLISIGTAGVPGAGIVMLTVILTQVGLPLEVVGFVAGVDPILGRIATMNNV 395
                                       ***************************************************************************** PP

                               SDF 378 tGdavaalivakl 390
                                       tGd++++++v k+
  gi|344210163|ref|YP_004786339.1| 396 TGDLAVSTVVGKW 408
                                       **********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); 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:                         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 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3027.37
//
Query:       gi|344210164|ref|YP_004786340.1|  [L=287]
Description: serine acetyltransferase [Haloarcula hispanica ATCC 33960]
Scores for complete 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   42.9   3.5    8.4e-07   28.5   2.3    2.6  2  Hexapep    Bacterial transferase hexapeptide (six repeats)
      8e-05   23.0   0.0    0.00015   22.1   0.0    1.3  1  SATase_N   Serine acetyltransferase, N-terminal
     0.0031   17.2   1.2     0.0031   17.2   1.2    2.4  2  Hexapep_2  Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.17   11.9   0.0    1.2  1  DUF1996    Domain of unknown function (DUF1996)


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 !   13.2   0.0   1.2e-05     0.056       2      35 ..     174     209 ..     170     210 .. 0.88
   2 !   28.5   2.3   1.9e-10   8.4e-07       4      35 ..     233     264 ..     230     265 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                                       EEEETTEEE-T..TEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgp..faviggnVkIGdnvkIgagvvig 35 
                                       + IG+  +I++  ++vig+ +++G+ v++   v++g
  gi|344210164|ref|YP_004786340.1| 174 AEIGDYFFIDHgtGVVIGETTTVGEWVRLYQDVTLG 209
                                       78999999999***************9998888776 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 1.9e-10
                                       EETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       IG++v+Ig++++++g +++Gd+v Iga++ ++
  gi|344210164|ref|YP_004786340.1| 233 IGDHVVIGAGTKVLGAITVGDHVSIGANSWVT 264
                                       9***************************9886 PP

>> SATase_N  Serine acetyltransferase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   3.4e-08   0.00015      57     103 ..      91     137 ..      86     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.4e-08
                                       HHHHHHHHH-THHHHHHHHHHHHHHHH-TT---THHHHHH-HHHHHH CS
                          SATase_N  57 elfeealeadpeiveaaraDlkAvlerDpAcksylepllyfKGFhAl 103
                                       e+++ ++++ p i++++++D++A ++ DpA+k+y+e++  + GF A+
  gi|344210164|ref|YP_004786340.1|  91 ETVDAVINRLPAIRTRLKRDVEAAFKGDPAAKTYMEIIRSYPGFMAI 137
                                       6788899999***********************************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   0.6      0.17   7.8e+02      17      21 ..     187     191 ..     166     210 .. 0.65
   2 !   17.2   1.2   6.8e-07    0.0031       4      33 ..     233     264 ..     232     265 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.17
                                       SEEE- CS
                         Hexapep_2  17 GvslG 21 
                                       Gv +G
  gi|344210164|ref|YP_004786340.1| 187 GVVIG 191
                                       33333 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 6.8e-07
                                       E-TT-EE-TT-EE.S.EEE-TT-EE-TT-EE- CS
                         Hexapep_2   4 IGdnCliGanagi.G.vslGdncvvgaGvvit 33 
                                       IGd ++iGa   + G +++Gd + +ga++ +t
  gi|344210164|ref|YP_004786340.1| 233 IGDHVVIGAGTKVlGaITVGDHVSIGANSWVT 264
                                       9***********8899************9988 PP

>> DUF1996  Domain of unknown function (DUF1996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.8e-05      0.17     117     158 ..      18      59 ..       5      68 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-05
                           DUF1996 117 eseekeeaeeetkelpkktkkkcasglraeilfpsCwdgknl 158
                                       + +e++ +++++ e+p++++++ +  +  +++fp+Cw+  +l
  gi|344210164|ref|YP_004786340.1|  18 QADEEPFPTQTQMEFPRREHRRPEVDILKRLFFPTCWNAAEL 59 
                                       34444445677999**88766667799***********9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2089.12
//
Query:       gi|344210165|ref|YP_004786341.1|  [L=66]
Description: hypothetical protein HAH_5224 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   14.0   1.8       0.21   11.8   0.2    2.2  2  zf-RING_7   C4-type zinc ribbon domain
       0.18   12.1   1.0       0.23   11.8   0.1    1.5  2  DUF3268     zinc-finger-containing domain


Domain annotation for each model (and alignments):
>> 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 ?    1.8   0.1     0.032   2.8e+02       2      29 ..       5      36 ..       4      38 .. 0.66
   2 ?   11.8   0.2   2.3e-05      0.21      21      30 ..      51      61 ..      41      61 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.032
                                      ETTT--B--CCHHHHH..CCS..TB-EE-TTT CS
                         zf-RING_7  2 CgGChmelppqvlsel..rag..devvtCpeC 29
                                      C+ Ch  ++p ++  +  r +   ev   ++C
  gi|344210165|ref|YP_004786341.1|  5 CYFCHGIVSPPEEGHIwlREHdsHEVYMHEQC 36
                                      77788777777766665544444677777777 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.3e-05
                                      TB.-EE-TTT- CS
                         zf-RING_7 21 de.vvtCpeCG 30
                                      +e ++tCpeCG
  gi|344210165|ref|YP_004786341.1| 51 GElLITCPECG 61
                                      3337******9 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.5e-05      0.23       4      53 ..       4      53 ..       1      56 [. 0.93
   2 ?   -1.1   0.1      0.26   2.3e+03       4      10 ..      56      62 ..      53      65 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.5e-05
                           DUF3268  4 rCpyCGekvilvsaseiYkerskgkllylCpkCdayvgvhkgtkiplGtl 53
                                       C +C + v   ++ +i+  ++  + +y+ ++C +   v +g + p G+l
  gi|344210165|ref|YP_004786341.1|  4 ECYFCHGIVSPPEEGHIWLREHDSHEVYMHEQCASGHNVIEGGQNPAGEL 53
                                      7*****************9889999**********************987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.26
                           DUF3268  4 rCpyCGe 10
                                      +Cp CGe
  gi|344210165|ref|YP_004786341.1| 56 TCPECGE 62
                                      5777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 422.76
//
Query:       gi|344210166|ref|YP_004786342.1|  [L=297]
Description: methylenetetrahydrofolate dehydrogenase [Haloarcula hispanica ATCC 33960]
Scores for 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-66  220.2   1.5    1.2e-65  219.8   1.5    1.2  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
      6e-34  116.8   0.0    9.1e-34  116.2   0.0    1.3  1  THF_DHG_CYH    Tetrahydrofolate dehydrogenase/cyclohydrolase,


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 !  219.8   1.5   1.3e-69   1.2e-65       1     158 [.     122     288 ..     122     290 .. 0.97

  Alignments for each domain:
  == domain 1  score: 219.8 bits;  conditional E-value: 1.3e-69
                                       SHHHHHHHHTT--SS--HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCT....T-EEEEE-TTSCCH CS
                     THF_DHG_CYH_C   1 hplnlgrlvkgeeallpctpkgvvellketgielegkkvvvvGrsnivgkplallLlek....natVtvchsktkdl 73 
                                       hp n+grlv+g+  + pctp+g+ ++l+etg+e+egk++vvvGrs+ivgkp+a lL +     nat+tvchs+t+dl
  gi|344210166|ref|YP_004786342.1| 122 HPENVGRLVAGNARYKPCTPHGIQKILAETGVETEGKDAVVVGRSDIVGKPMANLLIQYgpggNATTTVCHSRTDDL 198
                                       899*******************************************************77788************** PP

                                       HHHHCCSSEEEE-SS-TT-B-GGGS-TT-EEEE---EEC.....-TTEEE-SB-HHHHCTTSSEE--TTTSCHHHHH CS
                     THF_DHG_CYH_C  74 aeitreadivvvavGkpelikaemvkegavviDvGinrv.....ekgklvGDvdfeevkevasaitPvpgGVGpmTv 145
                                       ae+tr+adiv++a+G+pe+i+++m++ g++viDvGinrv     ++++lvGDvdfe++k++a aitPvpgGVGp+T+
  gi|344210166|ref|YP_004786342.1| 199 AEKTRNADIVIAAAGVPEMIDGSMLSAGTTVIDVGINRVdadteKGYELVGDVDFESAKAKADAITPVPGGVGPLTI 275
                                       *****************************************9988999***************************** PP

                                       HHHHHHHHHHHHC CS
                     THF_DHG_CYH_C 146 amllkntleaakr 158
                                       aml+ nt++aa+ 
  gi|344210166|ref|YP_004786342.1| 276 AMLMYNTVKAASL 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 !  116.2   0.0     1e-37   9.1e-34       1     116 []       4     119 ..       4     119 .. 0.99

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 1e-37
                                       E--HHHHHHHHHHHHHHHHHHHHHHT---EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHHHH CS
                       THF_DHG_CYH   1 lldGkalakeireelkeeveklkekgvkpkLavilvgddpasevYvrnkkkaceevGieseliklpedvseeellkl 77 
                                       ++dG+++ ++i + +++ +++l  + v+p+La++l+ dd ase+Yv++k++acee+Gie  ++++++d   e+l ++
  gi|344210166|ref|YP_004786342.1|   4 IIDGNEIGDQITAGVAACTDTLVGEAVTPGLATVLMSDDGASETYVSMKQQACEEIGIEGFHYEISADEPAETLFST 80 
                                       79*******************999999************************************************** PP

                                       HHHHHH-TT--EEEE-SS-STTS-HHHHHCCS-GGGBTT CS
                       THF_DHG_CYH  78 ieelneddsvdGilvqlPlpkhidekaileaispeKDVD 116
                                       i+eln+d++v+Gilvq+P+p+h+ ++ +le+i+p+KDVD
  gi|344210166|ref|YP_004786342.1|  81 IDELNADPAVHGILVQMPVPDHVPKRDVLERIDPMKDVD 119
                                       **************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1983.89
//
Query:       gi|344210167|ref|YP_004786343.1|  [L=503]
Description: anthranilate synthase component I [Haloarcula hispanica ATCC 33960]
Scores for 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-100  334.1   0.0    1.6e-99  332.7   0.0    1.7  3  Chorismate_bind  chorismate binding enzyme
    1.8e-08   34.7   0.0    4.9e-08   33.3   0.0    1.7  1  Anth_synt_I_N    Anthranilate synthase component I, N termina
  ------ inclusion threshold ------
      0.047   13.8   0.1       0.14   12.3   0.1    1.8  1  YqgC             Uncharacterized YqgC-like
       0.12   13.5   0.1       0.34   12.0   0.1    1.8  1  DUF3484          Membrane-attachment and polymerisation-promo


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 ?   -3.2   0.0       1.1   4.9e+03      39      59 ..      36      56 ..      25      84 .. 0.67
   2 ?   -2.6   0.0      0.72   3.2e+03     183     215 ..      86     123 ..      68     126 .. 0.74
   3 !  332.7   0.0  3.6e-103   1.6e-99       2     258 .]     219     472 ..     218     472 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.1
                                      -HHHHHHHHHCTBSSSEEEEE CS
                   Chorismate_bind 39 dplalyralrarnpapysfll 59
                                      dp+++yr+ r  n++ + +  
  gi|344210167|ref|YP_004786343.1| 36 DPFEAYRRARDGNTDGFYLET 56
                                      789999999999888776544 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.72
                                       SEESHHHHHHHHHHHSSS--T....TT.TSEEEEEETT CS
                   Chorismate_bind 183 tGaPkkrameiidelEearRg....vY.aGavgyldad 215
                                       +G P  ++++ + + E+ +Rg    +Y +Ga+g+l+ d
  gi|344210167|ref|YP_004786343.1|  86 GGSPSIETIDELLDREHLERGdctvPYpCGAFGWLSYD 123
                                       68888888888888888888855553558999998865 PP

  == domain 3  score: 332.7 bits;  conditional E-value: 3.6e-103
                                       HCHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEE CS
                   Chorismate_bind   2 redYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkve 78 
                                       ++++a++v+++k+++r+gd+++ ++s+rl+a+  aav+p+++++a+r+ npapys+lle+++ +l++aSPElll+v+
  gi|344210167|ref|YP_004786343.1| 219 EAAFADRVRQIKQYVRDGDTFQTNVSHRLTAP--AAVHPVDTFDAVRRVNPAPYSALLEFPGVDLVSASPELLLDVD 293
                                       5789****************************..99***************************************** PP

                                       TTSEEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEE CS
                   Chorismate_bind  79 ggrrietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhl 155
                                       g+ ++ tepiaGTr+rg+tp ede+le++l +deKeraEh+m+vdl rndLgkv++ gsv+v+e+++v+rysev+hl
  gi|344210167|ref|YP_004786343.1| 294 GD-QLLTEPIAGTRPRGATPSEDEDLEADLCSDEKERAEHAMLVDLERNDLGKVSEYGSVDVAEYRRVDRYSEVMHL 369
                                       77.************************************************************************** PP

                                       EEEEEEEESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETT CS
                   Chorismate_bind 156 vstiegelkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdk 232
                                       vs iegel++dvs++d+++a+fP+g++tGaPk r+meiide+E +rRg+Y+G++g++++d++a+l+++IRt+v+ d+
  gi|344210167|ref|YP_004786343.1| 370 VSLIEGELRDDVSIADAVAAVFPGGTITGAPKPRTMEIIDEVERTRRGPYTGSIGMFGFDDRATLNITIRTLVHYDG 446
                                       ****************************************************************************9 PP

                                       EEEEEEEEEEETT--HHHHHHHHHHH CS
                   Chorismate_bind 233 elrlgaGaGIvadSdpeaEyeEtlaK 258
                                       e+rl++G+GIv+dS peaEy+Etl+K
  gi|344210167|ref|YP_004786343.1| 447 EYRLRVGSGIVHDSVPEAEYRETLDK 472
                                       9***********************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 !   33.3   0.0   1.1e-11   4.9e-08       4     131 ..      36     152 ..      34     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.1e-11
                     Anth_synt_I_N   4 tplsvylklaeee.hkflLeSaeneggegrySfigldpflelkskngevevegpegeeleeee.pldalrellerfr 78 
                                       +p ++y++ ++ + + f Le     gg++ + + g+dp  ++++  +++  ++        ++ + ++++ell+r +
  gi|344210167|ref|YP_004786343.1|  36 DPFEAYRRARDGNtDGFYLETT---GGQSGWGYFGVDPVEQIEVSASATPAQD-------GGSpSIETIDELLDREH 102
                                       6999*******99*********...89999********555444444444444.......33358999999999999 PP

                     Anth_synt_I_N  79 saedseptelpfvgGlvGylgYDlvreieklpksakddlnlpdarlilydtli 131
                                          +  +  +p  +G++G l+YD+ re+e++p+++  +  lp +++ ++d + 
  gi|344210167|ref|YP_004786343.1| 103 -L-ERGDCTVPYPCGAFGWLSYDVARELEDIPETT-VSDGLPRLQFGVFDCIA 152
                                       .4.3457889**********************644.5566******9999875 PP

>> YqgC  Uncharacterized YqgC-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   3.1e-05      0.14      10      29 ..     212     231 ..     205     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.1e-05
                              YqgC  10 sRDaeCGerirtRtvRqvkq 29 
                                         ++eCGe ++   vRq+kq
  gi|344210167|ref|YP_004786343.1| 212 TFESECGEAAFADRVRQIKQ 231
                                       5578***************9 PP

>> DUF3484  Membrane-attachment and polymerisation-promoting switch
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   7.6e-05      0.34       4      22 ..     190     210 ..     188     245 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.6e-05
                           DUF3484   4 laqaAvsGeetlrrqPvd..p 22 
                                       laq A++Ge++++ qP+   +
  gi|344210167|ref|YP_004786343.1| 190 LAQDAIHGEKHVQSQPTAasQ 210
                                       9****************9431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 3023.96
//
Query:       gi|344210168|ref|YP_004786344.1|  [L=190]
Description: anthranilate synthase component II [Haloarcula hispanica ATCC 33960]
Scores for 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-46  156.7   0.0    6.5e-46  156.5   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    1.4e-07   31.5   0.8      6e-07   29.4   0.8    1.8  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.019   14.5   0.0      0.034   13.7   0.0    1.3  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 !  156.5   0.0   1.1e-49   6.5e-46       2     187 ..       4     184 ..       3     187 .. 0.94

  Alignments for each domain:
  == domain 1  score: 156.5 bits;  conditional E-value: 1.1e-49
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGI 77 
                                       +iDnyds+ +nlv+++ e++ +v+v+++da + e ++ + +pdgi+vs+Gpg+p+ ++ +i++  e    + P LG+
  gi|344210168|ref|YP_004786344.1|   4 IIDNYDSFAYNLVQYVGEFD-DVTVRRNDAIDVEGIH-ELDPDGIVVSPGPGTPAeAGVSIDVFAE---TEYPALGV 75 
                                       89******************.*********9999987.78***************99999998776...478***** PP

                                       THHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTE.E CS
                            GATase  78 CLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtaksedde.e 153
                                       CLG+Q+l+ + g +v ++     hg+ +++++d+t+l+ g ++++++ ++H+++v+  + +p++le ta ++d++  
  gi|344210168|ref|YP_004786344.1|  76 CLGHQALCAAHGTPVGHAP-SVVHGKPSEVRHDGTRLYDGINDPFEVGRYHSLAVEA-AALPDELEETAYTNDEQgV 150
                                       *******************.9***********************************8.99****9999988666569 PP

                                       EEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 154 lmeiiekknpfvgvQFHPEststpegpellfnfl 187
                                       +m++++ ++p +gvQFHPEs++t  g+++++nf+
  gi|344210168|ref|YP_004786344.1| 151 VMGVQHAEKPHIGVQFHPESILTDAGKQIVENFC 184
                                       ********************************96 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.8     1e-10     6e-07     102     216 .]      66     169 ..      61     169 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1e-10
                     Peptidase_C26 102 lergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqai 178
                                        e + P lg+C+G+q l  a  Gt + ++ +    + h +++      +v+   g+ l++ ++ + +ev  +H+ a+
  gi|344210168|ref|YP_004786344.1|  66 AETEYPALGVCLGHQAL-CAAHGTPVGHAPS----VVHGKPS------EVRH-DGTRLYDGIN-DPFEVGRYHSLAV 129
                                       57789************.6777777777775....3343343......3333.5777777777.79*********** PP

                     Peptidase_C26 179 ke..laeelrveAvaeD..gviEaieseeakafvlgvQwHPE 216
                                       +   l +el+ +A ++D  gv+  +++ e  ++ +gvQ+HPE
  gi|344210168|ref|YP_004786344.1| 130 EAaaLPDELEETAYTNDeqGVVMGVQHAE--KPHIGVQFHPE 169
                                       9866889******9986226666666665..68********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 ?   13.7   0.0   5.7e-06     0.034      31      73 ..       9      56 ..       5      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.7e-06
                                      GGGGGGT.......TS-BSBESSSB-HHHHHHH--SEEEE-GGG...G CS
                      Peripla_BP_2 31 pldadklee.....aivevgadgeidvEklaalkPDlvilskglgltd 73
                                       ++a++l +     + v+v+ ++ idvE + +l+PD +++s+g g+++
  gi|344210168|ref|YP_004786344.1|  9 DSFAYNLVQyvgefDDVTVRRNDAIDVEGIHELDPDGIVVSPGPGTPA 56
                                      5555655556667899*************************9985444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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 0.32s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1154.02
//
Query:       gi|344210169|ref|YP_004786345.1|  [L=618]
Description: glycine betaine transporter BetL [Haloarcula hispanica ATCC 33960]
Scores for 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-132  439.9  43.7   1.1e-131  439.6  43.7    1.1  1  BCCT      BCCT, betaine/carnitine/choline family transporter
  ------ inclusion threshold ------
      0.015   15.4   1.6      0.088   13.0   0.0    2.6  2  Pox_A9    A9 protein conserved region


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 !  439.6  43.7  1.3e-135  1.1e-131       1     483 [.     103     586 ..     103     588 .. 0.97

  Alignments for each domain:
  == domain 1  score: 439.6 bits;  conditional E-value: 1.3e-135
                              BCCT   1 vflvslliivlfvllalvfpealeevlsslnswilekfgwlylllvllflvfllvlafskygkikLGkddekpefst 77 
                                       ++++++l++++f+ l ++fp++ + +++++ +++l+  g l+l++v+l ++ +l+l++ ++g+ikLG++d++p++++
  gi|344210169|ref|YP_004786345.1| 103 ILAFPVLVFAAFFGLQIAFPARTTGAVDAAAATVLRGGGPLFLAAVFLSVCYCLFLLLGPWGEIKLGGPDTEPSYTY 179
                                       568999*********************************************************************** PP

                              BCCT  78 lsWfamlfaaglgigllfwgvaEplahylspppga..eagteeaaqeAlaytffhwGlhaWaiyalvalalayfayr 152
                                        ++f+++f+ag+++gl+fwg +E l+hy +ppp    +ag++ a++ Al yt+fhwG++aW+ ya++++ +ayfa++
  gi|344210169|ref|YP_004786345.1| 180 PTYFTLVFTAGIAAGLVFWGPTEALFHYDQPPPYIgaAAGSPGAVNGALVYTLFHWGVSAWSAYAVIGVPIAYFAFT 256
                                       *******************************96555699************************************** PP

                              BCCT 153 kglpltissalypllg.eringllgkvvDvlavlatvfGvatslGlgvlqinaglselfgieesltvqlaiivvita 228
                                       +g pl++s++l+pllg ++++++++++vD+lav+at+ G+ats++l   q+ ag+++ +++  +++  ++++  +t+
  gi|344210169|ref|YP_004786345.1| 257 RGAPLRVSTVLAPLLGvDELDSAWATLVDTLAVFATIGGIATSVALVSEQFLAGINYQWDVAAGEVGPVLFVGGLTL 333
                                       ****************559********************************************************** PP

                              BCCT 229 latvsavsGldkGikrlSnlnlvlalllllfvllvGptlfilntfvqslgdylqnlvalslatdaaeeaeewlasWT 305
                                       +++vs ++G+++Gi+r++ ln+vl+ l++l++  vGp lfil+  +q+lg+y+ ++v+lsl+t+     ++w+a+WT
  gi|344210169|ref|YP_004786345.1| 334 IFVVSSATGIHRGIRRIAGLNIVLFGLFALLIAAVGPRLFILQRGTQALGTYVVEFVPLSLHTG-----GQWVAAWT 405
                                       ***************************************************************4.....35****** PP

                              BCCT 306 vFyWawwiawapfvGlFiAriSrGRtiRefilgvllvptlvtflwftvlGgtaielelegeaelaea...aeasvea 379
                                       v+ W ww++wapf GlFiA  SrGR +R ++++ +++++++t++wf +lGgt++ ++++g+a++ +a      s ++
  gi|344210169|ref|YP_004786345.1| 406 VWNWSWWFSWAPFAGLFIAALSRGRRVRTVVFTSVVATSAATMVWFLLLGGTSLFIQQTGQADILAAiaqRGGSEAV 482
                                       **************************************************************999987534445588 PP

                              BCCT 380 alfalleqlplgsilsvlavvliiiffvTsaDSatlvlatltsggdenpprkqrvfWgvllgavaavlllaggleal 456
                                       a f l+++lplg++l++l+++lii+f++TsaD++tlv++ l+++    p+ ++ vfWg+++g va+ +ll+gg e+l
  gi|344210169|ref|YP_004786345.1| 483 AGFPLFASLPLGQLLMFLFLALIIVFMATSADTSTLVVSVLATRRGMAPSATHIVFWGIFQGSVAVSVLLLGGAETL 559
                                       99*************************************************************************** PP

                              BCCT 457 qsasiiaalPftlvlllmvvsllkalr 483
                                       q+++++++ Pf+++ l++v  l+ +++
  gi|344210169|ref|YP_004786345.1| 560 QALAVLTGGPFAVISLVAVGGLTVTWY 586
                                       *****************9998887765 PP

>> Pox_A9  A9 protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.8e-06     0.088      16      48 ..     431     463 ..     429     468 .. 0.85
   2 ?    0.2   0.5     0.093   8.4e+02      33      51 ..     496     514 ..     493     516 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.8e-06
                            Pox_A9  16 rlRpNsfafVvlksiisMvmyLvlGvaLlyiss 48 
                                       r+R+  f  Vv  s  +Mv +L+lG   l i +
  gi|344210169|ref|YP_004786345.1| 431 RVRTVVFTSVVATSAATMVWFLLLGGTSLFIQQ 463
                                       889999******************977766655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.093
                            Pox_A9  33 MvmyLvlGvaLlyissndd 51 
                                       ++m+L l ++++ ++   d
  gi|344210169|ref|YP_004786345.1| 496 LLMFLFLALIIVFMATSAD 514
                                       5899999999988887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 3508.23
//
Query:       gi|344210170|ref|YP_004786346.1|  [L=416]
Description: potassium channel-like protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   93.2   2.3    2.1e-26   92.5   2.3    1.4  1  TrkA_N          TrkA-N domain
    4.6e-14   52.1   7.5    4.6e-14   52.1   7.5    3.1  4  Ion_trans_2     Ion channel
     0.0016   17.7   0.2      0.003   16.8   0.2    1.5  1  Ion_trans       Ion transport protein
  ------ inclusion threshold ------
      0.011   15.4   8.3      0.016   14.9   7.9    1.6  1  tRNA-synt_2_TM  Transmembrane region of lysyl-tRNA synthetase
       0.89   10.0   3.6       0.21   12.0   0.3    1.6  2  NAD_binding_7   Putative NAD(P)-binding


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 !   92.5   2.3   5.8e-30   2.1e-26       1     116 []     264     378 ..     264     378 .. 0.99

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 5.8e-30
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       i+++G+G+v+ sl+eeL ++ + vvv+  dee+v++l+ e ++ + gd+tde+vL++a + +a++v++  +dd+  +
  gi|344210170|ref|YP_004786346.1| 264 IVVLGYGDVTASLLEELGDETE-VVVVTPDEETVASLQSEDVNLLTGDPTDEDVLRDARVGTASGVVVGSNDDARDV 339
                                       89*****************995.****************************************************** PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                       lav + k+ np+++++a a  ++h+e+++ +gad+vi+p
  gi|344210170|ref|YP_004786346.1| 340 LAVIATKNVNPDIRTVAAATAEKHVEKFRAVGADEVINP 378
                                       *************************************98 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       2.8     1e+04      60      71 ..      40      51 ..      34      58 .. 0.52
   2 ?   -2.6   1.2       1.5   5.5e+03      40      40 ..      95      95 ..      78     123 .. 0.52
   3 !   52.1   7.5   1.3e-17   4.6e-14       5      72 ..     166     235 ..     158     240 .. 0.83
   4 ?    0.0   0.0      0.24   8.5e+02      39      46 ..     267     274 ..     264     278 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.8
                                      HHHHHHHHHHHH CS
                       Ion_trans_2 60 llGlalfalfla 71
                                      l+G + +++f++
  gi|344210170|ref|YP_004786346.1| 40 LTGTVALLAFVT 51
                                      444444444443 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                                      - CS
                       Ion_trans_2 40 G 40
                                      G
  gi|344210170|ref|YP_004786346.1| 95 G 95
                                      2 PP

  == domain 3  score: 52.1 bits;  conditional E-value: 1.3e-17
                                       HTCHHHHHHHHT......T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2   5 lvlifgaviysl..eegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflav 72 
                                        v+++g+v  +   ++++e  s+ da+Y+++vt+ T+GYGdi+p+t+  r+f++ +il+G + f++++  
  gi|344210170|ref|YP_004786346.1| 166 GVVLYGTVGAYGlrGQFLELDSWGDAVYYVVVTIATVGYGDITPVTAEARWFSLSIILFGTGAFTVAVGA 235
                                       344444444444788889***************************8888****************99876 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.24
                                       S----SST CS
                       Ion_trans_2  39 iGYGdivp 46 
                                       +GYGd+++
  gi|344210170|ref|YP_004786346.1| 267 LGYGDVTA 274
                                       6*****96 PP

>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   8.3e-07     0.003     171     220 ..     180     230 ..      77     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.3e-07
                                       TTSSSSSSHHHHHHHHHHHHTTSSHHHHHHHHHHHS.HHHHHHHHHHHHHH CS
                         Ion_trans 171 ngntnFdnfftallwlfrlmttegwgdilyatldek.skvaliyfvifiil 220
                                        ++ + d+ ++a++ +++++ t+g+gdi+++t  ++  ++++i+f++  + 
  gi|344210170|ref|YP_004786346.1| 180 GQFLELDSWGDAVYYVVVTIATVGYGDITPVTAEARwFSLSIILFGTGAFT 230
                                       446678999***************************444555555544444 PP

>> tRNA-synt_2_TM  Transmembrane region of lysyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   7.9   4.5e-06     0.016      12      91 ..      43     122 ..      35     237 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.5e-06
                    tRNA-synt_2_TM  12 ivgvlavlsllasvspllrrlikvvrevvddyl..fnvPdtslawavvLllLAaAlaarkriAwwllvvylvlllll 86 
                                       +v++la +  l+ +s+    l  + ++vvd  l  +      + +a+vL ++  +l++rk++Aw ++ v+l+ l++l
  gi|344210170|ref|YP_004786346.1|  43 TVALLAFVTGLSNLSQASLALNGPLTAVVDLPLpfVR--FGGVLFAFVLGIVTVGLQRRKQLAWRVAAVVLLGLVVL 117
                                       3444444444444444444544555566665443233..46899**************************9999988 PP

                    tRNA-synt_2_TM  87 navll 91 
                                        + ++
  gi|344210170|ref|YP_004786346.1| 118 PLTTF 122
                                       76655 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 ?   -4.3   0.2         5   1.8e+04      12      35 ..      88     111 ..      87     115 .. 0.75
   2 ?   12.0   0.3   5.9e-05      0.21       7      80 ..     261     354 ..     257     371 .. 0.58

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 5
                     NAD_binding_7  12 vvGgGevAarkvrklleagakvtv 35 
                                       v G  +v++++ ++l+   a v++
  gi|344210170|ref|YP_004786346.1|  88 VLGIVTVGLQRRKQLAWRVAAVVL 111
                                       667778999998888877777765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5.9e-05
                     NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeee..........lekd............... 58 
                                       + +++v G G+v a+ ++ l ++  +v+vv+p+     e   +l++e+             d               
  gi|344210170|ref|YP_004786346.1| 261 EDHIVVLGYGDVTASLLEELGDE-TEVVVVTPDE----ETVASLQSEDvnlltgdptdE--Dvlrdarvgtasgvvv 330
                                       6799******************9.9********3....222223333322222223220..2333344444444444 PP

                     NAD_binding_7  59 ..legadlviaatddrelneriae 80 
                                          ++a  v+a++  +++n  i  
  gi|344210170|ref|YP_004786346.1| 331 gsNDDARDVLAVIATKNVNPDIRT 354
                                       445555555555555555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2522.27
//
Query:       gi|344210171|ref|YP_004786347.1|  [L=146]
Description: hypothetical protein HAH_5230 [Haloarcula hispanica ATCC 33960]
Scores for complete 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-12   46.4  19.3    4.8e-12   46.2  19.3    1.0  1  EamA             EamA-like transporter family
  ------ inclusion threshold ------
        3.9    6.9   8.2        4.9    6.6   1.3    2.1  2  DUF1129          Protein of unknown function (DUF1129)


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 !   46.2  19.3   5.3e-16   4.8e-12       3     136 ..      14     145 ..      12     146 .] 0.95

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 5.3e-16
                              EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlaf 79 
                                       ++l+ l  ++ w++++ +  +++++++p t++fv++ +a+++  i+ ++++ +  + + +++ +    g ++ +++ 
  gi|344210171|ref|YP_004786347.1|  14 AVLFGLGTMIAWGFWIAFGNVASSTMDPETAAFVSYAAATVVTGIYVVVSDASS-VVTNRGMMFAGAAG-VAAAVGV 88 
                                       6899**************************************************.88888888866666.7999999 PP

                              EamA  80 llffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       +  f +++ ++ s++s i  +  + +++++v+ +ge++tl++ +gi+l+l+++++i+
  gi|344210171|ref|YP_004786347.1|  89 VSTFVGVTVGPTSIVSTIGGMYFITAAVIGVIAFGESMTLTKAAGIGLALIAIVVIN 145
                                       ******************************************************997 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   1.3   0.00055       4.9     148     197 ..      13      62 ..       7      71 .. 0.90
   2 ?    4.7   0.7     0.002        18     154     200 ..      82     131 ..      63     137 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00055
                           DUF1129 148 krllilllllvvwlvlftlvallpaviNpvLpplvliiigviafvvryyl 197
                                         +l+ l+++++w +++++ ++  +++ p   ++v+ + + +  ++++++
  gi|344210171|ref|YP_004786347.1|  13 AAVLFGLGTMIAWGFWIAFGNVASSTMDPETAAFVSYAAATVVTGIYVVV 62 
                                       578999********************************999999998765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.002
                           DUF1129 154 llllvvwlvlftlvallpaviNpv...Lpplvliiigviafvvryylkkk 200
                                       +++ v  +  f+ v++ p++i  +   +  +  ++igviaf+  + l k 
  gi|344210171|ref|YP_004786347.1|  82 VAAAVGVVSTFVGVTVGPTSIVSTiggMYFITAAVIGVIAFGESMTLTKA 131
                                       44444444555555555555555511156677889******998888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 998.86
//
Query:       gi|344210172|ref|YP_004786348.1|  [L=126]
Description: endoribonuclease L-PSP [Haloarcula hispanica ATCC 33960]
Scores for complete 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-37  127.5   0.0      3e-37  127.3   0.0    1.0  1  Ribonuc_L-PSP    Endoribonuclease L-PSP
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.018   15.2   0.0    1.3  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 !  127.3   0.0   3.3e-41     3e-37       2     120 ..       8     124 ..       7     125 .. 0.97

  Alignments for each domain:
  == domain 1  score: 127.3 bits;  conditional E-value: 3.3e-41
                                       TTSTTTSSS-BSEEEETTEEEEEEE-SB-TTTSCB..-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEESSGG CS
                     Ribonuc_L-PSP   2 eaapaaaapYsqavkagnlvyvsGqlpldpetgelv.egdveeqtrqalenlkavLaaagaslsdvVkvtvFladie 77 
                                       ++apaa+++Ysqa  +g+l++++Gqlpl+  +gel   + v++qtrq+l n+ a+L++ ++sl+dv+k+tv+l di+
  gi|344210172|ref|YP_004786348.1|   8 DEAPAAVGAYSQATSNGDLLITAGQLPLT-TDGELLdGEPVADQTRQCLHNVAAILESEDLSLDDVLKTTVYLDDID 83 
                                       689*************************9.69999989999************************************ PP

                                       GHHHHHHHHHHHSSSSTS--EEEEEE-SBSGGG-SEEEEEEEE CS
                     Ribonuc_L-PSP  78 dfaevnevyaeafdelkeaParsaveVaaLpkgakvEIeaiav 120
                                       df  +ne+y e+f+ +   Parsav+V a+pkga+vEIeaia+
  gi|344210172|ref|YP_004786348.1|  84 DFDSFNEAYSEFFESEP--PARSAVGVGAVPKGAAVEIEAIAT 124
                                       ***************95..**********************96 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 ?   15.2   0.0     2e-06     0.018      12      49 ..       8      45 ..       2      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-06
                                      ------SSSS-SEEEETTEEEE--B--EETTEE--BS- CS
                   YjgF_endoribonc 12 pkvaaalGayepyaivasflttsfqlpylqekllyvGl 49
                                       +++aa+Gay   +  ++ l+t++qlp   +  l  G 
  gi|344210172|ref|YP_004786348.1|  8 DEAPAAVGAYSQATSNGDLLITAGQLPLTTDGELLDGE 45
                                      5899***********************98765555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 773.81
//
Query:       gi|344210173|ref|YP_004786349.1|  [L=89]
Description: hypothetical protein HAH_5232 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.075   13.2   0.0        0.1   12.8   0.0    1.2  1  DUF695    Family of unknown function (DUF695)


Domain annotation for each model (and alignments):
>> DUF695  Family of unknown function (DUF695)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.6e-06       0.1      60     100 ..       6      47 ..       2      59 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-06
                            DUF695  60 ekiedallealk.akpnalyvGritsngtrdlyfytkdteel 100
                                       e+++ +  +a++ a++  +y+G+i  +g +++yf  + +e+ 
  gi|344210173|ref|YP_004786349.1|   6 EEVKTEASAAITeADLRSVYTGIIHEDGRHEYYFGNDTEEAA 47 
                                       5555555666665899*****************976555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 572.33
//
Query:       gi|344210174|ref|YP_004786350.1|  [L=535]
Description: NADH dehydrogenase subunit F (ubiquinone) [Haloarcula hispanica ATCC 33960]
Scores for complete 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-18   65.0   0.0    8.8e-18   64.2   0.0    1.5  1  NADH_4Fe-4S   NADH-ubiquinone oxidoreductase-F iron-sulfur bi
    3.9e-16   59.3   0.0    6.1e-16   58.6   0.0    1.3  1  Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subu
  ------ inclusion threshold ------
      0.012   15.5   0.0       0.39   10.6   0.0    2.7  2  SLBB          SLBB domain
       0.11   13.0   1.2        1.7    9.1   0.1    3.0  3  HMA           Heavy-metal-associated domain


Domain annotation for each model (and alignments):
>> 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 !   64.2   0.0     2e-21   8.8e-18       6      85 .]     445     521 ..     440     521 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 2e-21
                                       HHHHHHHH--S--HHHHIIIIHHHHHHHHHTBT---HHHHHHHHHHHHHHSS--SSTHHHHHHHHHHHHHHHHHHHH CS
                       NADH_4Fe-4S   6 llefyaaesCGkCtpCreGtkrllelleriaagegteedldlleelaetikgtslCalgdsaanpvlsalrkFreef 82 
                                        ++f++ e+ G+C+p reGtk+l+ell++i +g+ +    d+++el+++++++s C+ g  a++pv +a+++F+ ef
  gi|344210174|ref|YP_004786350.1| 445 RARFASMENSGRCVPGREGTKQLAELLRDIYDGSFE---SDKIRELGRVMRQSSNCQTGAHAPRPVSTAIDEFEPEF 518
                                       589********************************9...799*********************************** PP

                                       HH. CS
                       NADH_4Fe-4S  83 eah 85 
                                       +ah
  gi|344210174|ref|YP_004786350.1| 519 RAH 521
                                       *98 PP

>> 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 !   58.6   0.0   1.4e-19   6.1e-16       5     151 ..     179     339 ..     176     340 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 1.4e-19
                      Complex1_51K   5 givGrGG..a..gfPthvKlkakakkkk.kylivNaaEcEPgltkDrllmreepheileGlkiaaealgaekgvigv 76 
                                       g+ GrG   a    P++  ++++++++  +++++Na+    + t D++l+  +p  +l+G++++ae + a  +v++v
  gi|344210174|ref|YP_004786350.1| 179 GLLGRGRgdAaaDEPVADTWETASETDGdPVVVCNANDASDLPTGDDTLLSGTPMAVLDGIAAVAEYVDAGDAVVYV 255
                                       66555541132256999999999996669************************************************ PP

                      Complex1_51K  77 rdekpeaiealekalaeakaaglldievvklagkYpaGeekaLiesltgr..evprgkpp..advgv.....vvnNv 144
                                       ++++++  ++l++a+++a +   +  ++v++++ + aGe +a +e+l+g     pr +pp  a+ g+     vv+  
  gi|344210174|ref|YP_004786350.1| 256 NESETDLQAHLREAIDAAADTLPVVPQLVAGPDEFRAGEPTAALEALEGAdrVEPRLQPPspAKRGLygrptVVHTP 332
                                       ******************87555999***********************99777888888889999999**99*999 PP

                      Complex1_51K 145 eTlaavy 151
                                        T+a+v+
  gi|344210174|ref|YP_004786350.1| 333 RTFAQVQ 339
                                       9999997 PP

>> SLBB  SLBB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.06   2.7e+02      14      35 ..      95     116 ..      91     128 .. 0.69
   2 ?   10.6   0.0   8.7e-05      0.39       1      24 [.     359     382 ..     359     389 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.06
                                       EEEETT-BHHHHHHTTT-SBSS CS
                              SLBB  14 yevpigttlsdlieqaGGltdd 35 
                                       y  p+ +t++dli++   +t +
  gi|344210174|ref|YP_004786350.1|  95 YSDPSPATVRDLIDELEAGTVP 116
                                       5668899******994444443 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 8.7e-05
                                       EEEEESSBSS-EEEEEETT-BHHH CS
                              SLBB   1 vVtVtGeVkrPgnyevpigttlsd 24 
                                       +VtVtG+V++  ++e+++ ++l+ 
  gi|344210174|ref|YP_004786350.1| 359 IVTVTGDVANQATVELRSSASLAA 382
                                       69***************9988765 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.7   1.6e+04      43      57 ..      97     111 ..      95     113 .. 0.74
   2 ?    0.9   0.1      0.14   6.3e+02      23      58 ..     236     272 ..     234     275 .. 0.78
   3 ?    9.1   0.1   0.00038       1.7      15      49 ..     337     372 ..     336     389 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.7
                               HMA  43 daestklrkiieaie 57 
                                       d++++++r++i ++e
  gi|344210174|ref|YP_004786350.1|  97 DPSPATVRDLIDELE 111
                                       556688999998887 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.14
                               HMA  23 lpgVesvkvdlatktvtVegdaestklrk.iieaiek 58 
                                       l+g+ +v   ++++ ++V +++++t+l + ++eai++
  gi|344210174|ref|YP_004786350.1| 236 LDGIAAVAEYVDAGDAVVYVNESETDLQAhLREAIDA 272
                                       577888888889999*********7774448888876 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00038
                               HMA  15 kvekvLselpgVesvkvdlatktvtVegdaes.tkl 49 
                                        v+++++e ++V++   d +t+ vtV+gd++  +++
  gi|344210174|ref|YP_004786350.1| 337 QVQRAVAEPDSVDADAADPGTRIVTVTGDVANqATV 372
                                       599*************************99876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.57
# Mc/sec: 2836.32
//
Query:       gi|344210175|ref|YP_004786351.1|  [L=1103]
Description: formate dehydrogenase alpha subunit [Haloarcula hispanica ATCC 33960]
Scores for 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-83  279.1   0.0    7.7e-83  278.8   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    8.5e-34  115.9   0.0    1.5e-33  115.1   0.0    1.4  1  Molydop_binding  Molydopterin dinucleotide binding domain
    1.1e-27   95.9   0.2    2.7e-27   94.6   0.2    1.8  1  Fer2_4           2Fe-2S iron-sulfur cluster binding domain
    3.4e-12   45.7   0.8    3.4e-12   45.7   0.8    2.5  2  NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur
    2.9e-09   36.8   0.1    1.1e-08   34.9   0.1    2.1  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
    4.9e-09   36.2   8.9    4.9e-09   36.2   8.9    2.8  3  Fer4_21          4Fe-4S dicluster domain
    5.4e-09   36.5  15.2    3.6e-08   33.9   8.7    3.6  3  Fer4_7           4Fe-4S dicluster domain
    3.5e-07   29.8  20.6    0.00017   21.2   1.0    3.6  3  Fer4             4Fe-4S binding domain
    5.8e-06   26.2  12.2    5.9e-05   23.0   3.0    3.7  3  Fer4_6           4Fe-4S binding domain
    5.9e-06   27.1   5.6     0.0017   19.3   0.1    3.6  3  Fer4_16          4Fe-4S double cluster binding domain
    2.9e-05   24.4   8.0    2.9e-05   24.4   8.0    3.4  3  Fer4_8           4Fe-4S dicluster domain
    4.4e-05   23.6  10.0    4.4e-05   23.6  10.0    3.9  4  Fer4_9           4Fe-4S dicluster domain
    0.00016   21.7  13.2    0.00016   21.7  13.2    3.5  4  Fer4_10          4Fe-4S dicluster domain
      0.002   18.3  13.1      0.038   14.2   1.5    2.7  2  Fer4_18          4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.01   15.9   2.8       0.01   15.9   2.8    4.5  4  Fer4_2           4Fe-4S binding domain
      0.055   13.7   0.0       0.13   12.4   0.0    1.7  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
       0.17   12.1   0.0       0.58   10.4   0.0    1.9  1  NIPSNAP          NIPSNAP
       0.17   12.6  18.3       0.11   13.3   3.5    4.6  4  Fer4_15          4Fe-4S single cluster domain
       0.42   11.5  16.1       0.36   11.7   1.3    3.8  3  Fer4_22          4Fe-4S dicluster domain
       0.53   10.9  15.6        2.3    8.8   4.1    3.0  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I


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 !  278.8   0.0   8.6e-86   7.7e-83       1     431 [.     448     873 ..     448     874 .. 0.95

  Alignments for each domain:
  == domain 1  score: 278.8 bits;  conditional E-value: 8.6e-86
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       R++ P++R   +++G++++ +W+eAl+++a++++++++++g d+    +s +  s+e+ ++ +k+++ + g  ++++
  gi|344210175|ref|YP_004786351.1| 448 RVTEPLLR---NDDGELEPTTWEEALDYVAERFTEIQDQHGIDSLGCLAS-SKGSNEEAYLVQKFARQVLG--TKNI 518
                                       9*******...99********************************96444.45559***************..9*** PP

                                       ECCGGGTTHHHH....CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSS CS
                     Molybdopterin  78 dwyadlppasaq....qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpr 150
                                       d++a+l+++s++    qt+g++      ++   ed+ ++d+ ++ GsN  e +p+l +ri + ++ + a ++v++pr
  gi|344210175|ref|YP_004786351.1| 519 DNCARLCHSSTVaalqQTLGYGAM----TNRINEDIGEADAYLISGSNTTESHPVLATRIKQNVRDG-ADLVVFDPR 590
                                       **********99555555555544....444445**********************99999999885.********* PP

                                       B-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHH CS
                     Molybdopterin 151 yaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarel 227
                                       +  ++++ad++  ++pg d+a ++++  +i++  ++d +f+++ t  +ee+++ +++ ++e+++   +v  +     
  gi|344210175|ref|YP_004786351.1| 591 KIGIAEHADQYTRTNPGYDVAWLNGLIRYIIEHDLHDADFIERNTRNFEEVREKVQAFTPEKVEDLAGVSPEELASA 667
                                       **************************************************************************999 PP

                                       HHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCC CS
                     Molybdopterin 228 arnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvksl 304
                                       a+ +a+++    + + +g++++++g++++ a++ Lal +g+vg+pg+g   ++Gq++++g++ ++g+lp  l+ ++ 
  gi|344210175|ref|YP_004786351.1| 668 AETLAEADS-VVFGWAMGMTQQSHGTENLIAMADLALVLGQVGKPGAGLSPFRGQNNVQGGGGDMGTLPGSLPGYQN 743
                                       999999999.999************************************************************9999 PP

                                       TT...HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSH CS
                     Molybdopterin 305 ke...ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrlts 378
                                       +      +kfa+ + +  ++ p+ ++ e+   ++ ++++ +y++g+np  + +d+++  +ale+l+++vv d+++t+
  gi|344210175|ref|YP_004786351.1| 744 PAddeVGEKFADAWGERPPKEPGLKVPEMLAEAHAGNLRGMYVVGENPALSEPDIQHAAEALEDLEFLVVQDIFMTE 820
                                       99888889********************************************************************* PP

                                       HHHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHHH CS
                     Molybdopterin 379 talyaDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaLak 431
                                       ta+yaD++LPaat  Ek++++tn+e+r+q+ ++  +ppg a++dw+I +aLa+
  gi|344210175|ref|YP_004786351.1| 821 TAEYADVVLPAATSPEKHGTFTNTERRIQRVRPTSEPPGKARQDWEITQALAR 873
                                       ***************************************************95 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.1   0.0   1.7e-36   1.5e-33       1     109 [.     964    1068 ..     964    1070 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.1 bits;  conditional E-value: 1.7e-36
                                        EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEE CS
                   Molydop_binding    1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvv 74  
                                        l+L++gr+l+++h++  tr+v+ l ++ + ++ve++pe+A++lGi+dG+ V+vesrrG ++v+a+vt+rv pG++
  gi|344210175|ref|YP_004786351.1|  964 LTLTSGRVLYHWHTGQITRRVEGLMSHVGeSFVEVHPETAEKLGIADGEYVRVESRRGDIVVKAQVTDRVGPGTL 1038
                                        78************************************************************************* PP

                                        EEESSHCC.....S-GHCTS--SCSTTT--CSTT- CS
                   Molydop_binding   75 fmpfgwweagekggnaNaltddatdplsgtpefks 109 
                                        f+p+++ +     g++N+lt + +dp++g+pe+k+
  gi|344210175|ref|YP_004786351.1| 1039 FIPMHFAA-----GAVNKLTGETFDPTAGIPEYKV 1068
                                        ******99.....********************96 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 !   94.6   0.2   3.1e-30   2.7e-27       2      82 .]      42     141 ..      41     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 3.1e-30
                            Fer2_4   2 rpvtltfDGkevtvpeGdtvasAllang................vdvprsckygrp...rgelcaggeCrnClVeve 59 
                                       +p+tlt+DG++vtv +G+t+++Al++ +                +dvp++c+y+r+   ++e+++++eCr+C+Ve++
  gi|344210175|ref|YP_004786351.1|  42 DPTTLTVDGERVTVAPGSTIIDALQDLDddivsvdpgaegveddADVPALCYYDRDgdcSDEIGPRSECRTCMVETD 118
                                       79*************************************************************************** PP

                            Fer2_4  60 gepnvracstpvedGlkvetqtg 82 
                                       +++ v++cs+p+edGl v+t+t+
  gi|344210175|ref|YP_004786351.1| 119 EHGLVPSCSFPAEDGLTVSTDTP 141
                                       ********************985 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 !   45.7   0.8   3.8e-15   3.4e-12       1      40 []     147     186 ..     147     186 .. 0.93
   2 ?   -3.3   2.8       7.9   7.1e+03      12      19 ..     253     260 ..     251     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 3.8e-15
                   NADH-G_4Fe-4S_3   1 RktilellLanHpldCltCdknGnCeLQdlayelgveesr 40 
                                       R  +l+l L+nH+l C+tC+ nG+CeLQd a    v++ r
  gi|344210175|ref|YP_004786351.1| 147 RSVNLDLVLSNHNLRCTTCSGNGRCELQDAAISEDVDHPR 186
                                       6789***************************999999876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.9
                   NADH-G_4Fe-4S_3  12 HpldCltC 19 
                                       H+ +C +C
  gi|344210175|ref|YP_004786351.1| 253 HDSECVSC 260
                                       9999**99 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   1.2e-11   1.1e-08       5      54 ..     392     444 ..     388     445 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.2e-11
                                       EEE-SSBTT--EEEEEEETTEEE...EEEE-TTSTTTTT---HHHHTCHHCCC CS
                    Molybdop_Fe4S4   5 ktaCpyCgvgCglevhvkdgkiv...kvegdpdhpvnegrlCvKGrtllervy 54 
                                        t+C +C vgC +e++ kdg       v+  +++p+n+  +CvKG++++e+ +
  gi|344210175|ref|YP_004786351.1| 392 ETTCGFCAVGCRFEMWGKDGDSLgvvPVDDPDNAPANNFSTCVKGKFGHEFAN 444
                                       79******************98844466667789****************988 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   8.9   5.5e-12   4.9e-09       2      53 ..     207     269 ..     206     274 .. 0.77
   2 ?   -0.9   0.3       2.1   1.9e+03      10      19 ..     394     403 ..     385     406 .. 0.73
   3 ?   -2.8   0.1       8.3   7.4e+03      13      27 ..     520     534 ..     517     543 .. 0.79

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 5.5e-12
                           Fer4_21   2 ridedkCigCgkCliaCedtshqai..........eidaktvl.......kvvedeCvGCnlCssvCPv 53 
                                       +id++kCi C++C+ aC+d  ++ +          +      +       ++ ++eCv C  C++vCP+
  gi|344210175|ref|YP_004786351.1| 207 QIDRNKCILCNRCVDACNDVQVEGVlrieghgedtR------IgfqsdaeTMHDSECVSCGHCATVCPT 269
                                       69*****************99999886655433331......2344444366789*************6 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.1
                           Fer4_21  10 gCgkCliaCe 19 
                                        Cg C++ C+
  gi|344210175|ref|YP_004786351.1| 394 TCGFCAVGCR 403
                                       6888888886 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 8.3
                           Fer4_21  13 kCliaCedtshqaie 27 
                                       +C+  C+ +++ a++
  gi|344210175|ref|YP_004786351.1| 520 NCARLCHSSTVAALQ 534
                                       799999988888775 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2       4.1   3.7e+03      37      44 ..     161     171 ..     125     173 .. 0.68
   2 !   33.9   8.7     4e-11   3.6e-08       1      51 [.     212     270 ..     212     271 .. 0.75
   3 ?    4.6   0.0     0.057        51       4      13 ..     394     426 ..     393     529 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.1
                            Fer4_7  37 kClgC...gaC 44 
                                       +C++C   g+C
  gi|344210175|ref|YP_004786351.1| 161 RCTTCsgnGRC 171
                                       55555222456 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 4e-11
                            Fer4_7   1 rCigCgaCvaaCp....vkaieldeeenekgt....ekveidpekClgCgaCvavCPtg 51 
                                       +Ci C++Cv+aC      ++++++ + ++ ++    +  +++ ++C++Cg+C++vCPtg
  gi|344210175|ref|YP_004786351.1| 212 KCILCNRCVDACNdvqvEGVLRIEGHGEDTRIgfqsDAETMHDSECVSCGHCATVCPTG 270
                                       7***********85555566666655444432445466699****************98 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.057
                            Fer4_7   4 gCgaCvaaC.......................p 13 
                                        Cg+C++ C                       p
  gi|344210175|ref|YP_004786351.1| 394 TCGFCAVGCrfemwgkdgdslgvvpvddpdnaP 426
                                       6********666666666655555555544441 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   4.3   1.8e-06    0.0016       1      18 [.     206     223 ..     206     223 .. 0.96
   2 !   21.2   1.0   1.9e-07   0.00017       6      23 ..     255     272 ..     251     273 .. 0.88
   3 ?   -0.1   1.2       1.1   9.8e+02      11      20 ..     395     404 ..     393     406 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.8e-06
                                       EEEETTTSSS-THHHHHS CS
                              Fer4   1 vvideekCigCGaCvevC 18 
                                       ++id +kCi C++Cv++C
  gi|344210175|ref|YP_004786351.1| 206 IQIDRNKCILCNRCVDAC 223
                                       68**************** PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.9e-07
                                       TTSSS-THHHHHSTTTEE CS
                              Fer4   6 ekCigCGaCvevCPvgAI 23 
                                       + C+ CG C+ vCP+g +
  gi|344210175|ref|YP_004786351.1| 255 SECVSCGHCATVCPTGSL 272
                                       78*************976 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.1
                                       -THHHHHSTT CS
                              Fer4  11 CGaCvevCPv 20 
                                       CG C+  C +
  gi|344210175|ref|YP_004786351.1| 395 CGFCAVGCRF 404
                                       *****99965 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   3.0   6.6e-08   5.9e-05       1      20 [.     205     224 ..     205     232 .. 0.89
   2 !   17.7   1.8   2.9e-06    0.0026       9      22 ..     257     270 ..     251     272 .. 0.88
   3 ?   -0.9   0.6       2.3     2e+03      12      20 ..     395     403 ..     393     407 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 6.6e-08
                            Fer4_6   1 vveidpdkCigCgdCvrvCP 20 
                                       +++id++kCi C++Cv++C 
  gi|344210175|ref|YP_004786351.1| 205 FIQIDRNKCILCNRCVDACN 224
                                       689****************5 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.9e-06
                            Fer4_6   9 CigCgdCvrvCPeg 22 
                                       C++Cg C++vCP+g
  gi|344210175|ref|YP_004786351.1| 257 CVSCGHCATVCPTG 270
                                       ************98 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.3
                            Fer4_6  12 CgdCvrvCP 20 
                                       Cg C++ C 
  gi|344210175|ref|YP_004786351.1| 395 CGFCAVGCR 403
                                       *****9996 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 !    8.1   0.3    0.0056         5       1      12 [.     212     223 ..     192     235 .. 0.88
   2 !   19.3   0.1   1.9e-06    0.0017       2      20 ..     257     275 ..     256     320 .. 0.85
   3 ?   -1.0   0.1       3.9   3.5e+03      53      64 ..     391     402 ..     363     405 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0056
                           Fer4_16   1 rCgtCgkCaevC 12 
                                       +C+ C++C+++C
  gi|344210175|ref|YP_004786351.1| 212 KCILCNRCVDAC 223
                                       588888888888 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.9e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C++Cg Ca vCPt+ ++ek
  gi|344210175|ref|YP_004786351.1| 257 CVSCGHCATVCPTGSLTEK 275
                                       ****************998 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 3.9
                           Fer4_16  53 aitgCdiCqdvC 64 
                                       + t C+ C+  C
  gi|344210175|ref|YP_004786351.1| 391 QETTCGFCAVGC 402
                                       446777777666 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   1.7       1.6   1.4e+03       7      55 ..     109     166 ..     108     174 .. 0.43
   2 !   24.4   8.0   3.2e-08   2.9e-05       3      64 ..     211     270 ..     209     271 .. 0.71
   3 ?    0.4   0.0         1     9e+02       7      16 ..     394     403 ..     392     470 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.6
                            Fer4_8   7 eCgaCq.........saCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcg 55 
                                       eC  C+          +C +  + +   + d+++  +++ ++ + +   +   +Cttc 
  gi|344210175|ref|YP_004786351.1| 109 ECRTCMvetdehglvPSCSFPAEDGlTVSTDTPDAEEARSVNLDLVL-SNHNLRCTTCS 166
                                       67777766666666666754444443444444444444222222211.22233444443 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 3.2e-08
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaae.....dvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       +kCi C +C +aC  ++ ++  + +  ge +      d+++ +         +C++cg+C++vCp+g
  gi|344210175|ref|YP_004786351.1| 211 NKCILCNRCVDACNDVQVEGVLRIEGHGEDTRigfqsDAETMHD-------SECVSCGHCATVCPTG 270
                                       69***********9777766444444444333335445555555.......9*************86 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1
                            Fer4_8   7 eCgaCqsaCp 16 
                                        Cg+C   C 
  gi|344210175|ref|YP_004786351.1| 394 TCGFCAVGCR 403
                                       5777777773 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.7       6.2   5.6e+03      35      40 ..     109     114 ..      89     127 .. 0.72
   2 !    7.9   8.2    0.0039       3.5       2      47 ..     162     224 ..     160     228 .. 0.61
   3 !   23.6  10.0   4.9e-08   4.4e-05       1      49 [.     212     270 ..     212     272 .. 0.77
   4 ?    1.7   0.2      0.34     3e+02       3      20 ..     393     410 ..     387     434 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6.2
                            Fer4_9  35 aCigCg 40 
                                       +C +C+
  gi|344210175|ref|YP_004786351.1| 109 ECRTCM 114
                                       355555 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0039
                            Fer4_9   2 CtgC...gaCveaCpagvvved.aaerkarlraase................eaCigCgaCveaCp 47 
                                       Ct C   g+C+   +  +++ed + +r+   +++ +                ++Ci C++Cv+aC+
  gi|344210175|ref|YP_004786351.1| 162 CTTCsgnGRCEL--QDAAISEDvDHPRYGVFDER-DqyepiddtssfiqidrNKCILCNRCVDACN 224
                                       666644445655..33333322022333333333.2468888888899999999***********7 PP

  == domain 3  score: 23.6 bits;  conditional E-value: 4.9e-08
                            Fer4_9   1 kCtgCgaCveaC....pagvvvedaaerkarlraase......eaCigCgaCveaCpkg 49 
                                       kC+ C++Cv+aC      gv + +  ++  r+  +s+      ++C++Cg C+ +Cp+g
  gi|344210175|ref|YP_004786351.1| 212 KCILCNRCVDACndvqVEGVLRIEGHGEDTRIGFQSDaetmhdSECVSCGHCATVCPTG 270
                                       7***********888855555555555555555555578899989************97 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.34
                            Fer4_9   3 tgCgaCveaCpagvvved 20 
                                       t Cg C   C ++++ +d
  gi|344210175|ref|YP_004786351.1| 393 TTCGFCAVGCRFEMWGKD 410
                                       568888888888887666 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       3.1   2.8e+03      44      51 ..     161     171 ..     142     174 .. 0.69
   2 !   21.7  13.2   1.8e-07   0.00016       2      56 .]     206     268 ..     205     268 .. 0.84
   3 !   13.7   2.3   5.5e-05     0.049       5      23 ..     253     271 ..     249     306 .. 0.79
   4 ?   -3.1   0.6       9.7   8.7e+03       7      13 ..     393     399 ..     387     405 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.1
                           Fer4_10  44 kCtgc...gaC 51 
                                       +Ct+c   g C
  gi|344210175|ref|YP_004786351.1| 161 RCTTCsgnGRC 171
                                       56666333455 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.8e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPadl.........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       ++id+++Ci C++Cv+aC  d+          + + + +  +++a+    ++C  cg C+ +CP
  gi|344210175|ref|YP_004786351.1| 206 IQIDRNKCILCNRCVDAC-NDVqvegvlrieGHGEDTRIGFQSDAETMHDSECVSCGHCATVCP 268
                                       689***************.5559******975555556666666777788*************9 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 5.5e-05
                           Fer4_10   5 dddtCirCgkCvkaCPadl 23 
                                        d+ C+ Cg C ++CP+  
  gi|344210175|ref|YP_004786351.1| 253 HDSECVSCGHCATVCPTGS 271
                                       5788************933 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 9.7
                           Fer4_10   7 dtCirCg 13 
                                        tC  C+
  gi|344210175|ref|YP_004786351.1| 393 TTCGFCA 399
                                       4555554 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   4.2    0.0024       2.1      84      98 ..     212     226 ..     203     236 .. 0.87
   2 !   14.2   1.5   4.3e-05     0.038      52      80 ..     248     276 ..     227     281 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0024
                           Fer4_18  84 eciscllcidacdkv 98 
                                       +ci c +c+dac++v
  gi|344210175|ref|YP_004786351.1| 212 KCILCNRCVDACNDV 226
                                       7************98 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.3e-05
                           Fer4_18  52 erkekgagdcidcescvkvcPtgidirkG 80 
                                       + ++  +++c++c++c +vcPtg    kG
  gi|344210175|ref|YP_004786351.1| 248 DAETMHDSECVSCGHCATVCPTGSLTEKG 276
                                       44567789**************9766666 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.3       7.5   6.7e+03      12      16 ..     109     113 ..     108     115 .. 0.77
   2 ?   -1.9   1.5       5.3   4.8e+03       9      16 ..     161     171 ..     157     173 .. 0.70
   3 ?   15.9   2.8   1.1e-05      0.01       3      20 ..     206     223 ..     204     224 .. 0.94
   4 ?   13.1   4.5   8.6e-05     0.077       6      22 .]     254     269 ..     251     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.5
                            Fer4_2  12 gCgaC 16 
                                       +C++C
  gi|344210175|ref|YP_004786351.1| 109 ECRTC 113
                                       69999 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.3
                            Fer4_2   9 rCigC...gaC 16 
                                       rC+ C   g C
  gi|344210175|ref|YP_004786351.1| 161 RCTTCsgnGRC 171
                                       78888544477 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 1.1e-05
                            Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                       +++d+++Ci C+ Cv+aC
  gi|344210175|ref|YP_004786351.1| 206 IQIDRNKCILCNRCVDAC 223
                                       789*************** PP

  == domain 4  score: 13.1 bits;  conditional E-value: 8.6e-05
                            Fer4_2   6 dtdrCigCgaCvsaCPa 22 
                                       d++ C++Cg C ++CP+
  gi|344210175|ref|YP_004786351.1| 254 DSE-CVSCGHCATVCPT 269
                                       667.************7 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 ?   12.4   0.0   0.00015      0.13      10      48 ..     989    1028 ..     981    1042 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                                        -CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCC.EEEEEE CS
                           CDC48_N   10 edvgrgivridpedmeelglepgdvveiegkrk.Tvaivw 48  
                                        ++vg + v ++pe+ e+lg+  g++v++e +r  +v+++ 
  gi|344210175|ref|YP_004786351.1|  989 SHVGESFVEVHPETAEKLGIADGEYVRVESRRGdIVVKAQ 1028
                                        489**************************97743555543 PP

>> NIPSNAP  NIPSNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00065      0.58       8      55 ..     461     508 ..     460     510 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00065
                                       E-TT-HHHHHHHHHHTHHHHHHHHH--EEEEEEEEESBSSEEEEEEEE CS
                           NIPSNAP   8 lkpgklaeflerfareiiaiqekhggeliGyfaseiGalnqvlhlway 55 
                                       l p + +e+l  +a+++ +iq +hg++ +G+ as+ G++ +++   ++
  gi|344210175|ref|YP_004786351.1| 461 LEPTTWEEALDYVAERFTEIQDQHGIDSLGCLASSKGSNEEAYLVQKF 508
                                       7899999*******************************9999987777 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 ?   -1.3   0.3       4.1   3.7e+03       6      33 ..     163     189 ..     162     203 .. 0.68
   2 ?   13.3   3.5   0.00012      0.11       1      23 [.     206     228 ..     206     256 .. 0.80
   3 ?    7.0   0.7     0.011       9.5       6      33 ..     255     284 ..     251     325 .. 0.68
   4 ?   -1.4   0.0       4.6   4.2e+03      19      48 ..     934     961 ..     918     964 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 4.1
                           Fer4_15   6 daCigcglCvaeapevfeldedglasvl 33 
                                       ++C g g+C   +   + +d d+  + +
  gi|344210175|ref|YP_004786351.1| 163 TTCSGNGRCELQD-AAISEDVDHPRYGV 189
                                       68*******8885.68888877765444 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00012
                           Fer4_15   1 VvvDrdaCigcglCvaeapevfe 23 
                                       + +Dr++Ci c++Cv+++ +v +
  gi|344210175|ref|YP_004786351.1| 206 IQIDRNKCILCNRCVDACNDVQV 228
                                       68****************77644 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.011
                           Fer4_15   6 daCigcglCvaeape..vfeldedglasvl 33 
                                       ++C +cg C++++p+  + e+  dg a++ 
  gi|344210175|ref|YP_004786351.1| 255 SECVSCGHCATVCPTgsLTEKGIDGAATLP 284
                                       68***********75214444447777554 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 4.6
                           Fer4_15  19 pevfeldedglasvllddgeiaegevpdde 48 
                                       +  f ++ dg+a+++ +dg    ge+pd+e
  gi|344210175|ref|YP_004786351.1| 934 EGNFNFE-DGKARFVPADGG-HPGEIPDEE 961
                                       5667777.999999955444.567888875 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.72   6.4e+02      74      90 ..     157     173 ..     127     178 .. 0.81
   2 ?    7.6   0.3    0.0075       6.7      76      93 ..     207     224 ..     193     227 .. 0.86
   3 ?   11.7   1.3    0.0004      0.36       1      15 [.     256     270 ..     245     276 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.72
                           Fer4_22  74 kekfgesgCvGCgRCie 90 
                                       +++   ++C G gRC+ 
  gi|344210175|ref|YP_004786351.1| 157 NHNLRCTTCSGNGRCEL 173
                                       55667789*******75 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0075
                           Fer4_22  76 kfgesgCvGCgRCieacp 93 
                                       ++++++C+ C+RC++ac+
  gi|344210175|ref|YP_004786351.1| 207 QIDRNKCILCNRCVDACN 224
                                       67999************7 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.0004
                           Fer4_22   1 rClsCgaCtlvCptC 15 
                                       +C+sCg+C++vCpt 
  gi|344210175|ref|YP_004786351.1| 256 ECVSCGHCATVCPTG 270
                                       488888888888875 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 ?    8.8   4.1    0.0026       2.3       1      19 [.     208     226 ..     208     229 .. 0.95
   2 ?    6.4   3.7     0.015        13       2      17 ..     254     268 ..     254     270 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0026
                           Fer4_13   1 VDrdtCiacgaCvelaPdv 19 
                                       +Dr++Ci c+ Cv+++ dv
  gi|344210175|ref|YP_004786351.1| 208 IDRNKCILCNRCVDACNDV 226
                                       8***************997 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.015
                           Fer4_13   2 DrdtCiacgaCvelaP 17 
                                       D ++C++cg C+ ++P
  gi|344210175|ref|YP_004786351.1| 254 D-SECVSCGHCATVCP 268
                                       5.89************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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):              20  [number of targets reported over threshold]
# CPU time: 0.87u 0.32s 00:00:01.19 Elapsed: 00:00:00.54
# Mc/sec: 6172.73
//
Query:       gi|344210176|ref|YP_004786352.1|  [L=243]
Description: creatininase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-68  230.9   2.0    1.7e-68  230.7   2.0    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 !  230.7   2.0   9.6e-73   1.7e-68       4     241 .]       7     231 ..       4     231 .. 0.92

  Alignments for each domain:
  == domain 1  score: 230.7 bits;  conditional E-value: 9.6e-73
                      Creatininase   4 twpeveealkeddvailPvGstEqHGphlplgtDtliaealaervaeklgakalvlPtlpyGvseehlgfpGTisls 80 
                                       tw++++++  e+++a+lPvGstEqHGph+plgtDtl aea+aer ae+++  ++v+P++p+Gv+eeh++f GT++ s
  gi|344210176|ref|YP_004786352.1|   7 TWTDMAAV--ETSLALLPVGSTEQHGPHAPLGTDTLDAEAVAERGAERYDDPVVVAPAVPVGVAEEHRAFTGTLWTS 81 
                                       999**999..99*************************************988************************* PP

                      Creatininase  81 petliavlrdileslarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaaeaaees 157
                                       ++t+++++rdi++sla hG++++vlvngHggn++al+e+  +++++ +a av        +++++++        + 
  gi|344210176|ref|YP_004786352.1|  82 ESTFRSYVRDIVRSLASHGWDHVVLVNGHGGNIDALREVSGKITRHDEAFAV--------PFTWFDA--------VG 142
                                       *********************************************9955443........2222222........22 PP

                      Creatininase 158 eeeegggHAgelEtSlmlalrpelVrmdraedpeeaklakeg.....vstaedaeelspsGvlGdpskataekGeal 229
                                       +++ ++gH+g+lEtSl+ +++pe V++dr++++++  ++ +g     v+ a d +e++++Gv+Gdp++ +ae+Ge l
  gi|344210176|ref|YP_004786352.1| 143 DHSADMGHGGPLETSLLRHMNPETVHEDRLDEAADGGSDGWGewqsgVNLAFDSDEFTENGVVGDPREGSAERGETL 219
                                       334499****************************99999999*********************************** PP

                      Creatininase 230 leaaveelaell 241
                                       le a+e+l++ll
  gi|344210176|ref|YP_004786352.1| 220 LELATESLVDLL 231
                                       *********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1590.66
//
Query:       gi|344210177|ref|YP_004786353.1|  [L=283]
Description: putative protease [Haloarcula hispanica ATCC 33960]
Scores for 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-14   52.3   8.5    5.7e-14   52.3   8.5    2.8  4  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 ?   -1.2   1.2      0.15   2.7e+03      63      64 ..      52      53 ..      10      95 .. 0.54
   2 ?   -0.6   0.9     0.096   1.7e+03      22      55 ..      67      96 ..      45     116 .. 0.55
   3 !   52.3   8.5   3.2e-18   5.7e-14       5      90 ..     122     226 ..     116     227 .. 0.86
   4 ?   -2.0   0.1      0.27   4.8e+03      52      72 ..     241     260 ..     230     269 .. 0.50

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.15
                                      HH CS
                              CPBP 63 al 64
                                      +l
  gi|344210177|ref|YP_004786353.1| 52 FL 53
                                      22 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.096
                                      HHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG CS
                              CPBP 22 lfRglllqllqergsstlailissilFglaHlpn 55
                                        R+ll +  +     + +i +  +++gl+ l+ 
  gi|344210177|ref|YP_004786353.1| 67 SPRSLLPPVRTL----IPVIGVVIAFWGLYNLVA 96
                                      444444443222....345666666666666554 PP

  == domain 3  score: 52.3 bits;  conditional E-value: 3.2e-18
                                       HHHHHHHHHHHHHHHHHHHTTCHHHHHHHH..S-.....HHHHHHHHHHHHHCSGGG.............HHH.HHH CS
                              CPBP   5 llvfllalllapllEEllfRglllqllqer.gss.....tlailissilFglaHlpn.............gps.vll 61 
                                       l+ ++  ll++++ EEllfR +l++++++  g+      ++ i + ++lF+l+Hlp              + + +l 
  gi|344210177|ref|YP_004786353.1| 122 LAALFSSLLFTAIPEELLFRTYLQEKFTRLaGGAtrravLAGIGLVAVLFALFHLPRwflasghgvgsalA-ArLLG 197
                                       67788899**********************633378899999**************976666666666532.236** PP

                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              CPBP  62 aalaGlvlgylylktgsllaaillHalln 90 
                                       ++l+Gl++g +y  tg+l+ ++l+Ha +n
  gi|344210177|ref|YP_004786353.1| 198 LTLMGLAYGSVYALTGNLWLVALFHASMN 226
                                       **************************998 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 0.27
                                       SGGGHHH.HHHHHHHHHHHHHH CS
                              CPBP  52 Hlpngps.vllaalaGlvlgyl 72 
                                       Hl+   s + +aa+++lv+  +
  gi|344210177|ref|YP_004786353.1| 241 HLVA--SvIEYAAIVSLVYLTV 260
                                       3333..2244555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); 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:                         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 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1856.81
//
Query:       gi|344210178|ref|YP_004786354.1|  [L=484]
Description: subtilase family protease [Haloarcula hispanica ATCC 33960]
Scores for complete 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   62.5   2.7    1.5e-15   57.3   0.0    2.7  2  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 !    3.2   1.4    0.0024        43      86     171 ..     167     248 ..     113     270 .. 0.59
   2 !   57.3   0.0   8.1e-20   1.5e-15     171     298 .]     353     467 ..     336     467 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0024
                                       STTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EE.SCETTCHHCHHHHHHHHHHHH.CCT-EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  86 apgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslg.estslpktgrsiealainravnkkgvlvviS 161
                                       ap+a+++ ++v      s    +   +a+++ ++ +vdvi   +   +   + tg + +   + ra+ ++g+++++ 
  gi|344210178|ref|YP_004786354.1| 167 APDADLYLARVD-----SV---DSYRQAVNWLVQADVDVIVAPVSfYGQPGDGTGPVAR--SATRAT-ESGSVFIAP 232
                                       555555533332.....21...3344688999999999766555521333333333333..778888.899999999 PP

                                       --SS-T-HH......E CS
                                       xxxxxxxxx......x RF
                      Peptidase_S8 162 aGNngktgs......s 171
                                       aGN  +++       +
  gi|344210178|ref|YP_004786354.1| 233 AGNLAQSHWsgqytsE 248
                                       9999844434433332 PP

  == domain 2  score: 57.3 bits;  conditional E-value: 8.1e-20
                                       EEE-TTCEECTTTSTTCEEEEEES.TTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 171 slqagspvgtpstsknvitvgayt.tegkiapfSsrGpssdgklkpdivapGgnivstwsrqsnnsaglssyqsmsG 246
                                       ++++  ++ +p+t++ +itvgay+   +++ pfSsrGp++d ++++d+vap  +        +         + + G
  gi|344210178|ref|YP_004786354.1| 353 HTTTRNSIVAPGTARKAITVGAYNsRIDQLEPFSSRGPTVDNRVGVDVVAPDRQ----FAAAA--------PDGFVG 417
                                       4566777889**************4558999********************999....33333........23479* PP

                                       HHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE......SSSSSSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 247 TSmAsPnaagaaAlllsalpkltpetvraallntAqdlgkadniesfaqGaG 298
                                       +S+A P + g aAlll+a+++l+p++ +++l++t +d+g++  ++++  G+G
  gi|344210178|ref|YP_004786354.1| 418 SSAAVPYVGGTAALLLDANESLSPRETEHLLERTTRDVGRP--GLDNGTGHG 467
                                       **************************************998..999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 2752.02
//
Query:       gi|344210179|ref|YP_004786355.1|  [L=205]
Description: ArsR family transcriptional regulator [Haloarcula hispanica ATCC 33960]
Scores for complete 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-14   52.5   0.0    6.4e-14   51.8   0.0    1.3  1  HTH_20    Helix-turn-helix domain
    6.6e-07   29.1   0.0    1.3e-06   28.1   0.0    1.5  1  MarR_2    MarR family
    4.2e-06   26.2   0.0      7e-06   25.5   0.0    1.4  1  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.27   11.1   0.0    1.6  1  HTH_IclR  IclR helix-turn-helix domain
       0.17   11.5   0.0        0.3   10.7   0.0    1.4  1  GerE      Bacterial regulatory proteins, luxR family
       0.18   11.7   0.0       0.33   10.8   0.0    1.4  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 !   51.8   0.0   2.1e-17   6.4e-14       1      58 [.      30      86 ..      30      88 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 2.1e-17
                                      HHHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20  1 dqiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      d++++ALa+ + r ++r L  +e+ t+se+a+r+d+s ++++yH+  Le+a+L+e v+
  gi|344210179|ref|YP_004786355.1| 30 DDVLDALASDTSRSLFRTL-YDEPGTPSEIADRCDTSVQNVHYHVSNLEDAELIEPVE 86
                                      789****************.***********************************875 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   4.5e-10   1.3e-06       8      53 ..      42      84 ..      35      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 4.5e-10
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      + +   L+++pg   t++e+a+r++ s ++v++++  L++a L+e 
  gi|344210179|ref|YP_004786355.1| 42 RSLFRTLYDEPG---TPSEIADRCDTSVQNVHYHVSNLEDAELIEP 84
                                      5677889*****...*****************************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 !   25.5   0.0   2.3e-09     7e-06      19      48 .]      54      83 ..      38      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.3e-09
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      + +e+A+r++ S+++v++++ +Le+++lI+
  gi|344210179|ref|YP_004786355.1| 54 TPSEIADRCDTSVQNVHYHVSNLEDAELIE 83
                                      679*************************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 ?   11.1   0.0   8.9e-05      0.27       7      49 ..      31      83 ..      31      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.9e-05
                                      HHHCT-CTTBSS..........-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  7 aiLdalaeapqe..........ltlselArrtglpkStvhRlLqtLvelGyve 49
                                      ++Ldala+ + +           t se+A+r++ +  +vh +++ L+   ++e
  gi|344210179|ref|YP_004786355.1| 31 DVLDALASDTSRslfrtlydepGTPSEIADRCDTSVQNVHYHVSNLEDAELIE 83
                                      69999999999999999999999***********************9988776 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   9.9e-05       0.3      21      41 ..      56      76 ..      53      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.9e-05
                                      HHHHHHHTS-HHHHHHHHHHH CS
                              GerE 21 keIAeelniSekTVkvhksni 41
                                       eIA++++ S ++V++h+sn+
  gi|344210179|ref|YP_004786355.1| 56 SEIADRCDTSVQNVHYHVSNL 76
                                      59*****************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 ?   10.8   0.0   0.00011      0.33      12      46 ..      49      83 ..      42      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                                      TTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 12 aegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                       +++ + +e+a+  + s  +v +H + L++a L+e
  gi|344210179|ref|YP_004786355.1| 49 YDEPGTPSEIADRCDTSVQNVHYHVSNLEDAELIE 83
                                      5678899**************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1206.56
//
Query:       gi|344210180|ref|YP_004786356.1|  [L=559]
Description: hypothetical protein HAH_5239 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   17.4   0.6        2.2    8.6   0.0    3.3  3  Ribosomal_L21p  Ribosomal prokaryotic L21 protein
     0.0064   17.1   0.1        1.1    9.9   0.0    3.6  3  Excalibur       Excalibur calcium-binding domain
     0.0081   16.3   0.2       0.19   11.9   0.1    2.4  2  YpM             Yersinia pseudo-tuberculosis mitogen
  ------ inclusion threshold ------
      0.015   15.2   5.3        1.9    8.5   0.0    4.3  4  RNase_II_C_S1   RNase II-type exonuclease C-terminal S1 domai
       0.14   12.4   0.1         13    6.1   0.0    3.0  3  NusG_II         NusG domain II
        1.5    9.2   6.7        1.3    9.3   0.2    3.7  4  AglB_L1         Archaeal glycosylation protein B long periphe


Domain annotation for each model (and alignments):
>> Ribosomal_L21p  Ribosomal prokaryotic L21 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.39   1.2e+03      27      69 ..      20      63 ..      13      89 .. 0.73
   2 ?    4.4   0.1     0.015        45      27      74 ..     255     301 ..     248     305 .. 0.76
   3 !    8.6   0.0   0.00074       2.2       7      66 ..     367     427 ..     365     440 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.39
                                      SSTTCEEEESSEEE....EE.ECTSSSES.STCEEEEEEEEEE- CS
                    Ribosomal_L21p 27 aevgdkveldkVllvgskddvkvGaplve.gakVeaevvehgkg 69
                                      ae+ ++v+ d+  l +++++v++G+ +++ g+++ +e+v+   +
  gi|344210180|ref|YP_004786356.1| 20 AEQQATVSEDSFPLHSDEQQVVTGETTLDpGTEIAVEIVSRESS 63
                                      55666677777777778888999999997468999999987544 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.015
                                       SSTTCEEEESSEEE....EE..ECTSSSESSTCEEEEEEEEEE---EEE CS
                    Ribosomal_L21p  27 aevgdkveldkVllvgskdd.vkvGaplvegakVeaevvehgkgkkiiv 74 
                                       +++g++ e+  V ++++ ++ + vG+++v+  +++a+v ++ ++ +++v
  gi|344210180|ref|YP_004786356.1| 255 VSQGETAEI-PVSMTDGGNKtLSVGSEAVN-YQINATVSDDDEDGEVLV 301
                                       568999999.566655544459*******6.9******98887777665 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00074
                                       CSTEEEEESSSEEEEEESS..SSSTTCEEEESSEEE....EE.ECTSSSESSTCEEEEEEEE CS
                    Ribosomal_L21p   7 tgGkqykVeegdvlkvekl..eaevgdkveldkVllvgskddvkvGaplvegakVeaevveh 66 
                                       t+++ + Vee   +  e+   ++++gd+ ++  Vl++ +  +v +G+p+ +  +++a+v + 
  gi|344210180|ref|YP_004786356.1| 367 TANEEFEVEETAEFGFEESvsRVQQGDTGRIPIVLATADAATVSIGSPATN-YEINATVRDG 427
                                       677788888888888886667789************999999******995.9*****9754 PP

>> Excalibur  Excalibur calcium-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00038       1.1       3      21 ..     119     137 ..     117     167 .. 0.85
   2 ?    1.9   0.0      0.12   3.5e+02      19      34 ..     281     297 ..     254     299 .. 0.74
   3 ?   -0.1   0.0      0.51   1.5e+03      11      33 ..     405     430 ..     400     431 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00038
                         Excalibur   3 nCtelrkagkggvakgapg 21 
                                       nCt++++a++ gva+++++
  gi|344210180|ref|YP_004786356.1| 119 NCTDATAAAEPGVAAKQQA 137
                                       9**************9887 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.12
                         Excalibur  19 apgYkan.kklDrDkDG 34 
                                       a  Y+ n + +D D DG
  gi|344210180|ref|YP_004786356.1| 281 AVNYQINaTVSDDDEDG 297
                                       44499999********9 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.51
                         Excalibur  11 gkggvakgapg..Ykan.kklDrDkD 33 
                                        ++ v+ g+p+  Y  n +  D+++D
  gi|344210180|ref|YP_004786356.1| 405 DAATVSIGSPAtnYEINaTVRDGNGD 430
                                       55566666444449999999***999 PP

>> YpM  Yersinia pseudo-tuberculosis mitogen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   6.3e-05      0.19      90     113 ..     278     301 ..     271     304 .. 0.89
   2 ?    1.6   0.0       0.1     3e+02      91     111 ..     413     433 ..     408     437 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.3e-05
                               YpM  90 ssetsnysldatvhddkedsdvlt 113
                                        se+ ny ++atv dd ed +vl 
  gi|344210180|ref|YP_004786356.1| 278 GSEAVNYQINATVSDDDEDGEVLV 301
                                       699******************985 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.1
                               YpM  91 setsnysldatvhddkedsdv 111
                                       s ++ny ++atv+d + d  v
  gi|344210180|ref|YP_004786356.1| 413 SPATNYEINATVRDGNGDDRV 433
                                       6679**********9988766 PP

>> 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 ?    3.8   0.0     0.019        57      28      46 ..      41      59 ..      38      67 .. 0.87
   2 ?    8.5   0.0   0.00064       1.9      29      51 ..     155     177 ..     152     182 .. 0.84
   3 ?    1.8   0.4     0.077   2.3e+02       4      42 ..     287     326 ..     285     332 .. 0.75
   4 ?   -2.5   0.1       1.7   5.2e+03      39      51 ..     396     408 ..     393     412 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.019
                     RNase_II_C_S1 28 veggaglplGervrVrLve 46
                                      v+g+++l++G+++ V++v+
  gi|344210180|ref|YP_004786356.1| 41 VTGETTLDPGTEIAVEIVS 59
                                      48999**********9986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00064
                     RNase_II_C_S1  29 eggaglplGervrVrLveADvat 51 
                                       +g+++l+ G++ +VrLv+ D  +
  gi|344210180|ref|YP_004786356.1| 155 TGETTLESGTEMTVRLVSEDASS 177
                                       7899*************988665 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.077
                     RNase_II_C_S1   4 dAvVvdvddrggtVqladPaVeArv.eggaglplGervrV 42 
                                        A+V d d++g +++l d a  ++  e+ + ++ G+ ++V
  gi|344210180|ref|YP_004786356.1| 287 NATVSDDDEDGEVLVLFDTAAAGTDaETLSVADDGDSLTV 326
                                       699********99999999988876455455555666655 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.7
                     RNase_II_C_S1  39 rvrVrLveADvat 51 
                                       r+ + L++AD at
  gi|344210180|ref|YP_004786356.1| 396 RIPIVLATADAAT 408
                                       6778899999987 PP

>> NusG_II  NusG domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0043        13      24      82 ..      70     128 ..      55     140 .. 0.85
   2 ?    2.5   0.0     0.056   1.7e+02      23      76 ..     182     235 ..     175     238 .. 0.83
   3 ?   -1.9   0.0       1.3   3.7e+03      21      41 ..     246     266 ..     237     295 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0043
                                       .EEEEEETTEEEEEEEE-TT--EEEEEEE-TTSEEEEEEETTEEEEEEE-SSS-HHHHH CS
                           NusG_II  24 ktavitvdgkvvktisLskedeektieiegeegtnvieikdgkvrvkeadCpdkiCvkt 82 
                                       + a+++ +g+   ++++s ++++++++++      ++  ++g+v+  e++C d +   +
  gi|344210180|ref|YP_004786356.1|  70 RDAKVQSNGTFAAQFDMSRVSANTSYKLSAYADADKLYERNGTVEECESNCTDATAAAE 128
                                       5799***********************8776667899999************9877655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.056
                                       ..EEEEEETTEEEEEEEE-TT--EEEEEEE-TTSEEEEEEETTEEEEEEE-SSS CS
                           NusG_II  23 aktavitvdgkvvktisLskedeektieiegeegtnvieikdgkvrvkeadCpd 76 
                                       +++++++ +g+ v ++++s + +++++e++ +    ++  + g+v   +++C d
  gi|344210180|ref|YP_004786356.1| 182 QREVRVQPNGTFVAQFDMSGVPANTSYELSAHVDGDTLFERTGTVAECDSNCTD 235
                                       67899*********************9987666566666678888888888887 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.3
                                       ....EEEEEETTEEEEEEEE- CS
                           NusG_II  21 keaktavitvdgkvvktisLs 41 
                                       +++ + v+tv + ++ +i+ s
  gi|344210180|ref|YP_004786356.1| 246 TDEDENVVTVSQGETAEIPVS 266
                                       444555566666666666653 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 ?    9.3   0.2   0.00044       1.3       4      46 ..      41      84 ..      39     124 .. 0.77
   2 ?    1.1   0.1      0.16   4.7e+02       4      44 ..     154     195 ..     152     228 .. 0.79
   3 ?   -2.6   0.1       2.3   6.8e+03      46      72 ..     263     288 ..     248     299 .. 0.54
   4 ?   -1.5   0.0       1.1   3.2e+03      22      72 ..     374     422 ..     361     453 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00044
                                      EEEEBSSSSEEEEEEEEE-.TTS-EEEEEEEEE.-BTTEEEEEE CS
                           AglB_L1  4 itGsaeagatvtasvelet.nqgrtftYrqeaeadedGefeltv 46
                                      +tG+++ +    ++ve+ + ++   f Y++ a+++++G+f+   
  gi|344210180|ref|YP_004786356.1| 41 VTGETTLDPGTEIAVEIVSrESSSPFVYKRDAKVQSNGTFAAQF 84
                                      6777777766667777777477899***************8655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.16
                                       EEEEBSSSSEEEEEEEEE-.TTS-EEEEEEEEE.-BTTEEEE CS
                           AglB_L1   4 itGsaeagatvtasvelet.nqgrtftYrqeaeadedGefel 44 
                                       itG+++ +    ++v+l + +    f  ++e++++++G+f  
  gi|344210180|ref|YP_004786356.1| 154 ITGETTLESGTEMTVRLVSeDASSPFLKQREVRVQPNGTFVA 195
                                       788888887777788877745678899999999999999964 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.3
                                       E---SS......-SSSS.EESS-EEEEE CS
                           AglB_L1  46 vPYstegeedgetnssv.eaagpYevta 72 
                                       +P s+++   g++  sv + a +Y++ a
  gi|344210180|ref|YP_004786356.1| 263 IPVSMTD--GGNKTLSVgSEAVNYQINA 288
                                       4555554..2333333312224555554 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.1
                                       -TTS-EEEEEEEEE.-BTTEE.EEEE---SS......-SSSSEESS-EEEEE CS
                           AglB_L1  22 tnqgrtftYrqeaeadedGef.eltvPYstegeedgetnssveaagpYevta 72 
                                       +++  +f +++++   ++G   ++ +  +t    d  t s  ++a++Ye+ a
  gi|344210180|ref|YP_004786356.1| 374 VEETAEFGFEESVSRVQQGDTgRIPIVLATA---DAATVSIGSPATNYEINA 422
                                       4444555555555444444321111222222...122333334445555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 3444.77
//
Query:       gi|344210181|ref|YP_004786357.1|  [L=92]
Description: photosystem reaction center subunit H-like protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   37.5   0.0    2.3e-09   37.2   0.0    1.1  1  PRC       PRC-barrel 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 !   37.2   0.0   1.3e-13   2.3e-09       1      78 [.       1      82 [.       1      83 [. 0.93

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.3e-13
                                      XEECCS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT...........-EEEEEGG.CEECCCTEEEET CS
                               PRC  1 edefrasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi......gekevliPfdlavkigkdriivd 73
                                      ++ + a++l + +V+++dG+++G+++++ +d+++g+++ +v++   + +i       + ++ +P    + +++d+++++
  gi|344210181|ref|YP_004786357.1|  1 MRTVLANQLSNVRVVSTDGREVGTLQNITLDTATGELQTIVINSEVQ-EIfgverdSDGDIRLPAS-LIESKRDHLTIQ 77
                                      5678899************************************9877.45699*************.************ PP

                                      TS-GG CS
                               PRC 74 apkel 78
                                      +p e+
  gi|344210181|ref|YP_004786357.1| 78 PPTEQ 82
                                      *9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); 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: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 623.08
//
Query:       gi|344210182|ref|YP_004786358.1|  [L=164]
Description: hypothetical protein HAH_5241 [Haloarcula hispanica ATCC 33960]
Scores for complete 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  16.5     0.0082   16.5   9.7    2.3  2  CopD      Copper resistance protein D
  ------ inclusion threshold ------
       0.13   12.5   9.8       0.16   12.3   6.4    2.4  2  DUF4149   Domain of unknown function (DUF4149)


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 !   12.5   1.2   1.6e-05      0.15      20      92 ..      41     111 ..      25     113 .. 0.80
   2 !   16.5   9.7   9.2e-07    0.0082       7      60 ..     103     158 ..     101     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                              CopD  20 vtGvvnallrvglagllttayGrlllaKlalllvllalaalnrfrlvprleaa..tgaggqalrhrlrrsaalel 92 
                                       v+ ++ a++    +g +   +G + la ++++ + ++ a+++ f+++p+++ +  +g++ + ++h++rr++ +++
  gi|344210182|ref|YP_004786358.1|  41 VSLAGFAWVE---TGTTLVDWG-VRLAHVGAFSLWFGGAMWHNFVVLPTVRSRpdAGEALKPQAHAFRRHLPVVI 111
                                       4444556666...555556799.99*************************888888888889999****998877 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 9.2e-07
                              CopD   7 FsrlalaavavvlvtGvvnallrvg..lagllttayGrlllaKlalllvllalaal 60 
                                       F r   +++ vv+vtGv+ ++ ++g    +ll+++ G l+ +Kl++l+vl+a+ a+
  gi|344210182|ref|YP_004786358.1| 103 FRRHLPVVISVVFVTGVYQTAGLIGlsALALLASPIGHLVAVKLLVLAVLTAMVAA 158
                                       66667788999**************75589999*****************998775 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1     0.085   7.6e+02      63      90 ..      23      50 ..       8      56 .. 0.68
   2 ?   12.3   6.4   1.8e-05      0.16       3      79 ..      68     156 ..      66     161 .. 0.55

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.085
                           DUF4149 63 klaseellqlllllvvllltllnafyle 90
                                        ++++ + ++ ll++ l++l+ + ++e
  gi|344210182|ref|YP_004786358.1| 23 SPTRRAVSVRSTLLLASLVSLAGFAWVE 50
                                      5566677778888888888888888876 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.8e-05
                           DUF4149   3 lglllGsqlwvtfvvapvlfrsLprhqfgelqskl...............Fplyfglglalsvlllltevavgsekl 64 
                                       ++l++G+ +w+ fvv p++ +  +  ++ + q++                  + +   ++ls+l+ll +++ +   l
  gi|344210182|ref|YP_004786358.1|  68 FSLWFGGAMWHNFVVLPTVRSRPDAGEALKPQAHAfrrhlpvvisvvfvtGVYQTAGLIGLSALALLASPIGH---L 141
                                       89*****************999433333333333333333555555544333333355667777777777655...3 PP

                           DUF4149  65 aseellqlllllvvl 79 
                                        + +ll l +l++++
  gi|344210182|ref|YP_004786358.1| 142 VAVKLLVLAVLTAMV 156
                                       333333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); 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:                         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 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1144.52
//
Query:       gi|344210183|ref|YP_004786359.1|  [L=155]
Description: iron dependent repressor [Haloarcula hispanica ATCC 33960]
Scores for complete 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   55.5   0.1    6.8e-15   55.0   0.1    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    1.3e-06   28.2   0.0    2.3e-06   27.4   0.0    1.4  1  MarR_2          MarR family
    2.8e-05   24.0   0.0    4.8e-05   23.2   0.0    1.3  1  MarR            MarR family
     0.0002   21.2   0.0     0.0003   20.7   0.0    1.2  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0014   19.1   0.0     0.0022   18.5   0.0    1.3  1  HTH_27          Winged helix DNA-binding domain
     0.0031   17.0   0.0     0.0044   16.5   0.0    1.2  1  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.016   15.4   0.0    1.2  1  Rio2_N          Rio2, N-terminal
      0.019   15.3   0.0      0.031   14.6   0.0    1.3  1  Rrf2            Transcriptional regulator
      0.067   13.2   0.0       0.12   12.4   0.0    1.4  1  Put_DNA-bind_N  Putative DNA-binding protein N-terminus
      0.073   13.0   0.0       0.12   12.4   0.0    1.5  1  HTH_12          Ribonuclease R winged-helix domain
       0.13   11.9   0.0        0.2   11.3   0.0    1.3  1  GntR            Bacterial regulatory proteins, gntR family
       0.14   11.2   0.0       0.16   11.0   0.0    1.1  1  Topoisom_bac    DNA topoisomerase
       0.15   12.0   0.0       0.24   11.3   0.0    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
       0.19   11.8   0.0       0.55   10.3   0.0    1.7  2  HTH_13          HTH DNA binding domain
        0.2   10.0   0.0       0.24    9.7   0.0    1.0  1  DUF505          Protein of unknown function (DUF505)


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 !   55.0   0.1   5.7e-18   6.8e-15       5      60 .]      23      79 ..      19      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 5.7e-18
                                      HHHHHHHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                    Fe_dep_repress  5 stEdYLetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                      s+  YL ++  lse   + v+t +l e+Lnv p+sV+em++kL++ G+v+yeky+g+
  gi|344210183|ref|YP_004786359.1| 23 SAGRYLFAVSVLSEsPTERVSTGELQEFLNVTPASVTEMVSKLDERGLVDYEKYQGV 79
                                      566799999999**8899*************************************97 PP

>> MarR_2  MarR family
   #    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      55 ..      33      75 ..      18      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.9e-09
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      +L  +p ++++ gel + l++++++v+ ++ +L ++GLv +++
  gi|344210183|ref|YP_004786359.1| 33 VLSESPTERVSTGELQEFLNVTPASVTEMVSKLDERGLVDYEK 75
                                      35666666*******************************9875 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0     4e-08   4.8e-05      12      48 ..      34      72 ..      28      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4e-08
                                      HHHSTTEEHH..HHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 12 lyeqgplsvs..eLakklgvskstvtrvldrLekkGlie 48
                                      l+e++  +vs  eL+++l+v++++vt+++ +L ++Gl++
  gi|344210183|ref|YP_004786359.1| 34 LSESPTERVStgELQEFLNVTPASVTEMVSKLDERGLVD 72
                                      555665555555*************************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 !   20.7   0.0   2.5e-07    0.0003      21      62 ..      41      84 ..      26      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.5e-07
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEES-H CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rgrr.irildl 62
                                      +++  el ++l++t+ +v+ + s+L ++gl++  +++ ++++d+
  gi|344210183|ref|YP_004786359.1| 41 RVSTGELQEFLNVTPASVTEMVSKLDERGLVDyEKYQgVTLTDR 84
                                      567788889***********************655445***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 !   18.5   0.0   1.8e-06    0.0022      15      68 .]      38      85 ..      27      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.8e-06
                            HTH_27 15 rrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      + +r++  +l ++lnv+ +++ ++++kL e+GLv         ++  v+lTd G
  gi|344210183|ref|YP_004786359.1| 38 PTERVSTGELQEFLNVTPASVTEMVSKLDERGLV------DYEKYQGVTLTDRG 85
                                      56788999**************************......33466678888876 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 !   16.5   0.0   3.7e-06    0.0044      16      47 ..      40      71 ..      32      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.7e-06
                            HTH_24 16 prisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                       r s  eL e l+++p+ v++ + +L e Gl+
  gi|344210183|ref|YP_004786359.1| 40 ERVSTGELQEFLNVTPASVTEMVSKLDERGLV 71
                                      58999*************************98 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   1.4e-05     0.016      12      70 ..      28      85 ..      17      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                            Rio2_N 12 LtavEmgmrn.hevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeG 70
                                      L av + + +  e V+t +++e+ +++  +v++ +s+l +++l+ ++  ky+G  Lt  G
  gi|344210183|ref|YP_004786359.1| 28 LFAVSVLSESpTERVSTGELQEFLNVTPASVTEMVSKLDERGLVDYE--KYQGVTLTDRG 85
                                      55666555432689********************************9..7******9887 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.6e-05     0.031      13      57 ..      30      73 ..      21      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-05
                                      HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 13 allyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      a+ +L++ ++e+ vs+ e+ e  n+ p  +  +++kL + glv  
  gi|344210183|ref|YP_004786359.1| 30 AVSVLSESPTER-VSTGELQEFLNVTPASVTEMVSKLDERGLVDY 73
                                      678899999998.******************************75 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    0.0001      0.12      12      44 ..      26      58 ..      24      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                                      HHHHHHHHHHHTT--EE-HHHHHHHCTS-HHHH CS
                    Put_DNA-bind_N 12 lYlryLeelkeegveriSSteLaealgvtaaqv 44
                                      +Yl +++ l+e+ +er+S  eL e l+vt+a v
  gi|344210183|ref|YP_004786359.1| 26 RYLFAVSVLSESPTERVSTGELQEFLNVTPASV 58
                                      69999*************************987 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 ?   12.4   0.0   9.9e-05      0.12      40      63 ..      63      86 ..      32      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.9e-05
                            HTH_12 40 rkleergltrrvgyagreltEkGl 63
                                       kl+ergl+    y g +lt++G 
  gi|344210183|ref|YP_004786359.1| 63 SKLDERGLVDYEKYQGVTLTDRGD 86
                                      68********************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 ?   11.3   0.0   0.00017       0.2      21      62 ..      39      79 ..      35      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                      TSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEE CS
                              GntR 21 GdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrGt 62
                                       ++  s  eL++ ++V+  +v e  ++L ++glv  ++ +G+
  gi|344210183|ref|YP_004786359.1| 39 TERV-STGELQEFLNVTPASVTEMVSKLDERGLVDYEKYQGV 79
                                      5667.788**************************99888876 PP

>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00013      0.16     342     399 ..      54     112 ..      37     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                      Topoisom_bac 342 tpaTraeiieklvergYverkk.kslvptelGkalvell.ekfkdlvspelTaeleekLd 399
                                       tpa+  e+++kl erg v+ +k + +  t+ G alv  +  +   +vs  + + l ++Ld
  gi|344210183|ref|YP_004786359.1|  54 TPASVTEMVSKLDERGLVDYEKyQGVTLTDRGDALVTEVgWR-FCVVSTFFESVLDTTLD 112
                                       9********************9999***********988433.35666666666666665 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    0.0002      0.24      24      56 ..      43      75 ..      34      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                                      HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 24 tadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      ++ e+ e l+v  ++v e++++L ++GlV+ ek
  gi|344210183|ref|YP_004786359.1| 43 STGELQEFLNVTPASVTEMVSKLDERGLVDYEK 75
                                      56799999*********************9886 PP

>> HTH_13  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00046      0.55      14      48 ..      42      76 ..      37      81 .. 0.89
   2 ?   -1.9   0.0       3.1   3.7e+03      28      40 ..      84      95 ..      78      96 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00046
                            HTH_13 14 VsagmvakeLkvtpraalklvkelglRElTGRgrf 48
                                      Vs+g  ++ L+vtp +++++v+ l+ R l   +++
  gi|344210183|ref|YP_004786359.1| 42 VSTGELQEFLNVTPASVTEMVSKLDERGLVDYEKY 76
                                      8999999******************9988777766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.1
                            HTH_13 28 raalklvkelglR 40
                                      r+ + lv+e+g R
  gi|344210183|ref|YP_004786359.1| 84 RG-DALVTEVGWR 95
                                      54.6799999987 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0002      0.24     473     531 ..      31      88 ..      20      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0002
                            DUF505 473 lkvlkkiPkrgvsveelveevdeleeeevrealeklearglvevlpdgnvvlTeaGeli 531
                                       ++vl++ P   vs  el e   ++    v+e ++kl+ rglv+  + ++v+lT  G+ +
  gi|344210183|ref|YP_004786359.1|  31 VSVLSESPTERVSTGELQEF-LNVTPASVTEMVSKLDERGLVDYEKYQGVTLTDRGDAL 88 
                                       67999999999999999555.58888999999999999999999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); 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:                        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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1028.57
//
Query:       gi|344210184|ref|YP_004786360.1|  [L=354]
Description: hypothetical protein HAH_5243 [Haloarcula hispanica ATCC 33960]
Scores for 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-82  268.9  16.5    9.2e-28   95.9   0.5    4.1  4  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 !   25.6   1.3   4.5e-10   8.1e-06       1      68 [.       4      71 ..       4      73 .. 0.89
   2 !   78.9   0.0   1.1e-26   1.9e-22       1      70 []      84     153 ..      84     153 .. 0.98
   3 !   77.9   0.5   2.1e-26   3.8e-22       3      70 .]     169     236 ..     167     236 .. 0.98
   4 !   95.9   0.5   5.1e-32   9.2e-28       1      70 []     268     337 ..     268     337 .. 0.97

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4.5e-10
                           DUF2249  1 tlDvRelppperhaaIfeafeaLapGetlelvndh..dPkpLlyqLearrpgffsweylergpgewrvli 68
                                      ++ +R+ ++++r ++ f+ ++  + G+t e+v+d+  dP+ ++yqLe+      +wey   + +  ++++
  gi|344210184|ref|YP_004786360.1|  4 EIQLRDQSERQRREQLFDVLSGAEVGDTIEVVADRdiDPQLVRYQLEQD--RSLEWEYAHPDVEPRELQV 71
                                      58899*****************************9555***********..999****988877777666 PP

  == domain 2  score: 78.9 bits;  conditional E-value: 1.1e-26
                           DUF2249   1 tlDvRelppperhaaIfeafeaLapGetlelvndhdPkpLlyqLearrpgffsweylergpgewrvlitk 70 
                                       t+DvR+l+p+ rh+a ++ f+ La+G++++lvndh+PkpL+++L+  +++ ++w+y  +g gew+v+i k
  gi|344210184|ref|YP_004786360.1|  84 TIDVRDLKPQRRHEALLDIFDGLAAGDGFVLVNDHNPKPLYHELKSMHGDVIEWDYTSQGGGEWQVEIVK 153
                                       79*****************************************************************976 PP

  == domain 3  score: 77.9 bits;  conditional E-value: 2.1e-26
                           DUF2249   3 DvRelppperhaaIfeafeaLapGetlelvndhdPkpLlyqLearrpgffsweylergpgewrvlitk 70 
                                       DvRe+p++erh++I+ ++  +++G t+el+++h+P+pL +++++r++++f+we++e +pg++rv+itk
  gi|344210184|ref|YP_004786360.1| 169 DVREIPKQERHPTIHHRYGMIPEGGTMELIAPHEPRPLQREFRQRYGDAFAWEVVESEPGRCRVQITK 236
                                       ******************************************************************97 PP

  == domain 4  score: 95.9 bits;  conditional E-value: 5.1e-32
                           DUF2249   1 tlDvRelppperhaaIfeafeaLapGetlelvndhdPkpLlyqLearrpgffsweylergpgewrvlitk 70 
                                       +lDvR+lpp++rh++Ifea+++L+ G +++lvndhdPkpL++q+ea+++ +f+w+y++++pge+rvli k
  gi|344210184|ref|YP_004786360.1| 268 ELDVRDLPPAQRHEQIFEAYAELDTGSGFVLVNDHDPKPLYHQFEAEAGPEFRWTYRQQDPGEFRVLIGK 337
                                       69**********************************************8888***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 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:                        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: 00:00:00.41
# Mc/sec: 2612.38
//
Query:       gi|344210185|ref|YP_004786361.1|  [L=236]
Description: Hemerythrin HHE cation binding domain-containing protein [Haloarcula hispanica ATCC 33960]
Scores for 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-20   71.7  20.0    8.6e-20   71.7  20.0    1.7  2  Hemerythrin   Hemerythrin HHE cation binding domain
    3.5e-18   65.0   1.3    4.3e-18   64.7   0.1    1.8  2  ScdA_N        Domain of Unknown function (DUF542)
      3e-05   23.5   6.5      3e-05   23.5   6.5    1.5  2  CorA          CorA-like Mg2+ transporter protein
     0.0073   16.5   0.0       0.15   12.3   0.0    2.9  3  DUF1858       Domain of unknown function (DUF1858)
  ------ inclusion threshold ------
      0.011   15.0   2.6      0.014   14.6   1.2    1.9  2  DLP_helical   Dynamin-like helical domain
      0.021   15.7   3.1      0.058   14.3   0.4    2.5  2  ERp29         Endoplasmic reticulum protein ERp29, C-terminal
      0.056   13.4   8.0      0.032   14.2   5.8    1.7  1  DinB          DinB family
      0.059   13.3   1.1        2.5    8.0   0.0    3.2  3  Prefoldin     Prefoldin subunit
      0.063   13.3   0.4       0.12   12.4   0.4    1.5  1  DUF3038       Protein of unknown function (DUF3038)
      0.063   13.4   3.5       0.11   12.6   0.7    2.5  2  RasGAP_C      RasGAP C-terminus
      0.092   13.1   0.4       0.32   11.3   0.0    2.1  3  Utp12         Dip2/Utp12 Family
       0.11   12.6   1.0       0.26   11.5   0.5    1.9  1  SesA          N-terminal domain on NACHT_NTPase and P-loop NT
       0.12   12.0   2.9       0.21   11.2   2.9    1.5  1  Exonuc_VII_L  Exonuclease VII, large subunit
       0.15   11.8   4.7       0.21   11.3   1.2    2.3  2  SHE3          SWI5-dependent HO expression protein 3
       0.41   10.8   5.3         22    5.2   0.0    3.6  2  ImpA_N        ImpA, N-terminal, type VI secretion system
       0.58    8.7   2.5        6.7    5.2   0.9    2.0  2  FapA          Flagellar Assembly Protein A
        1.2    9.2   2.7         18    5.4   1.7    2.7  3  DUF1664       Protein of unknown function (DUF1664)
        7.3    5.4  14.1         12    4.7   9.0    2.4  2  Spc7          Spc7 kinetochore protein
        7.5    7.3  15.6        1.3    9.7   5.1    2.8  3  DUF4404       Domain of unknown function (DUF4404)


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 ?    0.2   0.2       1.2   1.1e+03      83      92 ..      54      64 ..      38      84 .. 0.42
   2 !   71.7  20.0   9.1e-23   8.6e-20       4     130 ..      81     227 ..      78     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.2
                                      HHHHHHHHH.H CS
                       Hemerythrin 83 irelleelr.e 92
                                      +re+l+e+r +
  gi|344210185|ref|YP_004786361.1| 54 VREQLDEARrK 64
                                      22222222211 PP

  == domain 2  score: 71.7 bits;  conditional E-value: 9.1e-23
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC....HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH............ CS
                       Hemerythrin   4 ealdeeHralrallerlraladaaaevhga....lrklaelldelvdeleaHhaaEEellfPlle...........d 65 
                                       +++d +H++lr++l +l++la+++ +vh +    l+++++ + el++e+++H ++EE+ +fP++e           +
  gi|344210185|ref|YP_004786361.1|  81 HVVDSHHQYLREELPALEQLAEKVRSVHAEehpeLADIEREVLELAEEMRQHTTEEEQDVFPVIEkldsgdeltgkE 157
                                       7899*******************88888888899******************************************* PP

                                       CCC.HHHHHHHHHHHHHHHHHHHHHHHHCHTCGGSTCHHHHH.....HHHHHHHHHHHHHHHHHHTHHHH CS
                       Hemerythrin  66 rpggravldvlereHdeirelleelrellkgleepsaaafae.....lleeladllreHiakEesilfpl 130
                                       r++ ++ l++le +H++ +e le+++el +g++ p++a++ +     +le+l+++ + H++kE+++lfp 
  gi|344210185|ref|YP_004786361.1| 158 RARLDEALADLESDHEATAEHLERIAELSDGYAVPDDACPSYqslleRLETLEQDTHMHVHKENNVLFPQ 227
                                       *********************************************************************7 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 !   64.7   0.1   4.5e-21   4.3e-18       2      55 ..       8      61 ..       7      62 .. 0.96
   2 ?   -3.5   0.1       8.9   8.4e+03      34      53 ..     161     180 ..     159     182 .. 0.69

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 4.5e-21
                            ScdA_N  2 dqtvGeivaelpraakvFrkygIDFCCgGkvsLaeAckekgidleevlaeLeal 55
                                      d+++G +v e+p  a+vF+ +g+DFCCgG++ L++Ac+e+++dl++v ++L+++
  gi|344210185|ref|YP_004786361.1|  8 DRPLGALVRENPAFARVFEAVGLDFCCGGDQMLRTACTEADLDLDAVREQLDEA 61
                                      6899***********************************************986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.9
                            ScdA_N  34 LaeAckekgidleevlaeLe 53 
                                       L+eA+++ + d e+ +++Le
  gi|344210185|ref|YP_004786361.1| 161 LDEALADLESDHEATAEHLE 180
                                       67777777777777777776 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   6.5   3.2e-08     3e-05      77     222 ..      37     189 ..      32     192 .. 0.90
   2 ?    1.2   0.0      0.19   1.8e+02     173     210 ..     178     215 ..     175     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.2e-08
                              CorA  77 dnflitvrreplealdevikrlk...deggkpkspgellyrlldeivdrlfellekleeeldeledeledstkkeil 150
                                       d++l t + e    ld+v+++l+   ++++++ +  e + +l++ +vd+++++l++    l++l + + +s ++e++
  gi|344210185|ref|YP_004786361.1|  37 DQMLRTACTEADLDLDAVREQLDearRKREERGDEWESMTALIEHVVDSHHQYLREELPALEQLAEKV-RSVHAEEH 112
                                       6677778888877788999999988788899999999*******************************.******** PP

                              CorA 151 relaqlrrrlvkl.....rralapnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdty 222
                                        ela+++r++ +l     ++   + ++v+  + + + +++l+ +++ +l++ l +le+ +e +    er+  l+d y
  gi|344210185|ref|YP_004786361.1| 113 PELADIEREVLELaeemrQHTTEEEQDVFPVIEKLDSGDELTGKERARLDEALADLESDHEATAEHLERIAELSDGY 189
                                       *****************9999999*****99999************************8888888888888888876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.19
                              CorA 173 vlkrllakaddkllddedkeylrdlldelerllemlea 210
                                        l+r+ + +d+  ++d++ + ++ ll++le l+++++ 
  gi|344210185|ref|YP_004786361.1| 178 HLERIAELSDGYAVPDDACPSYQSLLERLETLEQDTHM 215
                                       577788889999999999999***********999985 PP

>> DUF1858  Domain of unknown function (DUF1858)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00016      0.15       1      37 [.       5      42 ..       5      52 .. 0.84
   2 ?   -1.6   0.0       3.4   3.2e+03      12      20 ..     110     118 ..     109     119 .. 0.89
   3 ?   -0.1   0.0       1.2   1.1e+03      31      51 ..     196     216 ..     193     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                      CETTSBHHHHHHH-GGGHHHHHHT..TGGGGGSCCHHTT CS
                           DUF1858  1 ItkdttIgelleeyPelaevLvel..Gfhclgcpsllkt 37
                                      I++d  +g l++e+P +a v+ ++   f c g++ +l+t
  gi|344210185|ref|YP_004786361.1|  5 IDPDRPLGALVRENPAFARVFEAVglDFCCGGDQ-MLRT 42
                                      99**********************5556666666.5665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.4
                                       HH-GGGHHH CS
                           DUF1858  12 eeyPelaev 20 
                                       ee+Pela++
  gi|344210185|ref|YP_004786361.1| 110 EEHPELADI 118
                                       79****997 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.2
                                       SCCHHTTHHHHSBHHHHHHHH CS
                           DUF1858  31 cpsllktvakvetleqaakvh 51 
                                       cps    + + etleq   +h
  gi|344210185|ref|YP_004786361.1| 196 CPSYQSLLERLETLEQDTHMH 216
                                       88877778899****966665 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.2   1.5e-05     0.014      65     136 ..      76     147 ..      53     154 .. 0.91
   2 ?   -1.4   0.0       1.1     1e+03     280     329 ..     160     212 ..     153     221 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                       DLP_helical  65 ksvirdvlerqlpeaeerleelekevekleesakriekelaelkkeieearielreelkayfsdLilqvkgl 136
                                        + i  v++ + ++ +e+l +le+ +ek ++ +++++ ela +++e+ e ++e+r+  ++ ++d+   ++ l
  gi|344210185|ref|YP_004786361.1|  76 TALIEHVVDSHHQYLREELPALEQLAEKVRSVHAEEHPELADIEREVLELAEEMRQHTTEEEQDVFPVIEKL 147
                                       56789999*************************************************999999987666655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                       DLP_helical 280 elkelkeelveklkdqrk..eilellndd.efietffpqylelekdleelees 329
                                       +l e+ ++l+++ + + +  e ++ l+d  ++  +  p+y++l ++le+le+ 
  gi|344210185|ref|YP_004786361.1| 160 RLDEALADLESDHEATAEhlERIAELSDGyAVPDDACPSYQSLLERLETLEQD 212
                                       44444444444433222211222333333366666667777777777766665 PP

>> ERp29  Endoplasmic reticulum protein ERp29, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2     0.027        25      23      82 ..      53     111 ..      37     116 .. 0.69
   2 ?   14.3   0.4   6.2e-05     0.058       3      77 ..      97     169 ..      94     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.027
                             ERp29  23 elleeakkaaeklksekekkaaeyYvkvmekiaekgeeyvekElkRLekllkkg.klaaek 82 
                                       ++ e++ +a +k +  +  ++ e  + ++e ++++ ++y+ +El  Le+l +k  +++ae+
  gi|344210185|ref|YP_004786361.1|  53 AVREQLDEARRKRE--ERGDEWESMTALIEHVVDSHHQYLREELPALEQLAEKVrSVHAEE 111
                                       44455555544444..666677777889999*******************98532666655 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 6.2e-05
                             ERp29   3 ieeldelaaefvaaakaereelleeakkaaeklksekekkaaeyYvkvmekiaekgeeyvekElkRLekllkkgk 77 
                                       +e+l e ++++ a++++e +++ +e+ ++ae++++++++++ +++  v+ek+ + + e   kE++RL++ l++ +
  gi|344210185|ref|YP_004786361.1|  97 LEQLAEKVRSVHAEEHPELADIEREVLELAEEMRQHTTEEEQDVF-PVIEKLDSGD-ELTGKERARLDEALADLE 169
                                       4566666777777779999***************88888888887.5899998777.***********9997444 PP

>> DinB  DinB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   5.8   3.4e-05     0.032      21     112 ..      50     144 ..      30     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.4e-05
                                       HHHHH.CT--CCCTT.--SSTTS--HHHHHHHHHHHHHHHHHHHHH...SSSGGGT---------HHHHHHHHHHHH CS
                              DinB  21 tldai.aaLpdeelk.aengegfqsvkqtlnHvldveelwlsrleg.eegapavddqterkeleeldalrealderl 94 
                                        lda+ ++L++   k  e+g    s+  ++ Hv+d+ +++l++     e+ +++   + ++e +el++  +++ e +
  gi|344210185|ref|YP_004786361.1|  50 DLDAVrEQLDEARRKrEERGDEWESMTALIEHVVDSHHQYLREELPaLEQLAEKVRSVHAEEHPELADIEREVLELA 126
                                       4455515566666668899***********************94448888888889999999999999999****** PP

                                       HHHHCT--HHHHHSEE-- CS
                              DinB  95 iafldqltdleretlldr 112
                                        ++ +  t++e++++++ 
  gi|344210185|ref|YP_004786361.1| 127 EEMRQHTTEEEQDVFPVI 144
                                       *********999998864 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.24   2.2e+02      12      39 ..      87     112 ..      76     127 .. 0.73
   2 ?   -0.3   0.0         1   9.5e+02      85     108 ..     157     180 ..     144     190 .. 0.56
   3 ?    8.0   0.0    0.0027       2.5       5      51 ..     182     225 ..     179     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHHHHHHHHHTT.-TT- CS
                         Prefoldin  12 laqlkeaieelektletlktlkkedegk 39 
                                       ++ l+e+++ le++ e ++++ +e+  +
  gi|344210185|ref|YP_004786361.1|  87 HQYLREELPALEQLAEKVRSVHAEE--H 112
                                       4558999999999999999998833..2 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  85 kleelekqlekleeeleklkdqit 108
                                       + + l+++l +le ++e  ++ ++
  gi|344210185|ref|YP_004786361.1| 157 ERARLDEALADLESDHEATAEHLE 180
                                       444555555555555554444443 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0027
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEE CS
                         Prefoldin   5 leslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyv 51 
                                       +++l + +a  ++a+++++++le+l+tl++   +++++v+ + ++ +
  gi|344210185|ref|YP_004786361.1| 182 IAELSDGYAVPDDACPSYQSLLERLETLEQ---DTHMHVHKENNVLF 225
                                       566666667778899***************...77788777777766 PP

>> DUF3038  Protein of unknown function (DUF3038)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   0.00013      0.12      64     106 ..      68     110 ..      53     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                           DUF3038  64 dveeakalvliichlakqlqeliRqllslleqleekkkepeqs 106
                                         +e ++++++i h+ + +++++R+ l +leql+ek ++++ +
  gi|344210185|ref|YP_004786361.1|  68 RGDEWESMTALIEHVVDSHHQYLREELPALEQLAEKVRSVHAE 110
                                       458999*****************************99988654 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.7   0.00012      0.11      32      91 ..      52     112 ..      50     149 .. 0.77
   2 ?    0.2   0.2      0.78   7.4e+02      39      75 ..     145     181 ..     118     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                          RasGAP_C  32 neIakdirnkgrlrekrkeElesleetlktL.seknnylesqlesYkayienvleqlkkkk 91 
                                       +++ + + + +r+re+r  E es+++ ++++ +++ +yl+++l  +++  e+v++  ++++
  gi|344210185|ref|YP_004786361.1|  52 DAVREQLDEARRKREERGDEWESMTALIEHVvDSHHQYLREELPALEQLAEKVRSVHAEEH 112
                                       6777888999*****************99963789**************999998876665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.78
                          RasGAP_C  39 rnkgrlrekrkeElesleetlktLseknnylesqles 75 
                                        ++++  e + +E  +l e+l++L++  +   ++le 
  gi|344210185|ref|YP_004786361.1| 145 EKLDSGDELTGKERARLDEALADLESDHEATAEHLER 181
                                       5556666677788888888888888888877777765 PP

>> Utp12  Dip2/Utp12 Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00034      0.32      36      90 ..      60     110 ..      45     128 .. 0.76
   2 ?   -2.3   0.0       5.8   5.4e+03      72      97 ..     160     185 ..     150     188 .. 0.62
   3 ?   -2.2   0.0       5.4   5.1e+03      32      49 ..     201     216 ..     197     220 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                                       HHHHHH.HTTTTHHHHHHHHHHHHHHHHHHHHHSH.HHHHHHHHHHHHHHHHHHH CS
                             Utp12  36 flaerlaeksphlelllrwlkallrvHgsylvaspsdlvpaLrslqkslrerlkt 90 
                                          + ++e++   e+++  ++ ++ +H++yl++   +l paL++l++++r+++++
  gi|344210185|ref|YP_004786361.1|  60 EARRKREERGDEWESMTALIEHVVDSHHQYLRE---EL-PALEQLAEKVRSVHAE 110
                                       4455567888899******************64...37.9********9998865 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.8
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Utp12  72 dlvpaLrslqkslrerlktlskllgl 97 
                                        l +aL+ l +  ++ +++l+++++l
  gi|344210185|ref|YP_004786361.1| 160 RLDEALADLESDHEATAEHLERIAEL 185
                                       56667777777777777766666665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5.4
                                       HHHHHHHHHH.HTTTTHH CS
                             Utp12  32 kLLeflaerlaeksphle 49 
                                        LLe l++ l e+ +h++
  gi|344210185|ref|YP_004786361.1| 201 SLLERLET-L-EQDTHMH 216
                                       57777777.5.3333433 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 ?   11.5   0.5   0.00027      0.26      22      84 ..      38     107 ..      33     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                              SesA  22 kglpeaFrevgkrLplvqetLedaksqlesskldedtesa.ikpvlescke....katkleeifekv..a 84 
                                       + l+ a  e+   L  v+e L++a+++ e++ +++++ +a i+ v++s ++    ++ +le++ ekv  +
  gi|344210185|ref|YP_004786361.1|  38 QMLRTACTEADLDLDAVREQLDEARRKREERGDEWESMTAlIEHVVDSHHQylreELPALEQLAEKVrsV 107
                                       668889999999*************************999999999998874444555566666666443 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 ?   11.2   2.9   0.00022      0.21     135     274 ..     101     194 ..      37     233 .. 0.42

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                      Exonuc_VII_L 135 Aelvvpdkaeleeqleeler...rlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlk 208
                                       Ae+v +++ae + +l+++er   +l ++++++ +e++q +  + ++l s +el+ ++r rlde+ ++le+  +++++
  gi|344210185|ref|YP_004786361.1| 101 AEKVRSVHAEEHPELADIERevlELAEEMRQHTTEEEQDVFPVIEKLDSGDELTGKERARLDEALADLES-DHEATA 176
                                       2222222222222222222222222233333333333333333344444444444444444444444444.223333 PP

                      Exonuc_VII_L 209 kkrerleelkerlkekleekkerlkklkerlelleekkerleeleeklealsplkvLkrGyaivrk 274
                                       ++ er+ e                                                L+ Gya+  +
  gi|344210185|ref|YP_004786361.1| 177 EHLERIAE------------------------------------------------LSDGYAVPDD 194
                                       33333333................................................3333333322 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 ?   11.3   1.2   0.00022      0.21      78     162 ..      40     124 ..      37     149 .. 0.87
   2 ?    1.8   0.7      0.18   1.7e+02     137     194 ..     160     181 ..     118     229 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                                       HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSX CS
                              SHE3  78 lkesveelklekkqlkkrlenssaseteleeelerlkvqYdalvdsqkeYkehYqqeieeLkesleklklenekqle 154
                                       l++   e+ l+ ++++++l++   + +e  +e e + +  + +vds+++Y       +e+L e++ + + e++ +l 
  gi|344210185|ref|YP_004786361.1|  40 LRTACTEADLDLDAVREQLDEARRKREERGDEWESMTALIEHVVDSHHQYLREELPALEQLAEKVRSVHAEEHPELA 116
                                       66777889999999*************************************999*****************998887 PP

                                       XXXXXXXX CS
                              SHE3 155 elqeriss 162
                                       + ++++ +
  gi|344210185|ref|YP_004786361.1| 117 DIEREVLE 124
                                       77766655 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHSSSXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SHE3 137 eLkesleklklenekqleelqerissndkdidtkldsynnkkknlesieeeknkkllk 194
                                       +L e+l +l+ ++e                                       ++l++
  gi|344210185|ref|YP_004786361.1| 160 RLDEALADLESDHE------------------------------------ATAEHLER 181
                                       34444444444433....................................32222222 PP

>> ImpA_N  ImpA, N-terminal, type VI secretion system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.024        22       2      27 ..       3      28 ..       2      31 .. 0.91
   2 ?    1.3   4.1      0.36   3.4e+02      16      55 ..      47      84 ..      42     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.024
                            ImpA_N  2 apisddspcGedlrydpefdaleear 27
                                      +pi++d+p G+ +r++p+f ++ ea+
  gi|344210185|ref|YP_004786361.1|  3 EPIDPDRPLGALVRENPAFARVFEAV 28
                                      7******************9998875 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.36
                            ImpA_N 16 ydpefdaleearnkarsdqsieakaadWkkveelaeelle 55
                                      +d + da++e++++ar++  +e++  +W+ + +l+e+++ 
  gi|344210185|ref|YP_004786361.1| 47 ADLDLDAVREQLDEARRK--REERGDEWESMTALIEHVVD 84
                                      566777777777777776..77777888887777776654 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.9    0.0071       6.7     326     411 ..      45     132 ..      27     145 .. 0.60
   2 ?    3.1   0.0     0.031        29     338     400 ..     157     219 ..     145     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0071
                              FapA 326 ievgldepelkeklkeleeeleeleeeleklkkkikklpklkaek..qlesekkeqlkklletkeklkeeleeleee 400
                                       +e+ ld  +++e+l+e +++ ee  +e e  ++ i+++ +++ ++  +  +  ++  +k++    +   el+++e+e
  gi|344210185|ref|YP_004786361.1|  45 TEADLDLDAVREQLDEARRKREERGDEWESMTALIEHVVDSHHQYlrEELPALEQLAEKVRSVHAEEHPELADIERE 121
                                       34444555677777777777777777777777778888885554300222233334444444446666666777777 PP

                              FapA 401 lkelkeelesk 411
                                         el ee++++
  gi|344210185|ref|YP_004786361.1| 122 VLELAEEMRQH 132
                                       77777777666 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.031
                              FapA 338 klkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleee 400
                                       ++++l+e l +le+  e   + ++++ +l+  ++++ +   ++++lle +e l+++ + + ++
  gi|344210185|ref|YP_004786361.1| 157 ERARLDEALADLESDHEATAEHLERIAELSDGYAVPDDACPSYQSLLERLETLEQDTHMHVHK 219
                                       447888888888888888888888888888899*****************9999988776655 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   1.7     0.019        18      38     107 ..      39     108 ..      30     156 .. 0.65
   2 ?    1.6   0.3      0.29   2.7e+02      88     115 ..     121     149 ..     114     189 .. 0.49
   3 ?   -0.7   0.0       1.4   1.4e+03      67      95 ..     160     188 ..     150     214 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.019
                           DUF1664  38 slsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                                        l+ a+++   +l+ v e+l +++r+ ++r d+ ++     +++  + ++ + e    l+++ e+v+sv+
  gi|344210185|ref|YP_004786361.1|  39 MLRTACTEADLDLDAVREQLDEARRKREERGDEWESMTALIEHVVDSHHQYLREELPALEQLAEKVRSVH 108
                                       5677777777777777777777777777666655555555555555555555555555555555555554 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.29
                           DUF1664  88 evtevredlse.igedvesvkeavegles 115
                                       ev e+ e++++ + e+ + v  ++e+l+s
  gi|344210185|ref|YP_004786361.1| 121 EVLELAEEMRQhTTEEEQDVFPVIEKLDS 149
                                       44444444432123333344444444443 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.4
                           DUF1664  67 ridrvdkkldeqkeiskeikeevtevred 95 
                                       r+d+  + l++  e+++e  e ++e++++
  gi|344210185|ref|YP_004786361.1| 160 RLDEALADLESDHEATAEHLERIAELSDG 188
                                       44444444555555555555555555555 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.017        16     204     246 ..      40      82 ..      38      84 .. 0.86
   2 ?    4.7   9.0     0.013        12     141     245 ..      80     184 ..      77     229 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.017
                              Spc7 204 lreelaelkaeieekkkelaelqeqleeleekieelkeqksel 246
                                       lr + +e++ ++++ +++l+e ++++ee  +++e++++ ++++
  gi|344210185|ref|YP_004786361.1|  40 LRTACTEADLDLDAVREQLDEARRKREERGDEWESMTALIEHV 82 
                                       7888899999999999999999999999999999999888766 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.013
                              Spc7 141 kegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeiee 217
                                       +++++++ + l+e+   Le+  e++ ++  e + e a++e+e+ +l e+ +++++ +++++  + e+l++ ++   +
  gi|344210185|ref|YP_004786361.1|  80 EHVVDSHHQYLREELPALEQLAEKVRSVHAEEHPELADIEREVLELAEEMRQHTTEEEQDVFPVIEKLDSGDELTGK 156
                                       56667777777777777777777777777777777777777777777766666666666666666666665554444 PP

                              Spc7 218 kkkelaelqeqleeleekieelkeqkse 245
                                        +++l+e  ++le+  e+ +e  e+++e
  gi|344210185|ref|YP_004786361.1| 157 ERARLDEALADLESDHEATAEHLERIAE 184
                                       4444444444443333333333333333 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   5.1    0.0014       1.3       5      77 ..      51     125 ..      48     129 .. 0.85
   2 ?    3.7   0.7       0.1        97      11      68 ..     146     176 ..     142     191 .. 0.57
   3 ?   -1.3   0.0       3.6   3.4e+03      24      39 ..     204     219 ..     197     225 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                           DUF4404   5 LekLheeLeqnesldeetralLeslaedieellaeedaaaeeee.laerlneave.rFeeeHPklagvlreilds 77 
                                       L++ +e+L++  +  ee  ++ es+   ie ++++  +   ee    e+l e v    +eeHP+la + re+l+ 
  gi|344210185|ref|YP_004786361.1|  51 LDAVREQLDEARRKREERGDEWESMTALIEHVVDSHHQYLREELpALEQLAEKVRsVHAEEHPELADIEREVLEL 125
                                       78889******************************99998887687777777765156899**********9986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.1
                           DUF4404  11 eLeqnesldeetralLeslaedieellaeedaaaeeeelaerlneaverFeeeHPkla 68 
                                       +L++ ++l  ++ra+L ++  d+e                             H   a
  gi|344210185|ref|YP_004786361.1| 146 KLDSGDELTGKERARLDEALADLESD---------------------------HEATA 176
                                       56666777777777777777777732...........................22222 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.6
                           DUF4404  24 alLeslaedieellae 39 
                                       ++Le+l++d  + +++
  gi|344210185|ref|YP_004786361.1| 204 ERLETLEQDTHMHVHK 219
                                       4566666665555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1443  (0.0804841); expected 358.6 (0.02)
Passed bias filter:                      767  (0.0427799); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.45
# Mc/sec: 1581.21
//
Query:       gi|344210186|ref|YP_004786362.1|  [L=86]
Description: hypothetical protein HAH_5245 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.5    7.7   5.3        1.7    7.5   5.3    1.1  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 ?    7.5   5.3   9.2e-05       1.7     257     305 ..      26      73 ..      19      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 9.2e-05
                              MMPL 257 tvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGra 305
                                       +  +a+l+L +   + ++++G  ++lG lv+ l+vl+ +PA+++l+  +
  gi|344210186|ref|YP_004786362.1|  26 ITLGALLSLPIFGTG-VRTLGSSLGLGRLVVPLLVLAHVPAVIALIALW 73 
                                       444455555555544.589**************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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: 00:00:00.39
# Mc/sec: 653.83
//
Query:       gi|344210187|ref|YP_004786363.1|  [L=196]
Description: transcription regulator [Haloarcula hispanica ATCC 33960]
Scores for 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   78.1   0.8    5.9e-22   78.1   0.8    1.7  2  TetR_C_6    BetI-type transcriptional repressor, C-terminal
    4.4e-10   39.2   0.7      8e-10   38.4   0.7    1.5  1  TetR_N      Bacterial regulatory proteins, tetR family
    1.8e-05   25.0   0.2      5e-05   23.5   0.0    1.9  2  TetR_C_24   Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
      0.013   16.2   0.0      0.027   15.1   0.0    1.6  1  TetR_C_37   Tetracyclin repressor-like, C-terminal domain
      0.014   15.4   0.4      0.052   13.6   0.1    2.3  1  TetR_C_27   Tetracyclin repressor-like, C-terminal domain
      0.016   15.3   0.3      0.061   13.4   0.3    1.8  2  HAD_2       Haloacid dehalogenase-like hydrolase
      0.037   13.5   0.0      0.067   12.7   0.0    1.4  1  Sigma70_r4  Sigma-70, region 4
      0.064   13.4   0.0       0.18   11.9   0.0    1.7  2  TetR_C_17   Tetracyclin repressor-like, C-terminal domain
      0.087   12.9   0.0       0.14   12.3   0.0    1.5  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 ?   -2.2   0.0       2.3   4.5e+03      38      53 ..      12      27 ..       8      40 .. 0.70
   2 !   78.1   0.8     3e-25   5.9e-22       1     114 [.      82     195 ..      82     196 .] 0.99

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.3
                                      HHHHHHHHHHHHHHHH CS
                          TetR_C_6 38 elaelqrenyarlrsn 53
                                      +  e+++++y++lr++
  gi|344210187|ref|YP_004786363.1| 12 QTEEIMQATYRALREH 27
                                      5566677777777764 PP

  == domain 2  score: 78.1 bits;  conditional E-value: 3e-25
                                       HHHHHHHHHHCCSTHSHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCTTSTHHHHHH CS
                          TetR_C_6   1 prerlraileallpldqerraelavwlafwaeaardpelaelqrenyarlrsnlrallaelaegglradadaeaaAe 77 
                                       p++rl+ +l++ll  +qe+++ + + l++ ++a++++++ +++r+n++ +r++l+a++ ++ ++g+++d+da+++++
  gi|344210187|ref|YP_004786363.1|  82 PEARLEILLDELLVKPQENPDLSVALLEMRSQAPYKEAFSDRFRQNDEYIRYMLKAVINHGIDEGVFSDVDADHVTR 158
                                       799************************************************************************** PP

                                       HHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHHT CS
                          TetR_C_6  78 rlaAlidGLwlraalapeeldaeraralvrrhldall 114
                                        l  +idG  +ra++ +++ + e+ar++++++ da+l
  gi|344210187|ref|YP_004786363.1| 159 SLLTIIDGARTRAVMLDDTEELETARQTASEYADAML 195
                                       **********************************998 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 !   38.4   0.7     4e-13     8e-10       1      46 [.      16      61 ..      16      62 .. 0.97

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 4e-13
                                      HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHH CS
                            TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLlea 46
                                      I+ a+ + + e+Gy+ +t+++IA++ G s +a+++y+++K++Ll+a
  gi|344210187|ref|YP_004786363.1| 16 IMQATYRALREHGYADLTIKRIADEYGKSTAAVHYYYDTKDDLLAA 61
                                      899*****************************************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 !   23.5   0.0   2.5e-08     5e-05       2      85 ..      80     165 ..      79     169 .. 0.83
   2 ?   -3.2   0.1       5.1     1e+04      98     111 ..     182     195 ..     178     196 .] 0.66

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.5e-08
                                       SSHHHHHHHHHHHHHHHHHHTHHHHHHHHHHGGG..S-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB-SS-HHHH CS
                         TetR_C_24   2 gspaerLralvrahveviaeereeaavllrelra..LspehreeiralrreyerllrdlieeGvaagefedldpkla 76 
                                       ++p++rL+ l+ +++    e+++  + ll+ + +   +++  +++r+  + ++ +l+++i+ G+++g+f+d+d++ +
  gi|344210187|ref|YP_004786363.1|  80 TDPEARLEILLDELLVKPQENPDLSVALLEMRSQapYKEAFSDRFRQNDEYIRYMLKAVINHGIDEGVFSDVDADHV 156
                                       68999********99999999998888775444411344456799999999999*********************** PP

                                       HHHHHHHHH CS
                         TetR_C_24  77 alailgmln 85 
                                       ++++l+++ 
  gi|344210187|ref|YP_004786363.1| 157 TRSLLTIID 165
                                       ****99875 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.1
                                       -HHHHHHHHHHHHH CS
                         TetR_C_24  98 speeiadqyadlll 111
                                       ++++ a +yad +l
  gi|344210187|ref|YP_004786363.1| 182 TARQTASEYADAML 195
                                       45666777777766 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 ?   15.1   0.0   1.4e-05     0.027      37     113 ..     117     193 ..     107     196 .] 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                                       -GGGHHHHHHHHHHHHHHHHHHHHTT--TTTBSS.-HHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH CS
                         TetR_C_37  37 ekeikekykkildsLrevLksklkelneekkiklknkeetaelIfvlvdgaYyylsleekkkayeeklkqykkevye 113
                                       ++++++++++  + +r +Lk  +++  +e+ ++  ++++++   ++++dga  ++ + +++++ e   +   +++  
  gi|344210187|ref|YP_004786363.1| 117 KEAFSDRFRQNDEYIRYMLKAVINHGIDEGVFSDVDADHVTRSLLTIIDGARTRAVMLDDTEELETARQTASEYADA 193
                                       68999****************************************************99999988776666666555 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 ?   13.6   0.1   2.6e-05     0.052      46      81 ..     129     164 ..      82     188 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                                       HHHHHHHHHHHHHHHHCT-STT--HHHHHHHHHHHS CS
                         TetR_C_27  46 eeleeqlaeIireGvaaGeFkaadpeaaaravfdat 81 
                                       e ++ +l+ +i++G+++G F+  d++   r +++ +
  gi|344210187|ref|YP_004786363.1| 129 EYIRYMLKAVINHGIDEGVFSDVDADHVTRSLLTII 164
                                       44567899*******************999987765 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3     3e-05     0.061       6      91 ..       6      93 ..       5     106 .. 0.87
   2 ?   -0.6   0.0       0.6   1.2e+03      73     112 ..     120     159 ..      97     165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                             HAD_2  6 DgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeee.kieellrkyneekkk.kevkpyd 82
                                      D T  d++e i+qa+ ++l+e+g+ +l+ + ++  +g s+  + +++  +++     ++ ll++++++ ++ +++ p  
  gi|344210187|ref|YP_004786363.1|  6 DRTFSDQTEEIMQATYRALREHGYADLTIKRIADEYGKSTAAVHYYYDTKDDLLAaFLDYLLERFVDSIHDvETTDPEA 84
                                      88999***********************************999888888766555688888999999999977777777 PP

                             HAD_2 83 gvkelLeeL 91
                                       ++ lL+eL
  gi|344210187|ref|YP_004786363.1| 85 RLEILLDEL 93
                                      777777776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.6
                             HAD_2  73 kkkkevkpydgvkelLeeLkeagyklgivTsksreaveek 112
                                         +++ +  + ++++L+ + ++g+  g+ ++ +++ v+++
  gi|344210187|ref|YP_004786363.1| 120 FSDRFRQNDEYIRYMLKAVINHGIDEGVFSDVDADHVTRS 159
                                       4444444455688899999999999999998877777665 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   0.0   3.3e-05     0.067       6      37 ..      10      48 ..       7      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.3e-05
                                      -HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHH CS
                        Sigma70_r4  6 pererevlelrf.......geglTleEIgerlgiSrerV 37
                                      +++  e+++  +       + +lT + I++++g S  +V
  gi|344210187|ref|YP_004786363.1| 10 SDQTEEIMQATYralrehgYADLTIKRIADEYGKSTAAV 48
                                      56778999999999999******************9877 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 ?   -2.4   0.0       2.5     5e+03      19      31 ..      57      69 ..      42      80 .. 0.57
   2 ?   11.9   0.0     9e-05      0.18      42      94 ..     121     176 ..     103     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.5
                                      SSHHHHHHHHHGG CS
                         TetR_C_17 19 slllakyEyflts 31
                                       ll+a+++y l +
  gi|344210187|ref|YP_004786363.1| 57 DLLAAFLDYLLER 69
                                      4444444444433 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9e-05
                                       HHHHHHHHH....HHHHHHHHHHHTTS---SS-HHHHHHHHHHHHHHHHHHHHHS-H CS
                         TetR_C_17  42 eeRyerlve....alkellqeGvergEfkPqlplesiakylisfldGliletlalge 94 
                                       ++R+ ++ e     lk+++++G+++g f+   +++++++ l+ ++dG  +++++l+ 
  gi|344210187|ref|YP_004786363.1| 121 SDRFRQNDEyiryMLKAVINHGIDEGVFS-DVDADHVTRSLLTIIDGARTRAVMLDD 176
                                       5566555441111578999*********9.5789***************99999985 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 ?   12.3   0.0   6.8e-05      0.14      15      80 ..      96     160 ..      82     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.8e-05
                                       HHHH-HHH.HHHHHHHHHS-TT--TTS--SS-.THHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHH CS
                         TetR_C_29  15 yhaanpef.vrLvsiEnlhrgrhlkksesirelnspliekleeilerGqaagvFrpgvdaldlylli 80 
                                         ++np++ v+L+ + +    +++  s+++r+  + +  +l+ +++ G ++gvF + vda ++  + 
  gi|344210187|ref|YP_004786363.1|  96 KPQENPDLsVALLEMRSQAPYKEA-FSDRFRQNDEYIRYMLKAVINHGIDEGVFSD-VDADHVTRSL 160
                                       555566542555555555555555.689999988888889**************88.***9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1353.41
//
Query:       gi|344210188|ref|YP_004786364.1|  [L=199]
Description: TetR family transcriptional regulator [Haloarcula hispanica ATCC 33960]
Scores for complete 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   2.3    1.7e-15   57.2   2.3    1.7  2  TetR_C_6   BetI-type transcriptional repressor, C-terminal
    7.9e-14   51.2   0.3    1.5e-13   50.3   0.3    1.5  1  TetR_N     Bacterial regulatory proteins, tetR family
    0.00035   20.9   1.9    0.00075   19.8   1.9    1.6  1  TetR_C_11  Tetracyclin repressor-like, C-terminal domain
    0.00047   20.2   0.8    0.00082   19.4   0.2    1.8  2  TetR_C_27  Tetracyclin repressor-like, C-terminal domain
    0.00065   20.0   0.3     0.0033   17.7   0.1    2.4  2  TetR_C_24  Tetracyclin repressor-like, C-terminal domain
     0.0018   18.3   0.1      0.008   16.3   0.0    2.0  2  TetR_C_17  Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
       0.12   12.4   0.1       0.25   11.4   0.1    1.8  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 ?   -1.3   0.1      0.95   2.4e+03      47      81 ..      11      39 ..       3      42 .. 0.54
   2 !   57.2   2.3   6.7e-19   1.7e-15       1     114 [.      75     189 ..      75     190 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.95
                                      HHHHHHHHHHHHHHHHHTTSCTTSTHHHHHHHHHH CS
                          TetR_C_6 47 yarlrsnlrallaelaegglradadaeaaAerlaA 81
                                      +a++r+++++  a+l         d +a+A+r  A
  gi|344210188|ref|YP_004786364.1| 11 DATYRALCQHGYAALTV------KDIAAEADRSKA 39
                                      44445555554444444......666666666555 PP

  == domain 2  score: 57.2 bits;  conditional E-value: 6.7e-19
                                       HHHHHHHHHHCCSTHSHHHH..HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH.TTSCTTSTHHH CS
                          TetR_C_6   1 prerlraileallpldqerr..aelavwlafwaeaardpelaelqrenyarlrsnlrallaelae.gglradadaea 74 
                                       pre l+ +l+++l++  +++  ++ ++ l++ a+a+++++++ ++++++a l+++lr+++a+++e g++ ++++++ 
  gi|344210188|ref|YP_004786364.1|  75 PREELDSLLDTVLTDGRQTPgqEFRTAILEIKAQAPYNDAFRTQLARFDAVLFDRLREIIAAGVEtGEFDSRVEPAV 151
                                       8*************9999986569999************************************************** PP

                                       HHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHHT CS
                          TetR_C_6  75 aAerlaAlidGLwlraalapeeldaeraralvrrhldall 114
                                       aAe l+  i G  +r++    + + +r  ++++r+ +++l
  gi|344210188|ref|YP_004786364.1| 152 AAEFLVTAITGAHTRHVAT--DRSIDRFKETITRYAETHL 189
                                       ****************999..8888999999999998876 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 !   50.3   0.3   5.7e-17   1.5e-13       1      46 [.       9      54 ..       9      55 .. 0.98

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 5.7e-17
                                      HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHH CS
                            TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLlea 46
                                      Ilda+ + + ++Gy+a+tv++IA++A  sk+++++y++sKe L+ +
  gi|344210188|ref|YP_004786364.1|  9 ILDATYRALCQHGYAALTVKDIAAEADRSKASIHYYYDSKENLFTE 54
                                      9******************************************976 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 !   19.8   1.9   2.9e-07   0.00075       6      91 ..      74     161 ..      70     186 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.9e-07
                         TetR_C_11   6 slrgDLrallralaealaspragallrallaeaqrdpelaealrerl...leprraalravlrrAvarGelradadv 79 
                                       + r+ L  ll+++ +  ++   g+ +r  + e+++ +   +a+r++l    +   ++lr++++ +v+ Ge +  + +
  gi|344210188|ref|YP_004786364.1|  74 TPREELDSLLDTVLTDGRQ-TPGQEFRTAILEIKAQAPYNDAFRTQLarfDAVLFDRLREIIAAGVETGEFDSRVEP 149
                                       6788899999999888888.46777777777777766666666665533156669********************** PP

                         TetR_C_11  80 elvldlllgpll 91 
                                       +++++ l+ ++ 
  gi|344210188|ref|YP_004786364.1| 150 AVAAEFLVTAIT 161
                                       **9999988775 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 ?   -2.9   0.0       2.8   7.1e+03      73      89 ..       5      22 ..       3      36 .. 0.50
   2 !   19.4   0.2   3.2e-07   0.00082      42      91 ..     120     170 ..     111     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.8
                                      HHHHHHHHSGG.GTSHHH CS
                         TetR_C_27 73 aaravfdatar.fhhPal 89
                                      +a  ++dat r ++++ +
  gi|344210188|ref|YP_004786364.1|  5 TATEILDATYRaLCQHGY 22
                                      555566666551333333 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 3.2e-07
                                       HHHHHHHHHHHHHHHHHHHHCT-STT-.-HHHHHHHHHHHSGGGTSHHHHH CS
                         TetR_C_27  42 ekhieeleeqlaeIireGvaaGeFkaa.dpeaaaravfdatarfhhPalaa 91 
                                       +++ + l + l eIi++Gv++GeF ++ +p++aa+ +++a++  h   +a+
  gi|344210188|ref|YP_004786364.1| 120 ARFDAVLFDRLREIIAAGVETGEFDSRvEPAVAAEFLVTAITGAHTRHVAT 170
                                       5666778899**************87549*******999999888766655 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 !   17.7   0.1   1.3e-06    0.0033      51      88 ..     126     164 ..      72     165 .. 0.85
   2 ?   -1.7   0.0       1.3   3.3e+03       4      20 ..     173     189 ..     170     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHHHHHHHHTTSB.-SS-HHHHHHHHHHHHHCHH CS
                         TetR_C_24  51 yerllrdlieeGvaagef.edldpklaalailgmlnwvy 88 
                                       + ++lr++i++Gv++gef ++++p++aa ++++++++ +
  gi|344210188|ref|YP_004786364.1| 126 LFDRLREIIAAGVETGEFdSRVEPAVAAEFLVTAITGAH 164
                                       55799***************************9998765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHHHH CS
                         TetR_C_24   4 paerLralvrahvevia 20 
                                         +r+++ + +++e+++
  gi|344210188|ref|YP_004786364.1| 173 SIDRFKETITRYAETHL 189
                                       67899999999988876 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 ?   -0.5   0.1      0.52   1.3e+03      25      48 ..      41      66 ..      26      72 .. 0.54
   2 !   16.3   0.0   3.1e-06     0.008      48      93 ..     126     171 ..      96     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.52
                                      HHHHHGGGG-..HHHHHHHHHHHHHH CS
                         TetR_C_17 25 yEyfltsyre..eerrayleeRyerl 48
                                      + y+  s+++  +e   +l eRy+  
  gi|344210188|ref|YP_004786364.1| 41 IHYYYDSKENlfTEFLDFLYERYTAK 66
                                      44444443331134445666666654 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3.1e-06
                                       HHHHHHHHHHHHHHTTS---SS-HHHHHHHHHHHHHHHHHHHHHS- CS
                         TetR_C_17  48 lvealkellqeGvergEfkPqlplesiakylisfldGliletlalg 93 
                                       l ++l e++ +Gve+gEf  +   +  a++l+  + G  ++++a +
  gi|344210188|ref|YP_004786364.1| 126 LFDRLREIIAAGVETGEFDSRVEPAVAAEFLVTAITGAHTRHVATD 171
                                       5689*******************************99888877766 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 ?   11.4   0.1   9.9e-05      0.25      42      74 ..     118     150 ..      75     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.9e-05
                                       -SS-.THHHHHHHHHHHHHHHHTTSS-SS--HH CS
                         TetR_C_29  42 sirelnspliekleeilerGqaagvFrpgvdal 74 
                                       +++++ + l+++l+ei++ G+++g F + v++ 
  gi|344210188|ref|YP_004786364.1| 118 QLARFDAVLFDRLREIIAAGVETGEFDSRVEPA 150
                                       5666777899****************9988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 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:                        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):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1390.01
//
Query:       gi|344210189|ref|YP_004786365.1|  [L=489]
Description: MATE family drug/sodium antiporter [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-64  216.7  34.1    7.8e-36  123.2  16.0    2.4  2  MatE             MatE
    0.00079   19.5  42.7      0.033   14.2  20.9    4.8  3  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 !  123.2  16.0   8.7e-40   7.8e-36       1     160 [.      34     193 ..      34     194 .. 0.99
   2 !   99.3  10.1   1.9e-32   1.7e-28      10     160 ..     279     430 ..     270     431 .. 0.96

  Alignments for each domain:
  == domain 1  score: 123.2 bits;  conditional E-value: 8.7e-40
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       Pi+++nl+++ ++l+dt+++g+++++alAa+s+a++ ++ll+++++g+s+a ++lv+q+ Ga+  ++a+ a+ q++ 
  gi|344210189|ref|YP_004786365.1|  34 PIVITNLFQTAYNLADTFWLGQYSTDALAAISFAFPMVFLLISLGMGISVAGSVLVAQFTGAGEERDAEYAASQTVT 110
                                       9**************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       +++++s+++ ++++l  + +lsl++++e+vl++a  y++++ lg+++++ ++v+ + +rg+g+t +p+ +++ s++l
  gi|344210189|ref|YP_004786365.1| 111 FAVIVSFVLGIAGYLGVDTFLSLMGASEDVLPMATSYMEVISLGLLFMFGFFVFVALMRGYGDTITPMLVMFGSVVL 187
                                       ***************************************************************************** PP

                              MatE 155 niplny 160
                                       ni++++
  gi|344210189|ref|YP_004786365.1| 188 NIIIDP 193
                                       ***986 PP

  == domain 2  score: 99.3 bits;  conditional E-value: 1.9e-32
                              MatE  10 sllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllslii 86 
                                        l+  ++ ++v++++++ +Aa++i+++++s++f+++++++ +++t++gq+ Ga +++ra++a+  +  +l+++  ++
  gi|344210189|ref|YP_004786365.1| 279 ALSMNLLLVIVAMFPDTVVAAYGIGTRVFSVVFLPAIAVARGVETMTGQNMGADKPDRAAKAAGLAATVLFGVLTLA 355
                                       5677788999******************************************************************* PP

                              MatE  87 allvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llniplny 160
                                        +lv++ + +i+ lft+d+ev+e++ ++lr+++l+  ++++  +++g +rgagkt ++++is++ l ++++p+++
  gi|344210189|ref|YP_004786365.1| 356 GVLVWFTAAPIADLFTTDPEVVEITTQFLRYVALSFGFIGIMRAYTGSFRGAGKTLTAAAISVLMLgIIRFPIAW 430
                                       ************************************************************************998 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 ?    2.2   2.9     0.019   1.7e+02      92     137 ..      70     127 ..      31     133 .. 0.74
   2 !   14.2  20.9   3.7e-06     0.033       2     134 ..     148     307 ..     147     366 .. 0.80
   3 !   10.8   3.3   4.1e-05      0.37       2      81 ..     384     464 ..     383     473 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.019
                   Polysacc_synt_C  92 lkpllaalvmgivvylllllllglllla..............alalllavlvgalvYlll 137
                                       ++ ll++l+mgi v + +l+   +   a              ++a++++ ++g++ Yl++
  gi|344210189|ref|YP_004786365.1|  70 MVFLLISLGMGISVAGSVLVAQFTG--AgeerdaeyaasqtvTFAVIVSFVLGIAGYLGV 127
                                       4778999999999554333333333..246999999999876668888888999988875 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.7e-06
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgi.................vGaaia 61 
                                       + +++l+++f++ + v+ +++ g g + +++++++ ++++++i+  +li  + +                  Gaaia
  gi|344210189|ref|YP_004786365.1| 148 MEVISLGLLFMFGFFVFVALMRGYGDTITPMLVMFGSVVLNIIIDPFLIFGWTVvenaplvgtvsfpelgiEGAAIA 224
                                       7899*********************************************8888788888888888888888****** PP

                   Polysacc_synt_C  62 tvlallvvavln...lyalrrllgikl.......ellrrllkpllaalvmgiv..vylllllllgllllaal..all 124
                                       tv++ ++++v+    +++ +r ++i+l       + lrrl+++ l a v g    +    + ll ++  + +  +++
  gi|344210189|ref|YP_004786365.1| 225 TVFSRALALVVGlaiMFRGNRGVQIHLrdmapdlSYLRRLVRIGLPASVEGTGraL---SMNLLLVIVAM-FpdTVV 297
                                       ****9999998754467777777777788888887788888888877777777321...22222222222.232444 PP

                   Polysacc_synt_C 125 lavlvgalvY 134
                                       +a ++g  v+
  gi|344210189|ref|YP_004786365.1| 298 AAYGIGTRVF 307
                                       4444444444 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 4.1e-05
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkial.kalvigalvklilnllliplfgivGaaiatvlallvvavlnlyal 77 
                                       L+++als+ f+++++ +++ + g g++ +a+ ++++   ++ + + ++    +g +G+ ++ +++ +++a++ + + 
  gi|344210189|ref|YP_004786365.1| 384 LRYVALSFGFIGIMRAYTGSFRGAGKTLTAAaISVLMLGIIRFPIAWFAAVPLGETGIWLSFAVSNVAGALIAYGWY 460
                                       8899**********************976651566666679*********99********************99887 PP

                   Polysacc_synt_C  78 rrll 81 
                                       rr +
  gi|344210189|ref|YP_004786365.1| 461 RRGT 464
                                       7755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); 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:                         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: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3254.19
//
Query:       gi|344210190|ref|YP_004786366.1|  [L=222]
Description: type 11 methyltransferase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-21   76.1   0.0    1.1e-20   74.0   0.0    1.9  2  Methyltransf_11  Methyltransferase domain
    6.3e-20   71.7   0.0    7.8e-20   71.4   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    7.4e-19   68.3   0.0    3.4e-18   66.2   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
    5.9e-14   52.1   0.0    1.1e-13   51.2   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
    1.1e-13   51.1   0.0    2.2e-13   50.1   0.0    1.4  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.4e-12   48.2   0.0    3.3e-12   47.0   0.0    1.7  2  Methyltransf_12  Methyltransferase domain
    0.00098   18.7   0.0     0.0023   17.5   0.0    1.6  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.019   14.9   0.0    1.3  1  Methyltransf_8   Hypothetical methyltransferase
      0.034   13.5   0.0      0.045   13.1   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.068   12.8   0.0       0.13   11.8   0.0    1.4  1  MetW             Methionine biosynthesis protein MetW
        0.1   13.7   0.0       0.21   12.7   0.0    1.7  1  Methyltransf_24  Methyltransferase domain
       0.17   11.6   0.0       0.25   11.1   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.18   11.4   0.0       0.27   10.8   0.0    1.2  1  NodS             Nodulation protein S (NodS)
       0.19   10.8   0.0        0.3   10.1   0.0    1.4  1  RrnaAD           Ribosomal RNA adenine dimethylase
       0.19   10.8   0.0       0.28   10.3   0.0    1.2  1  DREV             DREV 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 !   74.0   0.0   9.4e-24   1.1e-20       1      94 [.      48     144 ..      48     146 .. 0.94
   2 ?   -0.6   0.0       1.8   2.1e+03      51      65 ..     180     193 ..     156     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 9.4e-24
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       Ld+G+GtG+++ ++ + +   ++v ++++++ m+++a+eka+ +   + +  a ae lp+ +++fD+v++s+v++++
  gi|344210190|ref|YP_004786366.1|  48 LDLGAGTGAMFPYFNSVAnasTEVHAIEPDPHMRRQAEEKANAQATPIHIESAPAEALPYDEDTFDVVIASMVFCTI 124
                                       8**************444457******************9999999999**************************** PP

                                       CCHHHHHHHHHHHEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGll 94 
                                       +++e+a++ei+RvLkpgG l
  gi|344210190|ref|YP_004786366.1| 125 PEVESAISEIVRVLKPGGEL 144
                                       ******************87 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.8
                                       ECCCTSS-TT-EEEE CS
                   Methyltransf_11  51 daeklpfednsfDlv 65 
                                       + ++l ++++sfD+v
  gi|344210190|ref|YP_004786366.1| 180 TGTQL-VAEQSFDVV 193
                                       44454.678899998 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.0   6.5e-23   7.8e-20      10     164 ..      33     194 ..      23     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 6.5e-23
                   Methyltransf_23  10 sdklerllpklraggrvLdiGcGtGillevl...rengfsvtgvDlspeaveiaekakkaqkdqfdeqeaae..... 78 
                                       +  +e l+   + +g vLd+G+GtG + +++   +   ++v +++++p++   ae++ +aq ++ + ++a+      
  gi|344210190|ref|YP_004786366.1|  33 RPHREYLV--ANLDGTVLDLGAGTGAMFPYFnsvANASTEVHAIEPDPHMRRQAEEKANAQATPIHIESAPAealpy 107
                                       44556666..68999****************75444466****************9999999999888666645555 PP

                   Methyltransf_23  79 pqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpag..rhisffsarslke 153
                                       ++++fd++++++v++++p ++++++ i + lkpgG l + e+  ++ ++ ++++ l++  +   + +++ + ++  +
  gi|344210190|ref|YP_004786366.1| 108 DEDTFDVVIASMVFCTIPEVESAISEIVRVLKPGGELRFFEHVIDDGWRARVQSALAPLWRRlaGGCHL-TQQTGTQ 183
                                       777*******************************************9***9999766533322155555.5599999 PP

                   Methyltransf_23 154 lleeaGlevve 164
                                       l+ e+ ++vve
  gi|344210190|ref|YP_004786366.1| 184 LVAEQSFDVVE 194
                                       99999999987 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   2.8e-21   3.4e-18       1      97 []      47     142 ..      47     142 .. 0.93
   2 ?   -0.4   0.0       1.6   1.9e+03      48      70 ..     174     195 ..     156     208 .. 0.73

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 2.8e-21
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       vLdlG+GtG +  ++    + + +v+++++++ m ++a+e+a+++   ++++ + ae+lp+++++fD+v++s++++ 
  gi|344210190|ref|YP_004786366.1|  47 VLDLGAGTGAMFPYFNSVANaSTEVHAIEPDPHMRRQAEEKANAQATPIHIESAPAEALPYDEDTFDVVIASMVFCT 123
                                       9***********9999887569********************99999************************866665 PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                       +  +++e a++ei rvLkpgG
  gi|344210190|ref|YP_004786366.1| 124 I--PEVESAISEIVRVLKPGG 142
                                       5..5899*************9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.6
                                       EEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25  48 vefvqgdaedlpfedgsfDlvvs 70 
                                       +++ q+  ++l  +++sfD+v +
  gi|344210190|ref|YP_004786366.1| 174 CHLTQQTGTQLV-AEQSFDVVEI 195
                                       566667777775.5679999865 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   9.5e-17   1.1e-13       6     114 ..      46     159 ..      41     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 9.5e-17
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                       +vlDlG+GtG+    +++ ++   ev+ i+ ++++ ++A+e+ ++ + + ++ e +++e+l+  + +++fD++++  
  gi|344210190|ref|YP_004786366.1|  46 TVLDLGAGTGAMFPYFNSVANASTEVHAIEPDPHMRRQAEEK-ANAQATPIHIESAPAEALP--YDEDTFDVVIASM 119
                                       89***************999999******************6.5577889************..99*********** PP

                   Methyltransf_31  83 vlnaladpdkileeiervlkpggilliedpr........l 114
                                       v++++++ ++++ ei rvlkpgg+l   ++         +
  gi|344210190|ref|YP_004786366.1| 120 VFCTIPEVESAISEIVRVLKPGGELRFFEHViddgwrarV 159
                                       **************************99999444433331 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   1.9e-16   2.2e-13      50     153 ..      46     148 ..      27     152 .. 0.91
   2 ?   -2.7   0.0       2.5     3e+03     201     226 ..     178     203 ..     175     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 1.9e-16
                                       EEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-G CS
                   Ubie_methyltran  50 kvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGl 126
                                       +vlD+ +Gtg +   + + ++++ +v+ ++ +++m +++e+k++ +++  i+   a ae+Lp+++d+fDvv  s  +
  gi|344210190|ref|YP_004786366.1|  46 TVLDLGAGTGAMFPYFNSVANASTEVHAIEPDPHMRRQAEEKANAQAT-PIHIESAPAEALPYDEDTFDVVIASMVF 121
                                       79*****************************************99986.5777799********************* PP

                                       GG-S-HHHHHHHHHHHEEEEEEEEEEE CS
                   Ubie_methyltran 127 rnvtDklkaLkeayrvlkpGGrlvvle 153
                                         +++ + a+ e+ rvlkpGG+l  +e
  gi|344210190|ref|YP_004786366.1| 122 CTIPEVESAISEIVRVLKPGGELRFFE 148
                                       **********************98877 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHTTEEEEEEEEEGGGTE CS
                   Ubie_methyltran 201 qetlkeliedaGfksveyesltgGvv 226
                                       q+t  +l+ +  f+ ve e+l  G+ 
  gi|344210190|ref|YP_004786366.1| 178 QQTGTQLVAEQSFDVVEIERLNLGIT 203
                                       56667888888889999888888886 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   2.8e-15   3.3e-12       1      99 []      48     144 ..      48     144 .. 0.80
   2 ?   -2.4   0.0       7.2   8.6e+03      61      70 ..     184     193 ..     150     197 .. 0.66

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 2.8e-15
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnv 75 
                                       L++G+GtG++  ++       +e+++++++p++  +a+ek +++       +++e   ++ l+   ++fD+v+as v
  gi|344210190|ref|YP_004786366.1|  48 LDLGAGTGAMFPYFNSVAnASTEVHAIEPDPHMRRQAEEKANAQAT----PIHIESAPAEALPYDeDTFDVVIASMV 120
                                       8*********9998776678**************666666666553....44444443333322246********** PP

                   Methyltransf_12  76 lhhlkdirevldnirklLkpgGrl 99 
                                       ++ ++++++++++i ++LkpgG l
  gi|344210190|ref|YP_004786366.1| 121 FCTIPEVESAISEIVRVLKPGGEL 144
                                       **********************76 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.2
                   Methyltransf_12  61 ldggssfDlv 70 
                                       l  ++sfD+v
  gi|344210190|ref|YP_004786366.1| 184 LVAEQSFDVV 193
                                       2222577776 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.9e-06    0.0023      26     136 ..      38     145 ..      19     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.9e-06
                                       HCHCCTCSEEEEET-TTSHHHHHHHH.HTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEE..EE-STTTTSTTS-EE CS
                               MTS  26 tlpkelsgkvlDlGcGaGvlgaalak.espeaevtlvdvdarAlesakenleanklevev..vasdvleeveekkfd 99 
                                       +l ++l+g+vlDlG+G+G++   + + ++ ++ev++++ d +  + a+e ++a++  +++     ++l   +e+ fd
  gi|344210190|ref|YP_004786366.1|  38 YLVANLDGTVLDLGAGTGAMFPYFNSvANASTEVHAIEPDPHMRRQAEEKANAQATPIHIesAPAEALPY-DEDTFD 113
                                       56677999**********9987766514556669999999988888888777777775550044454444.45999* PP

                                       EEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEE CS
                               MTS 100 livsNPPfhagkatelavaeeliaeAkeaLkegGeLl 136
                                       +++    f +  +     +e  i e  ++Lk+gGeL+
  gi|344210190|ref|YP_004786366.1| 114 VVIASMVFCTIPE-----VESAISEIVRVLKPGGELR 145
                                       *998877777666.....5555566667777777776 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.6e-05     0.019     108     156 ..      97     146 ..      86     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                                       EEES-TTS-S--TT-EEEEEEES---S.S-HHHHHHHHHHHEEEEEEEEE CS
                    Methyltransf_8 108 vvacdlakvPledesvdvavfclslmg.tnladflkeanrvlkvGGllkv 156
                                       +++     +P ++++ dv++  + + +  ++++ + e+ rvlk+GG l  
  gi|344210190|ref|YP_004786366.1|  97 IESAPAEALPYDEDTFDVVIASMVFCTiPEVESAISEIVRVLKPGGELRF 146
                                       556666789***********99887652699***************9975 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.8e-05     0.045     162     256 ..      44     144 ..      35     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-05
                              PrmA 162 geevlDvGtGSGiL..aiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseell..keekadvivaNI 234
                                       + +vlD+G+G+G +     ++  +  +v+a+  D+   + a+e a+   +  ++e  +++e+l  +e ++dv++a +
  gi|344210190|ref|YP_004786366.1|  44 DGTVLDLGAGTGAMfpYFNSVANASTEVHAIEPDPHMRRQAEEKANAQATPIHIES-APAEALpyDEDTFDVVIASM 119
                                       459*********984435666777889**************998777766667765.455555354899*******9 PP

                              PrmA 235 Laevliel...aedikklvkeggll 256
                                       +   + e    +++i +++k+gg l
  gi|344210190|ref|YP_004786366.1| 120 VFCTIPEVesaISEIVRVLKPGGEL 144
                                       9988877622255666777888865 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011      0.13      15     101 ..      45     137 ..      37     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                              MetW  15 srvldlGcGdGellellkeekq..vdgrGleld....eegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtl 85 
                                        +vldlG+G G ++ +++   +   + + +e d    +++  ++ a+   ++ + +  +   +++++fd+v+ s  +
  gi|344210190|ref|YP_004786366.1|  45 GTVLDLGAGTGAMFPYFNSVANasTEVHAIEPDphmrRQAEEKANAQATPIHIESAPAEALPYDEDTFDVVIASMVF 121
                                       68***********9998765441155678887722223445566777788888889999999*************** PP

                              MetW  86 qatrnpkevldellri 101
                                        ++ + ++ ++e++r+
  gi|344210190|ref|YP_004786366.1| 122 CTIPEVESAISEIVRV 137
                                       ************9998 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00017      0.21       3      99 ..      50     142 ..      48     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                   Methyltransf_24   3 iGvysGvstlwllralrrngagrlvavdhdpgaeeaaalareaglddrvrlikads..eealaslaagsiDllfiDg 77 
                                       +G  +G  +++      +n+ ++++a+++dp   + ++ a+e + +++++ i+ +s   eal+  + +++D+++  +
  gi|344210190|ref|YP_004786366.1|  50 LG--AGTGAMFPYFNSVANASTEVHAIEPDP---HMRRQAEE-KANAQATPIHIESapAEALPYDE-DTFDVVIASM 119
                                       67..6666666666777888899********...88888887.66666666665554467788777.9999876544 PP

                   Methyltransf_24  78 .ghaaeavledleallprlapgg 99 
                                          +  +v  ++  + ++l+pgg
  gi|344210190|ref|YP_004786366.1| 120 vFCTIPEVESAISEIVRVLKPGG 142
                                       21234566666666666666665 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 ?   11.1   0.0   0.00021      0.25      67     129 ..      37      98 ..      29     145 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                                       HHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEE CS
                              PCMT  67 ellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivv 129
                                       e+l  +    vL++G+G+G     +  + ++++ v +ie  +++ ++a+++ +++++  +++ 
  gi|344210190|ref|YP_004786366.1|  37 EYLVANLDGTVLDLGAGTGAMFPYFNSVANASTEVHAIEPDPHMRRQAEEKANAQAT-PIHIE 98 
                                       6777677789***************************************99876543.45554 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00023      0.27      46     144 ..      46     146 ..      37     157 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                              NodS  46 dalevGcaaGalterlapyckrltvvdvv...eeaiararervkesshiswi.vsdvqqfst.dekfdlivvaevly 117
                                        +l++G  +Ga+   +  +++  t v  +   ++   +a e+ + ++  + i  +  + +   ++ fd+++ + v+ 
  gi|344210190|ref|YP_004786366.1|  46 TVLDLGAGTGAMFPYFNSVANASTEVHAIepdPHMRRQAEEKANAQATPIHIeSAPAEALPYdEDTFDVVIASMVFC 122
                                       577888888887655555555555444441103344445555554433233303334444431458**999999988 PP

                              NodS 118 yiedvaelraavrnlvsllapdgqlvf 144
                                        i +   + +a+ ++v++l+p+g+l f
  gi|344210190|ref|YP_004786366.1| 123 TIPE---VESAISEIVRVLKPGGELRF 146
                                       7766...568*************9976 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00025       0.3      33      80 ..      46      97 ..      40     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00025
                                      EEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT.TCCCEEE CS
                            RrnaAD 33 tvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls.kdeklkv 80
                                      tvl++g+G+G++   ++  a    +v ++E d+++    ++k + +++++ +
  gi|344210190|ref|YP_004786366.1| 46 TVLDLGAGTGAMFPYFNSVAnasTEVHAIEPDPHMRRQAEEKANaQATPIHI 97
                                      8**********98777666655599***********9999988866666655 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00023      0.28      95     135 ..      44      87 ..      29     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00023
                              DREV  95 dkklldlGaGdGeit...krvaptfeevyatelsetmrdrlkkk 135
                                       d ++ldlGaG G +    + va+   ev+a e   +mr + + k
  gi|344210190|ref|YP_004786366.1|  44 DGTVLDLGAGTGAMFpyfNSVANASTEVHAIEPDPHMRRQAEEK 87 
                                       679*********985333789999999***********998776 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:                      310  (0.0172904); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1401.94
//
Query:       gi|344210191|ref|YP_004786367.1|  [L=223]
Description: hypothetical protein HAH_5250 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   0.3    4.4e-28   98.4   0.3    1.0  1  AIM24     Mitochondrial biogenesis AIM24


Domain annotation for each model (and alignments):
>> AIM24  Mitochondrial biogenesis AIM24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   0.3   2.5e-32   4.4e-28       7     200 ..      23     212 ..      19     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 2.5e-32
                                       SS-EEEEEE-TT-EEEE-CCGEEEEETTEEEEE......--------------EEEEEEES.SS-EEEEE--SSSE. CS
                             AIM24   7 pssllsvtLspgeelyaerGalvamsgkvemet......gllkalkrlltgeslfllkftakissgtvllapklpg. 76 
                                       + +ll + L+   ++++++G++va++g+v++++      g+ +++k++++ge+  +++ +   +sg++++a + ++ 
  gi|344210191|ref|YP_004786367.1|  23 NNRLLDIPLD--GTVMVKAGSMVAYTGEVTFTGkssaegGITGFVKEAVSGEGTPVMEAE---GSGHLYVAENGKKv 94 
                                       5577788885..57******************9*****9*********************...56*********998 PP

                                       EEEEEEGGTT.EEEEEGGGEEEEETT-EEEEEEEE--SSGGGTS-EEEEEEESSSEEEEEEECSEEEEEEE.EEEEE CS
                             AIM24  77 tivtlelgggdwlivqkdafLAatgnveldikfqkglkglfggeglflqkltGrGlvalsgyGaiyeielkageelv 153
                                       +++ l+   g+++ v+   +LA++++++++i++ ++l+g+ +g gl +  ltG G val+ +G+++ ++     +++
  gi|344210191|ref|YP_004786367.1|  95 QVLALD--DGESISVNGTDVLAFESTIDYEINTVGSLSGMAAG-GLTNVYLTGPGEVALTTHGDPLVMTP----PVF 164
                                       888888..5779**********************999988866.9*************************....8** PP

                                       EEGGGEEEEETTEEEEEEEETT---STTTTS-EEEEEEE.EEEEEEES CS
                             AIM24 154 vdpghlvafsgslkfdiervgglkrrligGeglflkltG.pgtvllqs 200
                                        dp++ va+s++l+ +ie+++++    ++Ge++++++tG  g v++q+
  gi|344210191|ref|YP_004786367.1| 165 TDPDATVAWSSNLSPSIEMNKTFEIGQTSGESIQMEFTGdDGFVVIQP 212
                                       ***********************99999***********999*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1487.05
//
Query:       gi|344210192|ref|YP_004786368.1|  [L=837]
Description: polyphosphate kinase [Haloarcula hispanica ATCC 33960]
Scores for complete 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  231.9   0.0    5.3e-69  231.0   0.0    1.4  1  PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1
    1.3e-63  213.6   0.0    1.4e-61  206.9   0.0    2.5  2  PP_kinase_C    Polyphosphate kinase C-terminal domain 2
    4.1e-60  202.8   0.7    6.7e-60  202.1   0.7    1.3  1  PP_kinase      Polyphosphate kinase middle domain
    9.7e-36  122.4   0.1    2.7e-35  120.9   0.0    1.9  2  PP_kinase_N    Polyphosphate kinase N-terminal domain
    2.1e-12   47.1   0.0    1.2e-06   28.5   0.1    2.7  3  PLDc_2         PLD-like domain


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 !  231.0   0.0   1.5e-72   5.3e-69       1     164 [.     353     517 ..     353     520 .. 0.98

  Alignments for each domain:
  == domain 1  score: 231.0 bits;  conditional E-value: 1.5e-72
                                       SHHHHHHHS-EEEECTTB-S.CHHHHHHHHHHC-TTEEEEEEEES-S-S--HHHHHHHHHHHTT-EEEEEES--SSS CS
                     PP_kinase_C_1   1 sifeairkkdillhhPyesf.esvvelleeAaedpkvlaikitlYrvakdskivkaLieAaengkqvtvlvElkArf 76 
                                       s+f+ i++ dillhhPy++f ++v+++l++Aaedp+vla+k ++Yr+a+ds+i+++Li+Aaengkqv+v+vElkArf
  gi|344210192|ref|YP_004786368.1| 353 SVFRRIQDGDILLHHPYHDFtDTVQRFLSAAAEDPDVLAVKAAIYRTASDSQIIQSLITAAENGKQVAVMVELKARF 429
                                       589*****************999****************************************************** PP

                                       --HHHHHHHHHHHHHT-EEEE--TT--B--EEEEEEE---S---EEEEEESS-SS---SS-EEEEEEEE--HHHHHH CS
                     PP_kinase_C_1  77 deenNiewakkleeagvkvvygvvglkvhaklllvvrreeeklrryvhlgtGnynektaklYtDlslltadeelged 153
                                       de+nN+ew +klee+g++v+yg+vglk+h+k++lvvr+e+++++ y h+gtGny+++tak Y Dl+lltad+++g+d
  gi|344210192|ref|YP_004786368.1| 430 DEQNNLEWVRKLEENGIHVAYGTVGLKTHTKTALVVREEDDGVELYSHIGTGNYHSETAKGYVDLGLLTADRDIGRD 506
                                       ***************************************************************************** PP

                                       HHHHHHHHTT- CS
                     PP_kinase_C_1 154 veklfnvltgk 164
                                       ++k fn++tg 
  gi|344210192|ref|YP_004786368.1| 507 LTKEFNFFTGP 517
                                       *******9986 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 !    4.0   0.0    0.0087        31      39      61 ..     401     423 ..     374     431 .. 0.90
   2 !  206.9   0.0   3.9e-65   1.4e-61       1     172 []     526     709 ..     526     709 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0087
                       PP_kinase_C  39 edkeiidkLyeAsqaGVkikliv 61 
                                       +d++ii++L+ A++ G ++ ++v
  gi|344210192|ref|YP_004786368.1| 401 SDSQIIQSLITAAENGKQVAVMV 423
                                       799****************9998 PP

  == domain 2  score: 206.9 bits;  conditional E-value: 3.9e-65
                       PP_kinase_C   1 LlvaplnlrekllelidreieaakagkkakiilklNsledkeiidkLyeAsqaGVkiklivrgicclrpgvkglsen 77 
                                       Ll+ap+++r+++++ i+re+++a+ag++a+i++k+N led  i+++Ly+As aGV+i+livr+ic+lrpg +++sen
  gi|344210192|ref|YP_004786368.1| 526 LLIAPVTMRKEFTRCIRREAQHAQAGRPARIVAKINGLEDPGIVAELYRASMAGVDIDLIVRDICRLRPGLEDISEN 602
                                       89*************************************************************************** PP

                       PP_kinase_C  78 ikvisivdrfLEhaRiyifeng...........geeevyisSaDlmtRnldrRvevlvpvedeklkkelkeilelql 143
                                       i+v s+v+rfLEh+Ri++feng           g++e+yi+SaD+mtRnld Rve+++pv+++k++++l+ +l+l l
  gi|344210192|ref|YP_004786368.1| 603 ISVYSLVGRFLEHSRIFYFENGargdpateddwGDPEYYIGSADWMTRNLDYRVEAVTPVTSPKIQRQLRFTLDLLL 679
                                       ********************97444444444445789**************************************** PP

                       PP_kinase_C 144 kDnvkareldedgeykkvke.keekkvraQ 172
                                       +Dn k +e+d+dgey++  + ++e+ ++aQ
  gi|344210192|ref|YP_004786368.1| 680 SDNRKLWEMDSDGEYHQRYPdDGERVISAQ 709
                                       ****************99986777767766 PP

>> PP_kinase  Polyphosphate kinase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.1   0.7   1.9e-63   6.7e-60       2     202 .]     140     334 ..     139     334 .. 0.96

  Alignments for each domain:
  == domain 1  score: 202.1 bits;  conditional E-value: 1.9e-63
                                       HHHHHHHHHHHTTGGG---EE--TTTS-----TT-EEEEEEEESST-SS-..EEEEEE--TTS-SEEEE-T.TSS-. CS
                         PP_kinase   2 qkefleeyFeeevfpvLtplavdpshpfpflsnkslnlavelrkkekeekekefalvkvPsvlpRfielppeeegke 78 
                                       +++ l++yFee v+p Ltpl +dp+hpfpf+sn+sl+lav+ r++++e+   +f ++k+P + pR+++l    + ++
  gi|344210192|ref|YP_004786368.1| 140 EQSELRTYFEESVLPTLTPLSFDPAHPFPFISNRSLSLAVLTRHPNAED--PTFTRIKIPPNRPRLVQL---GD-DT 210
                                       6789****************************************95444..59****************...33.45 PP

                                       EEEEHHHHHHCCHHHH-TTSEEEEEEEEEEE-SSS----.---.-------------------EEEEETT--HHHHC CS
                         PP_kinase  79 rfilledvIeanldelFpgyevleaylfrvtRnadleidedeaedlleeiekeLkkRrrgevvRLeveaempeellk 155
                                       r++lle+vI+anld l p++e+++++lfr+tRna++  +++ aedl++++e+ L++Rr+++vvR+e++ ++++++++
  gi|344210192|ref|YP_004786368.1| 211 RYVLLEEVIRANLDLLLPNVEIVDTALFRLTRNAEVRRNQEIAEDLIDMVEDVLEQRRFASVVRMELSPDADSRIRS 287
                                       9**************************************9************************************* PP

                                       CHTTTT---TTT.EEEE-S--GGGGGCS...--TTTSSS----B--H CS
                         PP_kinase 156 fLlkeleldeedvyeidgpldltdlmklvgkdrpeLkyppftpqtpp 202
                                       +L+ +l+lde+++y+++gpld +d+ +l++ drp+L  +++tpq++p
  gi|344210192|ref|YP_004786368.1| 288 TLATQLGLDEREIYDLSGPLDYRDFAELTDLDRPDLSLDEWTPQPHP 334
                                       ****************************99***************97 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 !  120.9   0.0   7.5e-39   2.7e-35       1     106 [.      25     130 ..      25     131 .. 0.99
   2 ?   -3.3   0.0       3.2   1.1e+04      82     105 ..     424     447 ..     397     448 .. 0.67

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 7.5e-39
                                       XXXHHHHHHHHHHHHHHHHH-TTS-HHHHHHHHHHHHHHHHHHHHHCCHHHHH.HTT-..-----------HHHHHH CS
                       PP_kinase_N   1 ylnRelSwLkFneRVLeeAedervplleRlkFlaIfssNlDEFfmvRvaslkrqleakvekksedgltpeeqlkais 77 
                                       ylnRelS L+F++RVL+eA d+r+plleR++FlaI++ NlDEF m R+++lk+q+ea+v+++ +dg+tpeeql+a++
  gi|344210192|ref|YP_004786368.1|  25 YLNRELSALAFQRRVLHEALDQRNPLLERVRFLAIVTRNLDEFTMKRIGGLKQQIEADVTETAPDGRTPEEQLAAVH 101
                                       89*************************************************************************** PP

                                       HHHHHHHHHHHHHHHHTHHHHHHHTTEEE CS
                       PP_kinase_N  78 eeveelveeqekileeellpeLaeegikl 106
                                       e+++ ++++q +++++ ++p+La+egi++
  gi|344210192|ref|YP_004786368.1| 102 ETLRPMLATQARCYRDAIRPALAAEGIEI 130
                                       ***************************98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.2
                                       HHHHHHHHHHHHTHHHHHHHTTEE CS
                       PP_kinase_N  82 elveeqekileeellpeLaeegik 105
                                       el +++++  + e +++L+e+gi+
  gi|344210192|ref|YP_004786368.1| 424 ELKARFDEQNNLEWVRKLEENGIH 447
                                       445555555556678888888887 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       3.2   1.1e+04     101     123 ..      19      41 ..      19      45 .. 0.79
   2 !   28.5   0.1   3.2e-10   1.2e-06      15     130 ..     395     512 ..     389     514 .. 0.86
   3 !   15.4   0.0   3.6e-06     0.013      21     126 ..     564     672 ..     548     678 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.2
                            PLDc_2 101 ltkrgldlnlElnvviedkelak 123
                                       lt+++l ln+El     ++++ +
  gi|344210192|ref|YP_004786368.1|  19 LTDSSLYLNRELSALAFQRRVLH 41 
                                       68999999999998888777665 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 3.2e-10
                            PLDc_2  15 atyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfetllgslHaKlylidg 91 
                                       a+y   sd++i+++l+ aa++g++v +++     +a++ ++ +l + ++l  e+g+ v   +      H+K++l+ +
  gi|344210192|ref|YP_004786368.1| 395 AIYRTASDSQIIQSLITAAENGKQVAVMVEL---KARFDEQNNLEWVRKL-EENGIHVAYGTV-GLKTHTKTALVVR 466
                                       56666799**********************9...7777666777777777.******987543.3568*******64 PP

                            PLDc_2  92 k.......tvivGSsNltkrgldlnlElnvviedkelakeleeeFe 130
                                       +       +  +G+ N+  +  ++  +l++ + d+++   l++eF+
  gi|344210192|ref|YP_004786368.1| 467 EeddgvelYSHIGTGNYHSETAKGYVDLGLLTADRDIGRDLTKEFN 512
                                       44789999999*******************************9997 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 3.6e-06
                            PLDc_2  21 sdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfetllgslHaKlylidgk..... 92 
                                        d+ i+++l++a+  gv++ +++++      ++ ++ l  ++e +  + +  r+   l+   H+ ++ +++      
  gi|344210192|ref|YP_004786368.1| 564 EDPGIVAELYRASMAGVDIDLIVRD-----ICRLRPGLEDISENISVYSLVGRF---LE---HSRIFYFENGargdp 629
                                       57789*******************9.....677777888887774444444332...34...*******84456778 PP

                            PLDc_2  93 .........tvivGSsNltkrgldlnlElnvviedkelakele 126
                                                  ++GS+ + +r+ld++ E+   +++++++ +l+
  gi|344210192|ref|YP_004786368.1| 630 ateddwgdpEYYIGSADWMTRNLDYRVEAVTPVTSPKIQRQLR 672
                                       888999999****************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (837 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.45
# Mc/sec: 5567.85
//
Query:       gi|344210193|ref|YP_004786369.1|  [L=236]
Description: serine/threonine protein phosphatase [Haloarcula hispanica ATCC 33960]
Scores for 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   49.5   0.1      1e-12   49.0   0.1    1.3  1  Metallophos    Calcineurin-like phosphoesterase
    2.6e-07   31.0   0.0    6.6e-07   29.7   0.0    1.8  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 !   49.0   0.1   1.2e-16     1e-12       3     172 ..      26     177 ..      25     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1.2e-16
                                       EEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHH CS
                       Metallophos   3 ilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegfee 79 
                                       i v+gD+H     g+ ++l++ll++l +     lv+++GDlv  g+ +  +++++++  +    + +++GN e    
  gi|344210193|ref|YP_004786369.1|  26 IYVVGDVH-----GCRPTLERLLNRLDPT-PDELVVFVGDLVRKGPDSAGVVDMVRHTPN----FLTVRGNNE---- 88 
                                       89******.....*************666.66788889****************999999....7********.... PP

                                       HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE.EEEEEEESECEEE....THHHHHHHHHHHSCHHHHCC.HHH CS
                       Metallophos  80 ellnkygylgifsepwrsdaevfnnlplaslgsgs.lkvlllhGgspel....lvsldklgslnleleapepg.dew 150
                                         + + +  +  + +  +d +++  lp+a     s ++ l++hGg  ++     ++l++l +     +    +   w
  gi|344210193|ref|YP_004786369.1|  89 --QKLIDGRKSIPSLTDDDLSWMASLPVAI----SwDDSLVVHGGVDHRksiaEHELTELLNMRSLVPDGSYDrPYW 159
                                       ..444444444477788889*******999....5558*******44445666455555555555544444443566 PP

                                       HHHHHHHTTCSEEEEEESSESS CS
                       Metallophos 151 lkdlekrekadwvivlgHsply 172
                                       ++     ++ad+ i++gH  l+
  gi|344210193|ref|YP_004786369.1| 160 FET----RRADPRIFFGHTVLS 177
                                       666....999********9887 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 !   29.7   0.0   7.3e-11   6.6e-07       3     127 ..      26     174 ..      25     215 .. 0.65

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 7.3e-11
                     Metallophos_2   3 laiiSDlHsnldaleavlealkevgvdaiihaGDl..eeeepevleellela.pvlaVrGNnDeevveedvlreaae 76 
                                       + ++ D+H+ +  le++l++l+ +  ++++++GDl  ++ +   + ++ + +  +l+VrGNn+ + +++ +   +  
  gi|344210193|ref|YP_004786369.1|  26 IYVVGDVHGCRPTLERLLNRLDPTPDELVVFVGDLvrKGPDSAGVVDMVRHTpNFLTVRGNNE-QKLIDGRKSIPSL 101
                                       679*********************9999******9554444443344444346**********.4455555555555 PP

                     Metallophos_2  77 lgtdlpeeaelel..agekvlliHgdpl.....................gvkdalaellkeaeegsd.vvvcGHt 127
                                        ++dl   a l +    ++ l++Hg  +                      ++++  + +++   ++d  +++GHt
  gi|344210193|ref|YP_004786369.1| 102 TDDDLSWMASLPVaiSWDDSLVVHGGVDhrksiaeheltellnmrslvpDGSYDRPYWFET--RRADpRIFFGHT 174
                                       5555554444443224445788888744666655555555555554444333333333333..223336666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1749.99
//
Query:       gi|344210194|ref|YP_004786370.1|  [L=72]
Description: hypothetical protein HAH_5253 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); 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 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 500.89
//
Query:       gi|344210195|ref|YP_004786371.1|  [L=81]
Description: hypothetical protein HAH_5254 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   11.5   2.0       0.31   11.4   2.0    1.1  1  DUF5533   Family of unknown function (DUF5533)
        3.1    7.7   5.5        4.5    7.2   5.5    1.3  1  DUF3487   Protein of unknown function (DUF3487)


Domain annotation for each model (and alignments):
>> DUF5533  Family of unknown function (DUF5533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.0   3.5e-05      0.31      64     121 ..       3      57 ..       1      70 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.5e-05
                           DUF5533  64 lltsllfvalsvlflleyvsirlllrlqyklsvlllllgrrrvdfsvlneliiysihv 121
                                       l+t+   v++ v+ ll  + ir +  l   l+++l+llg    d++++n ++  + h 
  gi|344210195|ref|YP_004786371.1|   3 LFTA---VVVFVVGLLSGIVIRWVAGLAAALALVLVLLGATTPDIGLINFVMEQYYHG 57 
                                       5554...4445666788999*****************************988655553 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   5.5    0.0005       4.5      27      63 ..       4      39 ..       2      52 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0005
                           DUF3487 27 vlaglglvvglvlglllallvgslaliptialllvll 63
                                      ++a++ +vvgl+ g+++ +++g la  ++++l+l+++
  gi|344210195|ref|YP_004786371.1|  4 FTAVVVFVVGLLSGIVIRWVAG-LAAALALVLVLLGA 39
                                      5677889999999999999999.66666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 593.41
//
Query:       gi|344210196|ref|YP_004786372.1|  [L=281]
Description: hypothetical protein HAH_5255 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   53.3   0.0    2.5e-14   53.0   0.0    1.1  1  DUF726         Protein of unknown function (DUF726)
      6e-12   45.6   0.0    8.2e-12   45.1   0.0    1.1  1  DUF900         Alpha/beta hydrolase of unknown function (DUF9
    0.00044   20.9   8.8    0.00073   20.2   8.8    1.5  1  Abhydrolase_6  Alpha/beta hydrolase family
  ------ inclusion threshold ------
      0.016   14.5   0.0      0.024   13.9   0.0    1.1  1  Lipase         Lipase
      0.036   13.2   0.0      0.045   12.9   0.0    1.1  1  LCAT           Lecithin:cholesterol acyltransferase
      0.096   12.3   0.0       0.22   11.1   0.0    1.5  1  Tudor_4        Histone methyltransferase Tudor domain
       0.14   12.3   0.1       0.26   11.5   0.1    1.4  1  CAF1A          Chromatin assembly factor 1 subunit A


Domain annotation for each model (and alignments):
>> DUF726  Protein of unknown function (DUF726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   9.6e-18   2.5e-14     179     330 ..     108     266 ..      63     277 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 9.6e-18
                            DUF726 179 PlaLlkvakildnpwnvsleraakaGklLAdallsraq.GeRpvtLiGfslGARviyvCLlelakkkalglvenvil 254
                                       P  ++ ++   d  w+ + + a++  ++LA+ l++ a+   Rpv L+ +slG Rv  + L++la++ a++ +  v l
  gi|344210196|ref|YP_004786372.1| 108 PTPVIAYSWDSDVEWEQAKDNAEANSTHLAQWLVEWAEtDGRPVHLLAHSLGGRVTGETLRVLAERGATDALASVSL 184
                                       55566666666889********************9987578************************************ PP

                            DUF726 255 lGaPvtteakv....wlkvrsvvsgRlvnvysenDylLgflyRtssaqfrvaglqriel..dvekvenvdvselveg 325
                                       lG  ++ ++ v    +  + + v   + n ys+nD +L+++yR+s+   +v  +++ +     ++ + v+v++lv  
  gi|344210196|ref|YP_004786372.1| 185 LGGAIPYDSVVqggrYGDAIAAVDAPVSNFYSHNDKVLSWVYRASDRTHAVGHAGTRDAgpLPDGYQEVNVTDLVAD 261
                                       **98887764322228899999***********************99887755555554325789************ PP

                            DUF726 326 HldYr 330
                                       H +Y 
  gi|344210196|ref|YP_004786372.1| 262 HYSYF 266
                                       *9996 PP

>> DUF900  Alpha/beta hydrolase of unknown function (DUF900)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   3.2e-15   8.2e-12      15     185 ..      72     239 ..      66     267 .. 0.81

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 3.2e-15
                            DUF900  15 ksaakeilvfvhGynnsFedav..lraaqiaddlknqgaivvfsWPsagklldynyDresaeasrdalekllrylat 89 
                                       +++a e+ +fvhG+ +  e a     +aq+a d   +  ++ +sW s    ++ +  +++aea  ++l++ l + a+
  gi|344210196|ref|YP_004786372.1|  72 FDDASEVFLFVHGFSTDAERARdnAYTAQVALDGTRPTPVIAYSWDSD---VEWEQAKDNAEANSTHLAQWLVEWAE 145
                                       67889***********999996224579*****************998...6688999999999************* PP

                            DUF900  90 kksakkihllaHSmGtwlvlealrqlaieadepaveakikeviLaAPDidvdvfkkqle...slgkeskeltvyvsr 163
                                       + + + +hllaHS G +++ e+lr la +  +      ++ v L+   i  d + +  +   +++  + ++  ++s+
  gi|344210196|ref|YP_004786372.1| 146 T-DGRPVHLLAHSLGGRVTGETLRVLAERGAT----DALASVSLLGGAIPYDSVVQGGRygdAIAAVDAPVSNFYSH 217
                                       9.8999*********************99874....57889999988888877766655556777788********* PP

                            DUF900 164 dDraLklSaliegdasRlGald 185
                                       +D++L+   + +  +  +G+++
  gi|344210196|ref|YP_004786372.1| 218 NDKVLSWVYRASDRTHAVGHAG 239
                                       ****986655555555555555 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   8.8   2.9e-07   0.00073       1     154 [.      79     234 ..      79     279 .. 0.51

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.9e-07
                                       EEEE--GC.....G....CHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHH..HHHHCCTT......TTSE CS
                     Abhydrolase_6   1 vlllHGagssassW....lvapLaallaagvhvlapDlpGhGrsdpppldledladl..aalldelaa....gggpv 67 
                                       +l++HG++++a+      ++a++a  +++   v+a+++     sd  +    d a+    +l++ l++    +g+pv
  gi|344210196|ref|YP_004786372.1|  79 FLFVHGFSTDAERArdnaYTAQVALDGTRPTPVIAYSWD----SDVEWEQAKDNAEAnsTHLAQWLVEwaetDGRPV 151
                                       69****998866665443355664444444666999994....433333333312222344555554466669**** PP

                                       EEEEETCHHHHHHHHHHCC.........EEEEES-..----TTTS----TTHHHHHHTT-CCCCHCCHS-HSCCCCH CS
                     Abhydrolase_6  68 vlvGHSlGGalalaaapla.......lvvgvlldppptalpagllaaalelllallallrllawlsreplprlflad 137
                                       +l++HSlGG +  ++++++             l++   +  +g + ++ +++++ +   + +a ++  p++  f++ 
  gi|344210196|ref|YP_004786372.1| 152 HLLAHSLGGRVTGETLRVLaergatdA-----LAS---VSLLGGAIPYDSVVQGGRYGDAIAAVDA--PVS-NFYSH 217
                                       **********99994444434333431.....333...2233333333333332222222223332..111.33333 PP

                                       HHCCCCHCHCCCGHHHH CS
                     Abhydrolase_6 138 edadaawrarlarlaal 154
                                       +d+  +w++r ++  + 
  gi|344210196|ref|YP_004786372.1| 218 NDKVLSWVYRASDRTHA 234
                                       33333333333333333 PP

>> Lipase  Lipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.5e-06     0.024      65     164 ..      71     166 ..      64     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.5e-06
                                       S--TTSEEEEEE--TT-TT.TTTHHHHHHHHHHTT..--EEEEEEE-HHHHSS-HHHHHHHHHHHHHHHHHHHHHHH CS
                            Lipase  65 efntskktrliihgftvkgleeswlsklvkalekv..ekvnvivvdwksgsealyaqavenirvvgaevakllseLe 139
                                        f   +++ l +hgf+ ++ e    +   +++  +  +++ vi+  w s    + +qa  n +  + + a+ l+e +
  gi|344210196|ref|YP_004786372.1|  71 SFDDASEVFLFVHGFSTDA-ERARDNAYTAQVALDgtRPTPVIAYSWDS--DVEWEQAKDNAEANSTHLAQWLVEWA 144
                                       577889999*********9.66665666555555534777777777765..567899******99999887777666 PP

                                       HHH---GGGEEEEEETCHHHHHHHH CS
                            Lipase 140 eelnyseenvhliGsslgaHvaGva 164
                                          +     vhl+ +slg  v+G+ 
  gi|344210196|ref|YP_004786372.1| 145 ---ETDGRPVHLLAHSLGGRVTGET 166
                                       ...556677*************986 PP

>> LCAT  Lecithin:cholesterol acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.8e-05     0.045      94     146 ..     122     174 ..      99     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                              LCAT  94 WRlsleerdkYfskLkelieealklsgkkvvliaHSmGnllvlyflkwveaea 146
                                       W  + ++ +   ++L++ + e  +++g++v l+aHS+G+ ++ ++l+ + + +
  gi|344210196|ref|YP_004786372.1| 122 WEQAKDNAEANSTHLAQWLVEWAETDGRPVHLLAHSLGGRVTGETLRVLAERG 174
                                       555555555666789999999999*********************99876655 PP

>> Tudor_4  Histone methyltransferase Tudor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.7e-05      0.22      20      47 ..     204     231 ..     196     233 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.7e-05
                           Tudor_4  20 vlkVDaSLvkllfesdkrtEWIYRGStR 47 
                                       +  VDa   + + ++dk + W+YR S R
  gi|344210196|ref|YP_004786372.1| 204 IAAVDAPVSNFYSHNDKVLSWVYRASDR 231
                                       789***********************99 PP

>> CAF1A  Chromatin assembly factor 1 subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1    0.0001      0.26      35      55 ..     110     129 ..      93     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                             CAF1A  35 keldYdyDSdaEWeeeeeeeg 55 
                                       + + Y+ DSd EWe+ ++ ++
  gi|344210196|ref|YP_004786372.1| 110 PVIAYSWDSDVEWEQAKD-NA 129
                                       5588*********77544.43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1821.06
//
Query:       gi|344210197|ref|YP_004786373.1|  [L=200]
Description: tellurite resistance protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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-12   46.6   0.0    6.2e-12   46.1   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    1.6e-09   38.3   0.0    2.6e-09   37.6   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
      3e-09   36.9   0.0    7.1e-09   35.7   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
    1.8e-07   30.8   0.0    2.2e-07   30.5   0.0    1.1  1  TehB             Tellurite resistance protein TehB
    2.4e-07   30.3   0.0    3.3e-07   29.9   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.5e-06   27.1   0.0    3.1e-06   26.9   0.0    1.1  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    1.3e-05   25.0   0.0    1.7e-05   24.7   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    0.00018   22.2   0.0    0.00034   21.3   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    0.00025   20.7   0.0    0.00036   20.1   0.0    1.2  1  MTS              Methyltransferase small domain
    0.00073   19.3   0.0      0.001   18.8   0.0    1.1  1  UPF0020          Putative RNA methylase family UPF0020
     0.0096   15.7   0.0      0.013   15.2   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.053   13.3   0.0      0.068   12.9   0.0    1.1  1  Met_10           Met-10+ like-protein
       0.12   11.7   0.0       0.16   11.3   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


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 !   46.1   0.0   4.5e-15   6.2e-12       2      72 ..      36     106 ..      35     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 4.5e-15
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEES CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssg 72 
                                       Ld+++GtGr++l +a+++  ++v +vD s + l +are+a+e g+  ++e++q+d++++ ++++++D++++s+
  gi|344210197|ref|YP_004786373.1|  36 LDVATGTGRNALPVAAAG--YRVDAVDQSRAGLHIARENAREVGVedDIEWIQADLDSFGYPASTYDVITVSF 106
                                       9****************5..**********************99999**********************9963 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   1.9e-12   2.6e-09       1      69 [.      36     106 ..      36     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.9e-12
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvsse 69 
                                       Ldv++GtGr+a ++a +g+rv +vD s + l +a+e+a+e g+   +e+++ad+ ++ ++ +++D++++s+
  gi|344210197|ref|YP_004786373.1|  36 LDVATGTGRNALPVAAAGYRVDAVDQSRAGLHIARENAREVGVedDIEWIQADLDSFGYPASTYDVITVSF 106
                                       8********************************************9*********************9875 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   5.2e-12   7.1e-09      13     125 ..      23     144 ..      12     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 5.2e-12
                   Methyltransf_23  13 lerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae............kakkaqkdqfdeqeaa 77 
                                       ler lp  +++gr Ld+++GtG+++   ++ g+ v++vD+s++  +ia+            + ++a  d+f      
  gi|344210197|ref|YP_004786373.1|  23 LERYLP-TFPPGRALDVATGTGRNALPVAAAGYRVDAVDQSRAGLHIARenarevgveddiEWIQADLDSF-----G 93 
                                       678887.89***************************************87777777666666666666666.....7 PP

                   Methyltransf_23  78 epqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl........k 125
                                       +p+ ++d+I+ +++      p   l  i + l++gG l+++ +l+           
  gi|344210197|ref|YP_004786373.1|  94 YPASTYDVITVSFY-----RPVDRLPDIIEALADGGCLFIQHHLRTTddvdggpsG 144
                                       7999*****98765.....5666677788888899999999998866566666543 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   1.6e-10   2.2e-07      28     172 ..      29     170 ..       4     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.6e-10
                                       CS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHH.HHHHTT-TTEEEEE--GGG---.-S-EEEEEEE CS
                              TehB  28 ivkpgkvldlgcgqgrnslylsllgydvtawdknensiaflee.ikekenlknistalydineakl.derydfilst 102
                                       +  pg++ld+  g grn+l +++ gy v+a+d+    +   +e  +e    ++i+    d+++       yd i  t
  gi|344210197|ref|YP_004786373.1|  29 TFPPGRALDVATGTGRNALPVAAAGYRVDAVDQSRAGLHIAREnAREVGVEDDIEWIQADLDSFGYpASTYDVI--T 103
                                       5679*******************************999877551566667788999999999988735689988..4 PP

                                       SSGGGS-GGGHHHHHHHHHHTEEEEEEEEEEEEB.--SSS-.-SS--S--B-TTHHHHHTTTSEEEEEE--E CS
                              TehB 103 vvlmfleaeripsiienmqectkvggynlivaam.stddvp.ctvpfsftfkegelkeyykdwellkynedv 172
                                       v  ++   +r+p+iie +      gg  +i   +  tddv   + +  + f+++el +   +  +l+y+e  
  gi|344210197|ref|YP_004786373.1| 104 V-SFYRPVDRLPDIIEALA----DGGCLFIQHHLrTTDDVDgGPSGERYRFASNELLRAGLGLTVLHYDERT 170
                                       4.45678899*****9875....4777777766625677752578889999999999999999999998876 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   2.4e-10   3.3e-07      48     125 ..      32     107 ..      22     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.4e-10
                                       TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEEEEE CS
                   Ubie_methyltran  48 gakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvvtvs 123
                                       + ++lDva+Gtg  a+ ++    + ++v+ +D +   L+++++ ++e g+  +ie++qa+   + +   ++Dv+tvs
  gi|344210197|ref|YP_004786373.1|  32 PGRALDVATGTGRNALPVA---AAGYRVDAVDQSRAGLHIARENAREVGVEdDIEWIQADLDSFGYPASTYDVITVS 105
                                       5679********9998875...45679***********************989************************ PP

                                       S- CS
                   Ubie_methyltran 124 fG 125
                                       f 
  gi|344210197|ref|YP_004786373.1| 106 FY 107
                                       94 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 !   26.9   0.0   2.2e-09   3.1e-06       4      60 ..      35      91 ..      33     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.2e-09
                   Methyltransf_15  4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe 60
                                       lD+ +G+G n+   a  + +v a++ ++  l +a +Na+  gv+d i ++++d+ +
  gi|344210197|ref|YP_004786373.1| 35 ALDVATGTGRNALPVAAAGYRVDAVDQSRAGLHIARENAREVGVEDDIEWIQADLDS 91
                                      69****************99**********************************876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.2e-08   1.7e-05       6     112 ..      34     131 ..      32     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.2e-08
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsn 81 
                                       r lD+++GtG+ ++  a  +  + +v  +D s   +  Arena++ g++  +e  q+d  ++   +  +++D+i+  
  gi|344210197|ref|YP_004786373.1|  34 RALDVATGTGRNALPVA-AA--GYRVDAVDQSRAGLHIARENAREVGVEdDIEWIQADLDSFG--YPASTYDVITV- 104
                                       579**************.44..45677**********************9*************..999*****999. PP

                   Methyltransf_31  82 evlnaladpdkileeiervlkpggilliedp 112
                                            ++ p + l  i+++l +gg l i+++
  gi|344210197|ref|YP_004786373.1| 105 ----SFYRPVDRLPDIIEALADGGCLFIQHH 131
                                       ....599999999999999999999999887 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.5e-07   0.00034       1      74 [.      36     106 ..      36     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.5e-07
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg..ssfDlvvasn 74 
                                       L++ +GtG+++ +++++  + ++ +vD s++ ++ a+e  ++ +    + +e+ + dl d++g   s++D++++s+
  gi|344210197|ref|YP_004786373.1|  36 LDVATGTGRNALPVAAA--GYRVDAVDQSRAGLHIARENAREVGV--EDDIEWIQADL-DSFGYpaSTYDVITVSF 106
                                       89***************..**************888887777775..66899998885.4555578******9885 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.6e-07   0.00036      25     101 ..      25     102 ..      20     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.6e-07
                                       HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTT.TSTTS-E CS
                               MTS  25 etlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvle.eveekkf 98 
                                       ++lp+   g++lD+++G+G  ++ +a++  +  v++vd++ + l++a+en+++ ++e  +e ++ d+ +   +   +
  gi|344210197|ref|YP_004786373.1|  25 RYLPTFPPGRALDVATGTGRNALPVAAAGYR--VDAVDQSRAGLHIARENAREVGVEddIEWIQADLDSfGYPASTY 99 
                                       5677777899****************98777..9**********************999999999998723445666 PP

                                       EEE CS
                               MTS  99 dli 101
                                       d+i
  gi|344210197|ref|YP_004786373.1| 100 DVI 102
                                       666 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   7.3e-07     0.001      77     125 ..      54     102 ..      35     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.3e-07
                                       --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EE CS
                           UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvi 125
                                       +++ ++D  r+ ++ areNa++ gv+d ie+ qad  ++  + + +dvi
  gi|344210197|ref|YP_004786373.1|  54 YRVDAVDQSRAGLHIARENAREVGVEDDIEWIQADLDSFGYPASTYDVI 102
                                       557799*******************************999888788887 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   9.6e-06     0.013      67     171 ..      25     128 ..      10     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.6e-06
                                       HHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-G.GGTTGGG- CS
                              PCMT  67 ellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDG.rkGyeeka 141
                                        +l   +  r+L+v +G+G ++  +a       rv ++++++   + a++n ++ ++e ++  + +D    Gy++ +
  gi|344210197|ref|YP_004786373.1|  25 RYLPTFPPGRALDVATGTGRNALPVAAA---GYRVDAVDQSRAGLHIARENAREVGVEdDIEWIQADLdSFGYPA-S 97 
                                       5666666779***********9876654...446669*******************9989999***961568875.7 PP

                                       SEEEEEESSB..BSS--HHHHHTEEEEEEEEE CS
                              PCMT 142 PYdaihvgaa..apeiPealidQLkeGGrlvv 171
                                        Yd+i v+    ++ +P+ +i+ L++GG l +
  gi|344210197|ref|YP_004786373.1|  98 TYDVITVSFYrpVDRLPD-IIEALADGGCLFI 128
                                       8******97522567885.89*******9976 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     5e-05     0.068     104     195 ..      35     124 ..      24     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5e-05
                                       EEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE--TTTG CS
                            Met_10 104 VvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvmnlpksa 180
                                        +dv  G G  a+p+a    + rv a+d   +  +  +en +   ve+ ++ i++D   +  +  +  v+    ++ 
  gi|344210197|ref|YP_004786373.1|  35 ALDVATGTGRNALPVAA--AGYRVDAVDQSRAGLHIARENAREVGVEDDIEWIQADLDSFGYPASTYDVITVSFYRP 109
                                       589*************7..9999*************************************88777777777777788 PP

                                       GGGHHHHHHHEEEEE CS
                            Met_10 181 ieFldkvlaalkdgg 195
                                       ++ l ++++al dgg
  gi|344210197|ref|YP_004786373.1| 110 VDRLPDIIEALADGG 124
                                       888888888888876 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.16     164     242 ..      34     113 ..      22     130 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                              PrmA 164 evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk....eekadvivaNILa 236
                                       + lDv tG+G  a+ +a  g  +v avD     +++a+eNa+  +ve+ +e  ++++l +    ++++dvi      
  gi|344210197|ref|YP_004786373.1|  34 RALDVATGTGRNALPVAAAG-YRVDAVDQSRAGLHIARENAREVGVEDDIEW-IQADLDSfgypASTYDVITVS-FY 107
                                       67999888886666665555.5799***********************9986.344444333456889988654.44 PP

                              PrmA 237 evliel 242
                                       +++ +l
  gi|344210197|ref|YP_004786373.1| 108 RPVDRL 113
                                       566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); 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:                        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 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1351.49
//
Query:       gi|344210198|ref|YP_004786374.1|  [L=133]
Description: PilT protein domain-containing protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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-10   40.0   2.9    5.6e-10   39.8   2.9    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 !   39.8   2.9   3.1e-14   5.6e-10       1     112 [.       1     113 [.       1     123 [. 0.84

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 3.1e-14
                                       EEE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEE.BCH CS
                               PIN   1 ivlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilp.ida 75 
                                       +++ T +l all +++  ++aa+++lee ++++ts+l++aE+l     r+  +++ ++ ++   ll+ + i+p   +
  gi|344210198|ref|YP_004786374.1|   1 MYVETDFLTALLkDDDWLQDAAVRALEEHDDIHTSILAYAEVLVLFYDREAAEYEIDAPRAITNLLELVPIVPeEHE 77 
                                       699*********99999**************************9999956666666666666666********7778 PP

                                       HHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ES CS
                               PIN  76 eiaeeaaeialkygllpnDaliaAtAkehgikliatf 112
                                       ++++ aa++ ++y+l+p+Dal+a +      +++ + 
  gi|344210198|ref|YP_004786374.1|  78 DAVLAAAAFLDEYDLTPFDALHAGLVTTGEERVL-ST 113
                                       888999999**************98877776666.54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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 0.34s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 749.07
//
Query:       gi|344210199|ref|YP_004786375.1|  [L=88]
Description: hypothetical protein HAH_5258 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 524.68
//
Query:       gi|344210200|ref|YP_004786376.1|  [L=580]
Description: cytochrome c oxidase subunit I [Haloarcula hispanica ATCC 33960]
Scores for 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-145  483.2  61.7     7e-145  483.2  61.7    1.6  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 ?   -2.7   0.3      0.11     2e+03       9      27 ..      10      28 ..       3      37 .. 0.50
   2 !  483.2  61.7  3.9e-149    7e-145       1     431 [.      66     518 ..      66     533 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.11
                                      HHHHHHHHHHHHHHHHHHH CS
                              COX1  9 lalvlllvggllgllirlq 27
                                      ++l+++l+ g++g+l+r++
  gi|344210200|ref|YP_004786376.1| 10 TVLMAILLVGIAGILARIE 28
                                      3344444444444444443 PP

  == domain 2  score: 483.2 bits;  conditional E-value: 3.9e-149
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCTCT.....-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS CS
                              COX1   1 kigllylilalvlllvggllgllirlqlafp.....dletynqlrtlHgnlmiflfatpfilgfgnylvplllgard 72 
                                       +ig+ly ++a+v++++gg++ +l+r++l++p     ++  yn l+t Hg++m+flf tp++++f+nyl+pll+ga+d
  gi|344210200|ref|YP_004786376.1|  66 DIGILYGVFAVVAFAWGGIAVVLMRFELMYPaedflSASAYNGLLTTHGITMLFLFGTPMLAAFSNYLIPLLIGADD 142
                                       599***************************98888888*************************************** PP

                                       -S-HHHHHHHHHHHHHHHHHHHHHHHCS........S-STTTTTTTC.......SHHHHHHHHHHHHHHHHHHHHHH CS
                              COX1  73 lafprlnalsfwlvvlgvvllllsllga........attgwteYapls......evdlwllglllvvvssllgainf 135
                                       +afpr+na++fwl++ +++l++ ++lg+        a+t wt+Y+pls      +vdl+llgl+l++v++++gainf
  gi|344210200|ref|YP_004786376.1| 143 MAFPRINAIAFWLLPPAALLIWGGVLGGpfleniepAQTAWTMYTPLSieqqnpGVDLMLLGLHLSGVAATMGAINF 219
                                       *************************94446677777***************************************** PP

                                       HHHHHHHHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT.-SSSC..E-HHHHHHHHHHHHTHH CS
                              COX1 136 ivtilkrrapgmtvaklplfvwavlatailillalpvlalalllllldrslg.kffsp..gdplldqhlfWffgHpe 209
                                       i+ti++ r++ +t+a l +f w+vl+ ++ il+a+p l  al++llldr+lg +ff+   g pll+qhlfWffgHpe
  gi|344210200|ref|YP_004786376.1| 220 IATIFTERSEDVTWATLDIFSWTVLVQSAQILFAFPLLGSALVMLLLDRNLGtTFFTLdgGGPLLWQHLFWFFGHPE 296
                                       ********************************************************7777***************** PP

                                       HHHHHHHHHHHHHHHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHHHHHHTHHHHHHCC CS
                              COX1 210 VyililpalgivyyilpkfagrplfsyklsvlafililflsflvwaHHlfttglpewlkalgsvfslliavPsglkv 286
                                       Vyil+lp +g+v+yilpkf+gr+lf+ k++v++++++++lsf vwaHH+f tg+++ l+a ++++s++ia+Ps++k+
  gi|344210200|ref|YP_004786376.1| 297 VYILVLPPMGLVSYILPKFCGRKLFGFKFVVYSTLALGVLSFGVWAHHMFATGMDPRLRASFMAVSIAIAIPSAVKT 373
                                       ***************************************************************************** PP

                                       CHHHHCCTTS-CHCHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTHHHHHHHHHHHHHH CS
                              COX1 287 fnwlatlwrgsirfktpmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllgavvfllfaaiyyll 363
                                       fnw+at+w+g++r ++p+lf++gf+  fiigG+tGv+ a+ +v++++h+ty vvaHfH+v++g+++f++fa+iyy++
  gi|344210200|ref|YP_004786376.1| 374 FNWMATMWNGALRTTAPFLFCVGFVGNFIIGGVTGVFEAAIPVDLILHDTYHVVAHFHYVIMGGIAFAVFAGIYYWF 450
                                       ***************************************************************************** PP

                                       HHHHSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHBSSSST--SCCCCHHHCHHHHHHHHHHHH CS
                              COX1 364 pkltgrmlserlaklhfwllfiGlvlmflpmhilGllgmprraadyksfletvpelqplnvlrtiggv 431
                                       p  tgr++++ lak+hfwl+++G++++f+pm++lG++gmprr+a+y   +  v+ ++ l++l+t+g v
  gi|344210200|ref|YP_004786376.1| 451 PLYTGRWYQRSLAKWHFWLTLVGTNVTFFPMVLLGYAGMPRRYATYALTAGPVDLFTLLHQLATLGVV 518
                                       **********************************************97788899**********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3765.54
//
Query:       gi|344210201|ref|YP_004786377.1|  [L=123]
Description: cupin 2 barrel domain-containing protein [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-07   30.5   0.3    3.1e-07   30.0   0.3    1.2  1  Cupin_2         Cupin domain
     0.0073   16.0   0.1      0.011   15.4   0.1    1.3  1  Cupin_3         Protein of unknown function (DUF861)
  ------ inclusion threshold ------
      0.011   15.4   0.1      0.013   15.2   0.1    1.1  1  AraC_binding_2  AraC-binding-like domain
      0.055   13.5   0.0       0.23   11.5   0.0    1.9  2  Inhibitor_I78   Peptidase inhibitor I78 family
      0.066   12.9   0.4      0.077   12.7   0.4    1.3  1  Cupin_6         Cupin
       0.15   11.9   0.0       0.19   11.6   0.0    1.1  1  AraC_binding    AraC-like ligand 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 !   30.0   0.3     1e-10   3.1e-07       5      70 ..      35      99 ..      33     100 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1e-10
                                      EETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2  5 lppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70
                                      ++pG+ +p h  p +d  ++V +G g ++ ++ e  +e+Gd+v+++a t  +++ ++d+ ++ l v
  gi|344210201|ref|YP_004786377.1| 35 FEPGQFIPVHA-PASDVAIHVQSGSGIVRDGDTERAVEPGDVVVVEADTDRGVKADEDGRLEALLV 99
                                      68999999999.8889*************999***************************9999876 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 !   15.4   0.1   3.6e-06     0.011      23      60 ..      45      82 ..      28      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.6e-06
                                      ESSEEEE.EEEECEEEEEETTTEEEEEETTEEEEE-TTE CS
                           Cupin_3 23 yeedEfc.yileGevkvtpeggetvelraGDlvvlpkgl 60
                                       +++  + ++ +G   v++ g  ++++++GD+vv+++++
  gi|344210201|ref|YP_004786377.1| 45 APASDVAiHVQSGSGIVRD-GDTERAVEPGDVVVVEADT 82
                                      5554444499*******99.9999************998 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 ?   15.2   0.1   4.3e-06     0.013      61     108 ..      54     105 ..      30     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.3e-06
                    AraC_binding_2  61 plsGraeveqggrevvlgpgdavvldpgrpyrlrwsadce..qlvlrip..r 108
                                         sG++ v+ g++e  ++pgd+vv+ ++ +  +  ++d +   l+++ p  +
  gi|344210201|ref|YP_004786377.1|  54 VQSGSGIVRDGDTERAVEPGDVVVVEADTDRGVKADEDGRleALLVTAPppT 105
                                       469*******************************999888335555555553 PP

>> Inhibitor_I78  Peptidase inhibitor I78 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.23   6.9e+02      35      56 ..      36      57 ..      15      63 .. 0.64
   2 ?   11.5   0.0   7.8e-05      0.23      28      62 ..      64      97 ..      43      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.23
                     Inhibitor_I78 35 kPGqvvtleynpaRlniivega 56
                                       PGq + +   ++ + i v+  
  gi|344210201|ref|YP_004786377.1| 36 EPGQFIPVHAPASDVAIHVQSG 57
                                      6888887777777777776654 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.8e-05
                     Inhibitor_I78 28 sdsvRvlkPGqvvtleynpaRlniivegaGkisal 62
                                       d+ R + PG+vv +e ++ R  +  +++G++ al
  gi|344210201|ref|YP_004786377.1| 64 GDTERAVEPGDVVVVEADTDR-GVKADEDGRLEAL 97
                                      57889**************99.7999****99887 PP

>> Cupin_6  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   2.6e-05     0.077      33      82 ..      48      95 ..      15     120 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                           Cupin_6 33 g.lalhvvlrGscwlidpasgepvrLsagdvvllpggephvladspgtapl 82
                                      + +a+h v +Gs  ++d++  + +++++gdvv++  ++   +  +++ + +
  gi|344210201|ref|YP_004786377.1| 48 SdVAIH-VQSGSGIVRDGD--TERAVEPGDVVVVEADTDRGVKADEDGRLE 95
                                      445555.689******777..569************998888555443222 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 ?   11.6   0.0   6.3e-05      0.19      27      70 ..      52      95 ..      32     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.3e-05
                                      EEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEE CS
                      AraC_binding 27 hyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgwe 70
                                      + v++G+g++r ++ +  ++pGd++ +  ++     +d++ ++e
  gi|344210201|ref|YP_004786377.1| 52 IHVQSGSGIVRDGDTERAVEPGDVVVVEADTDRGVKADEDGRLE 95
                                      7899**********************999987777777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 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:                        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 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 797.15
//
Query:       gi|344210202|ref|YP_004786378.1|  [L=307]
Description: alkanal monooxygenase [Haloarcula hispanica ATCC 33960]
Scores for complete 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  162.0   4.7    3.7e-47  161.3   1.7    1.9  2  Bac_luciferase  Luciferase-like monooxygenase
  ------ inclusion threshold ------
       0.02   14.9   0.3      0.094   12.7   0.0    2.2  2  DUF2761         Protein of unknown function (DUF2761)


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 !  161.3   1.7   4.2e-51   3.7e-47      16     235 ..      33     253 ..      20     255 .. 0.92
   2 ?    1.6   0.1     0.017   1.5e+02      25      47 ..     268     290 ..     255     301 .. 0.78

  Alignments for each domain:
  == domain 1  score: 161.3 bits;  conditional E-value: 4.2e-51
                    Bac_luciferase  16 gaas.aslrylvelaraaEelGfdavwvaehhggpgga......ldaftllaalaaaTerirlgtavtplytrhPav 85 
                                          s ++++  ++la +aE +Gfda+w+ +  + +         +d+++ll+++aa+Te + lgta  +l++rhP++
  gi|344210202|ref|YP_004786378.1|  33 E--StPDIDAELRLASHAETVGFDALWARDVPTYWPRFgdaggaFDPWSLLSHVAAHTESVALGTASIVLPLRHPLH 107
                                       2..1469***********************99888776789************************************ PP

                    Bac_luciferase  86 lAqqaatLdhlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsv.kgalllpr 161
                                       +A++aat+d+ls+GR++lg+ +g + +e+ +fGvd + r +  rE ve+lr lwr+e ++ +G + ++  ++++lp+
  gi|344210202|ref|YP_004786378.1| 108 MAKSAATVDRLSDGRLVLGVASGDRDPEYPAFGVDPENRGQLVRESVEALRVLWREEYPTLDGSWGYLdGELDVLPK 184
                                       ******************************************************99*********777699****** PP

                    Bac_luciferase 162 pgqgpiPvyvaaaspaglelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadtee 235
                                       p  + +P++  +   ++ e+ a+ +dg+++   p+  ++ +++++r+ a+e  +   ++++++++ +++++t+e
  gi|344210202|ref|YP_004786378.1| 185 PTTDTLPLFPTGNARQSTEWIAENGDGWIFYHLPESTLESYLDTWRSHASE--K---PFTIAVQVEFAADPTAE 253
                                       *9999*****************************************95555..3...88999999999998876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.017
                    Bac_luciferase  25 lvelaraaEelGfdavwvaehhg 47 
                                       ++e+ r++Ee+G+d v v+ ++ 
  gi|344210202|ref|YP_004786378.1| 268 FREYFRRLEEHGLDHVIVGLRAA 290
                                       7899************9987765 PP

>> DUF2761  Protein of unknown function (DUF2761)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     1e-05     0.094      28      60 ..      59      91 ..      45     117 .. 0.88
   2 ?   -1.2   0.0      0.24   2.1e+03      27      55 ..     208     237 ..     203     251 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1e-05
                           DUF2761 28 gdapayfyseeaeglgldpwrlvegvdahtags 60
                                       d+p+y+      g  +dpw l+  v aht+  
  gi|344210202|ref|YP_004786378.1| 59 RDVPTYWPRFGDAGGAFDPWSLLSHVAAHTESV 91
                                      69******9999999**************9865 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.24
                           DUF2761  27 ngdapayfyseeae.glgldpwrlvegvda 55 
                                       ngd   +++ +e+  +  ld wr      +
  gi|344210202|ref|YP_004786378.1| 208 NGDGWIFYHLPESTlESYLDTWRSHASEKP 237
                                       788887777666542778999997655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 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:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1857.54
//
Query:       gi|344210203|ref|YP_004786379.1|  [L=248]
Description: 3-beta hydroxysteroid dehydrogenase/isomerase family protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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-36  124.8   2.4    4.1e-36  124.6   2.4    1.1  1  NAD_binding_10   NAD(P)H-binding
    2.5e-11   43.6   0.0    3.5e-11   43.1   0.0    1.3  1  NmrA             NmrA-like family
    5.2e-09   35.5   0.0    7.1e-09   35.1   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    5.7e-07   29.3   0.0      7e-07   28.9   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
      6e-05   23.5   0.1    8.9e-05   22.9   0.1    1.3  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
     0.0042   17.3   0.2      0.016   15.4   0.1    2.0  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.021   15.1   0.0      0.037   14.3   0.0    1.4  1  TrkA_N           TrkA-N domain
      0.059   13.3   0.0       0.11   12.5   0.0    1.5  1  ADH_zinc_N       Zinc-binding dehydrogenase
      0.067   13.6   0.5        5.5    7.4   0.1    2.3  2  HsbA             Hydrophobic surface binding protein A


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 !  124.6   2.4   2.1e-39   4.1e-36       1     180 [.      13     200 ..      13     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 2.1e-39
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC.... CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk.... 73 
                                       GA+G++Gr+ ++ l +r   +v+al+ +p+k+++l+a+ + evv+ d++++ +laeal+++d+V+sa+g++ +    
  gi|344210203|ref|YP_004786379.1|  13 GASGGTGRATLRLLSSR-VPTVRALTSTPSKTDDLQAAGADEVVVDDLLNPTALAEALSDVDVVLSAVGSNITdvws 88 
                                       9***********99999.59***************999999***************************999998887 PP

                                       .....HHHHHHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHHHHHHHHHSSSEEEEEEE-C CS
                    NAD_binding_10  74 .....deegaknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaakraaeellrasgldwTivrpgg 145
                                            d  g++n++d a  agv+ fv+ saigvgde ++++ +  + +++++ +ak++ae+ +r+  +  Ti+rpg 
  gi|344210203|ref|YP_004786379.1|  89 rdeyvDGAGTINLLDTAVDAGVEAFVMESAIGVGDEPASPLATAFDVVIQPIQRAKAEAEAAIRDAPVRHTILRPGV 165
                                       655545455********************************999999****************************** PP

                                       EE-ST--S.EEEEETTSS----EEEHHHHHHHHHHH CS
                    NAD_binding_10 146 Ltdepttk.yrvvekgepfkggsisradVAdvlvav 180
                                       Lt++p+t+ + v+e g ++  gs+sradVA++++a+
  gi|344210203|ref|YP_004786379.1| 166 LTNGPRTDtVSVAEPGAKL-WGSVSRADVARLMIAS 200
                                       *****66615555556655.569**********985 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   1.7e-14   3.5e-11       1     144 [.       9     166 ..       9     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.7e-14
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTT.EEEES-TT-HHHHHHHHTT-SEEEE---GG. CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGv.elvkgdlddkeslvealkgvdvvfsvtgfy. 75 
                                       + v Ga+G  G++  r l ++  +vral+  +++   + l++aG+ e+v +dl +   l+eal++vdvv s++g++ 
  gi|344210203|ref|YP_004786379.1|   9 VFVAGASGGTGRATLRLLSSRVPTVRALTSTPSK--TDDLQAAGAdEVVVDDLLNPTALAEALSDVDVVLSAVGSNi 83 
                                       5799*************************88865..689*****94466*************************999 PP

                                       .....S-HHHHH...HHHHHHHHHHS-SEEEEEE---GG.G......T.SSS---TTTHHHHHHHHHHHHCTS-EEE CS
                              NmrA  76 .....skeiedg...kklvdAakeaGvkhfiySslgddndr......snaeepavphfdsKaeieeyvralgipytf 138
                                            ++e  dg    +l d a+ aGv+ f+  s     d+      +  +    p+  +Kae e ++r + +++t+
  gi|344210203|ref|YP_004786379.1|  84 tdvwsRDEYVDGagtINLLDTAVDAGVEAFVMESAIGVGDEpasplaTAFDVVIQPIQRAKAEAEAAIRDAPVRHTI 160
                                       999*9888888844469***************9877666541111113334445566669***************** PP

                                       EEE-EE CS
                              NmrA 139 vyagff 144
                                       +++g+ 
  gi|344210203|ref|YP_004786379.1| 161 LRPGVL 166
                                       *99975 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 !   35.1   0.0   3.6e-12   7.1e-09       2     122 ..      11     123 ..      10     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 3.6e-12
                         3Beta_HSD   2 vtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvd 78 
                                       v G++G  Gra  + L ++  + +vr+l     p++ ++l+  + ++v+  D+++   l eal +vdvv+     ++
  gi|344210203|ref|YP_004786379.1|  11 VAGASGGTGRATLRLLSSR--VPTVRAL--TSTPSKTDDLQAAGADEVVVDDLLNPTALAEALSDVDVVLSA-VGSN 82 
                                       8899999999988766554..5799986..67888899*******************************987.4566 PP

                         3Beta_HSD  79 vagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgp 122
                                       ++ + ++de+  v   GT n+l+++v+agv+++v  S+++v g+
  gi|344210203|ref|YP_004786379.1|  83 ITDVWSRDEY--VDGAGTINLLDTAVDAGVEAFVMESAIGV-GD 123
                                       7778889955..7789*********************9987.43 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   3.5e-10     7e-07       1     114 [.       9     117 ..       9     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 3.5e-10
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.EEEE--TT-HHHHHHHHHHHT-SEEEE--S--- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.elveldltdrsalerlfkeeqpdavihlAavgg 76 
                                       ++V+Ga+G  G+a+++ l ++  +v +l++ +s+    + + + e+v  dl++++al+++++  ++d+v+ + + ++
  gi|344210203|ref|YP_004786379.1|   9 VFVAGASGGTGRATLRLLSSRVPTVRALTSTPSKTDDLQAAGAdEVVVDDLLNPTALAEALS--DVDVVLSAVG-SN 82 
                                       68*****************************7777666666659******************..7999999855.55 PP

                                       HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEE CS
                         Epimerase  77 vaassedpadfieknlqgtlnlleaarkagvkrllfls 114
                                       + + +++ ++    + +gt nll+ a +agv+ ++  s
  gi|344210203|ref|YP_004786379.1|  83 ITDVWSRDEY---VDGAGTINLLDTAVDAGVEAFVMES 117
                                       5555555555...78****************9988655 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 !   22.9   0.1   4.5e-08   8.9e-05       2      83 ..       9      88 ..       8     112 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.5e-08
                                      EEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHH CS
                    Semialdhyde_dh  2 vaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvs 79
                                      v + Ga+G +G++ lrlL++  p v  ++ + s+  +  + a a      + dl   ++ +e+l++vd+v++a++++++
  gi|344210203|ref|YP_004786379.1|  9 VFVAGASGGTGRATLRLLSSrVPTVRALTSTPSKT-DDLQAAGA--DEVVVDDLLNPTALAEALSDVDVVLSAVGSNIT 84
                                      7899****************566555555444444.55555544..334455555445788889************998 PP

                                      HHHH CS
                    Semialdhyde_dh 80 kela 83
                                        + 
  gi|344210203|ref|YP_004786379.1| 85 DVWS 88
                                      7665 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 !   15.4   0.1   8.2e-06     0.016       1      79 [.       9      81 ..       9      86 .. 0.82
   2 ?   -1.7   0.0       1.6   3.1e+03      15      44 ..     127     154 ..     120     177 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.2e-06
                                      EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE-.-TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaial.daenyeavLaallkegdlvvnls 77
                                      v + Ga G++G+a+++ll+ + +    +   + + +k + l a      ++ + + d  n++a La++l++ d+v++++
  gi|344210203|ref|YP_004786379.1|  9 VFVAGAsGGTGRATLRLLSSRVPT---VRALTSTPSKTDDLQA----AGADEVVVdDLLNPTA-LAEALSDVDVVLSAV 79
                                      5688****************9876...9999999999888854....4555555515677788.*************98 PP

                                      SG CS
                   Sacchrp_dh_NADP 78 pp 79
                                      ++
  gi|344210203|ref|YP_004786379.1| 80 GS 81
                                      75 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.6
                                       HHHHCTCCT-GEEEEEESSHHHHHHHHCHH CS
                   Sacchrp_dh_NADP  15 ellarhfdvdaeitvadrskeklealaaka 44 
                                         la  fdv   i  + r k+++ea++ +a
  gi|344210203|ref|YP_004786379.1| 127 SPLATAFDV--VIQPIQRAKAEAEAAIRDA 154
                                       556666666..6777777777777777654 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   0.0   1.8e-05     0.037       7      73 ..      16      82 ..       9      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                                      SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSE.EEES-TTSHHHHHHTTGGGESEEEE-SSSH CS
                            TrkA_N  7 GrvGrslaeeLseggkdvvvidkdeerveelreegle.vvvgdatdeevLeeagiekadaviaatgdd 73
                                      G +Gr+ ++ Ls++ + v +  + +++ + l++ g++ vvv d  ++ +L+ea ++++d+v+ a+g++
  gi|344210203|ref|YP_004786379.1| 16 GGTGRATLRLLSSRVPTVRALTSTPSKTDDLQAAGADeVVVDDLLNPTALAEA-LSDVDVVLSAVGSN 82
                                      889**********9989******************555************998.89999999998876 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.3e-05      0.11      16      70 ..      32      83 ..      17     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.3e-05
                                      EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHH CS
                        ADH_zinc_N 16 eviavdsseeklelakklGadevinykea.dlverikeltggegvdvvfecvGsga 70
                                      +v a  s+++k + ++  Gadev+   +  ++ +  ++l    +vdvv+ +vGs+ 
  gi|344210203|ref|YP_004786379.1| 32 TVRALTSTPSKTDDLQAAGADEVVVD-DLlNPTALAEALS---DVDVVLSAVGSNI 83
                                      56788999*****************9.7767777777777...9*********765 PP

>> HsbA  Hydrophobic surface binding protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0028       5.5      79     116 ..      34      71 ..      25      73 .. 0.92
   2 ?    4.2   0.0     0.027        55      27      54 ..     115     149 ..      96     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0028
                                       HHHHHHHHTHHHHHHHT-HHHHHHHHHHHHHHHHHHHH CS
                              HsbA  79 aaldaliaKkpafdkagltslvlssLqdlkaasdaLsd 116
                                        al++  +K +++++ag+  +v ++L +  a+++aLsd
  gi|344210203|ref|YP_004786379.1|  34 RALTSTPSKTDDLQAAGADEVVVDDLLNPTALAEALSD 71 
                                       6899999****************************998 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.027
                                       S......H...HHHHHHHHHHHHHHHHHHHHHHHT CS
                              HsbA  27 G......g.asalpilsasnalvsaikkattdaqa 54 
                                              g   a p+ +a++ +++ i+ a + a+a
  gi|344210203|ref|YP_004786379.1| 115 MesaigvGdEPASPLATAFDVVIQPIQRAKAEAEA 149
                                       14455577789*******************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1718.66
//
Query:       gi|344210204|ref|YP_004786380.1|  [L=332]
Description: DMT(drug/metabolite transporter) superfamily permease [Haloarcula hispanica ATCC 33960]
Scores for 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-38  129.9  39.1    1.1e-19   71.0  16.9    2.0  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
       0.03   13.7   8.6       0.22   10.8   4.3    2.2  2  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 !   65.1  14.2   7.8e-22     7e-18       6     136 ..      21     153 ..      19     154 .. 0.93
   2 !   71.0  16.9   1.2e-23   1.1e-19       2     135 ..     166     302 ..     165     304 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 7.8e-22
                              EamA   6 lallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkd..wllllllgllgtvlafl 80 
                                       l++l a++++ +fv++k +lr+++p+ ++++rf +a++ ll +++l++ +  +l+++   +  +   +l+ ++l ++
  gi|344210204|ref|YP_004786380.1|  21 LFVLLAVLFGGSFVAIKTGLRELPPVLFAGLRFDLAAVTLLGYIVLTRPRSTWLPRTRadFVGIGMAALFLIALNNG 97 
                                       66788999***************************************9999455444444888899999******** PP

                              EamA  81 lffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       l+f ++  t+++ as++  l P+++ +++++llg +l+++  lgi+++l Gv+li+
  gi|344210204|ref|YP_004786380.1|  98 LLFLGQGATTPAAASVMYGLNPILAPVFAWWLLGDRLSWLGALGIGIALSGVILIV 153
                                       ******************************************************97 PP

  == domain 2  score: 71.0 bits;  conditional E-value: 1.2e-23
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl...aklslkdwllllllgllgt 75 
                                       +g ll+l aa   a++ v+ +++  ++++  lt++ + ++++ll i +ll ++++     + ++ +++++ +g+ +t
  gi|344210204|ref|YP_004786380.1| 166 IGQLLVLGAAAAVALGSVFLQRVGPQMDSTPLTAWAMAVGAVLLHIASLLAGEPPtavIGIGPETIASIVAVGIPST 242
                                       699*****************************************************999999999************ PP

                              EamA  76 vlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       ++a+ ++f ++k++++ +a l+ +++P+f+++++++llg +++l++++g++++++G +li
  gi|344210204|ref|YP_004786380.1| 243 AVAYAIYFGLIKRIGPVRANLVAYVVPIFAALMGWVLLGSSVSLWTFVGFLVVVAGFALI 302
                                       *********************************************************998 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1    0.0017        15     257     288 ..     120     151 ..      85     152 .. 0.80
   2 ?   10.8   4.3   2.4e-05      0.22      36     134 ..     199     301 ..     192     311 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0017
                               TPT 257 vvvIvlsvlvfknpvsllnaiGtavaivGvfl 288
                                       ++  v++  ++++++s+l a+G  +a+ Gv+l
  gi|344210204|ref|YP_004786380.1| 120 ILAPVFAWWLLGDRLSWLGALGIGIALSGVIL 151
                                       555566667899******************87 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 2.4e-05
                               TPT  36 avqllvgsvlilvlwal.glkkrpkisse..flkailplalvktlghvlavvslsk.vaVSfthtvKasePiFtvil 108
                                       a  ++vg vl+ ++  l g   ++ i     ++++i+ +++  t++  +  + l k +    ++ v  + PiF++++
  gi|344210204|ref|YP_004786380.1| 199 AWAMAVGAVLLHIASLLaGEPPTAVIGIGpeTIASIVAVGIPSTAVAYAIYFGLIKrIGPVRANLVAYVVPIFAALM 275
                                       555666666665544443555544444333488888888888888888888887652444468999999******** PP

                               TPT 109 srlllgeklsllvylsLlpivgGval 134
                                         +llg ++sl+ ++  l++v+G al
  gi|344210204|ref|YP_004786380.1| 276 GWVLLGSSVSLWTFVGFLVVVAGFAL 301
                                       ***********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2186.96
//
Query:       gi|344210205|ref|YP_004786381.1|  [L=279]
Description: aldehyde reductase/aldo/keto reductase family oxidoreductase [Haloarcula hispanica ATCC 33960]
Scores for 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-56  189.4   0.0    3.3e-53  180.8   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 !  180.8   0.0   1.9e-57   3.3e-53       2     293 ..      20     263 ..      19     264 .. 0.97

  Alignments for each domain:
  == domain 1  score: 180.8 bits;  conditional E-value: 1.9e-57
                                       EEEE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTS CS
                      Aldo_ket_red   2 lglGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeik 78 
                                       lglGtwq       + e+ +e +r+aleaG++++DtA++Y    +e  +G  l+++ ++r+++++atKv      + 
  gi|344210205|ref|YP_004786381.1|  20 LGLGTWQND-----DAEQCAESVRTALEAGYRHIDTAQAY---DNESAVGDGLAAADVDRDDIFLATKV------WI 82 
                                       799999877.....589***********************...**************************......** PP

                                       SSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHHHHTTT- CS
                      Aldo_ket_red  79 sglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqlekakkkkkv 155
                                       s+ls+++++e  eesl +Lg+d vDll++H+   +++  ee+l a++elv+ G+i ++GvSnf+  ++e a      
  gi|344210205|ref|YP_004786381.1|  83 SNLSHDDVIETTEESLDKLGVDSVDLLYVHWAAGEYE-PEETLPAFDELVDRGLIDNVGVSNFEPHHVETAMDVLDA 158
                                       *************************************.*********************************999999 PP

                                       -EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHH CS
                      Aldo_ket_red 156 kivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeel 232
                                       ++ a+qve +++  l++++l+e +++++  l+ayspl++G   g                              + +
  gi|344210205|ref|YP_004786381.1| 159 PVFANQVETHPF--LQQSELREHAAEQDYELVAYSPLARGEVFG-----------------------------HDVI 204
                                       ************..************************998883.............................3569 PP

                                       HHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHHH CS
                      Aldo_ket_red 233 selakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldell 293
                                       +++a +h+ s aq++l+++   ++++++ip+a++ ++++dnl++l+l ls+ e++++d+++
  gi|344210205|ref|YP_004786381.1| 205 EAIADDHDASEAQVSLAWLR--EKGVTAIPKATSEAHITDNLASLDLSLSDAEIDRIDSID 263
                                       ********************..************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1710.68
//
Query:       gi|344210206|ref|YP_004786382.1|  [L=184]
Description: hypothetical protein HAH_5265 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   13.4   0.0      0.033   13.4   0.0    1.1  1  Peptidase_M19  Membrane dipeptidase (Peptidase family M19)


Domain annotation for each model (and alignments):
>> Peptidase_M19  Membrane dipeptidase (Peptidase family M19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.8e-06     0.033     243     273 ..      72     105 ..      26     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-06
                                       S--BHHHHHHHHHHHHHHT-GGGEEE---T...T CS
                     Peptidase_M19 243 aeatledvvdhidyivelaGidhVGlGsDf...d 273
                                         a l++v++ i y+v+   + +VG+G+Df    
  gi|344210206|ref|YP_004786382.1|  72 LAAALRHVIAGISYVVAATAVGAVGIGLDFaasS 105
                                       56899*************************5432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1310.90
//
Query:       gi|344210207|ref|YP_004786383.1|  [L=76]
Description: hypothetical protein HAH_5266 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       174  (0.00970495); expected 358.6 (0.02)
Passed bias filter:                      138  (0.00769703); 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 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 532.40
//
Query:       gi|344210208|ref|YP_004786384.1|  [L=84]
Description: hypothetical protein HAH_5267 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); 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 0.27s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 548.49
//
Query:       gi|344210209|ref|YP_004786385.1|  [L=274]
Description: putative protease HtpX protein [Haloarcula hispanica ATCC 33960]
Scores for 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-39  133.7   0.0    8.6e-39  133.3   0.0    1.1  1  Peptidase_M48  Peptidase family M48
    2.8e-06   26.8   0.1    6.2e-06   25.6   0.0    1.7  2  Peptidase_M56  BlaR1 peptidase M56
  ------ inclusion threshold ------
      0.062   13.2   0.0      0.092   12.6   0.0    1.2  1  SprT-like      SprT-like family
        4.9    7.9   8.1         19    6.0   1.7    2.3  2  PrgI           PrgI family protein


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 !  133.3   0.0   1.9e-42   8.6e-39       2     193 ..      70     273 ..      69     274 .] 0.84

  Alignments for each domain:
  == domain 1  score: 133.3 bits;  conditional E-value: 1.9e-42
                                       --SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   2 lreaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhr 78 
                                       +r+++++++v++l + +++  ++++++v+++   NAFa+g+     +v++++L+ qll+++el++V++HEl+Hik+r
  gi|344210209|ref|YP_004786385.1|  70 QRFGYVHQMVRRLCRDMNI--EEPRLMVMDMGVPNAFAVGRKGAGVVVVSSELM-QLLDDDELEGVIAHELAHIKNR 143
                                       6899***************..*********************999*********.********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHH.TT-SHHHHHTT--S---HHHHHHHHHHTTHHHHHHHHHHHHHHHHTTT.HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  79 hsvvslivsllasillllglall.israeedaagafldalavliglliillflalSRkrEyqADeagvellkrakdl 154
                                       +++++++ +++ +++ +++++++ ++ +++  + +++ ++  l+ +l ++ +la+SR+rEy AD+ + +++   + l
  gi|344210209|ref|YP_004786385.1| 144 DVITMVVGQSIGMLVGYVAYFAVlFGGERNVGSWIMAMIASSLANALVMVFVLAISRYREYVADADARRAIGTGEPL 220
                                       *****888888888888776554055555555555555666666777777788************************ PP

                                       HHHHHHHHHHTT-.........-S---HHHH............HHS-SS--HHHHHHHHH CS
                                       xxxxxxxxxxxxx.........xxxxxxxxx............xxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 155 vraliklakdler.........qdvsaslrs............ellstHPplleRiqalk 193
                                       +ral k+++++e+         +       +            +l+stHPp+++Riq+l+
  gi|344210209|ref|YP_004786385.1| 221 ARALEKISRGAEGreskvedsmN-------AlcifnadkglfeKLFSTHPPTEKRIQRLR 273
                                       **********9995544444440.......2666666666666***************98 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.4e-09   6.2e-06     178     224 ..     111     157 ..      35     161 .. 0.77
   2 ?   -2.3   0.1      0.43   1.9e+03       4      22 ..     182     200 ..     177     218 .. 0.57

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.4e-09
                     Peptidase_M56 178 kprIvlPadflkklsdeeleyillHElaHlkrkDllvnllvavlqcl 224
                                         ++v+++++++ l+d+ele +++HElaH+k++D++  ++ + + +l
  gi|344210209|ref|YP_004786385.1| 111 AGVVVVSSELMQLLDDDELEGVIAHELAHIKNRDVITMVVGQSIGML 157
                                       4589*******************************998876666555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.43
                     Peptidase_M56   4 lkasiaaaiavllvlllrr 22 
                                       +++s+a a+++++vl++ r
  gi|344210209|ref|YP_004786385.1| 182 IASSLANALVMVFVLAISR 200
                                       3444444444444444433 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     2e-05     0.092      46      77 ..     111     142 ..      72     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                         SprT-like  46 hasIeLseklldsrsedrllntLaHElcHlal 77 
                                          +  s++l++  ++d+l+ ++aHEl+H+ +
  gi|344210209|ref|YP_004786385.1| 111 AGVVVVSSELMQLLDDDELEGVIAHELAHIKN 142
                                       5567889999*******************876 PP

>> PrgI  PrgI family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.7    0.0043        19      21      64 ..       7      45 ..       4      72 .. 0.62
   2 ?    5.5   0.6    0.0061        28      26      69 ..     153     204 ..     142     214 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0043
                              PrgI 21 QliflvlallvaiglylllrafleelasvlvillavPvaalgfy 64
                                      Q+ +lv++++  +++y++   +l    svl+ l  vPv ++g+ 
  gi|344210209|ref|YP_004786385.1|  7 QVRMLVVGAI-LFAFYVFAGTAL----SVLLGLPLVPVLLVGIL 45
                                      4445555555.566666666666....67777777787777665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0061
                              PrgI  26 vlallvaiglylllrafl...eelasvlvill.......avPvaalgfykkdgl 69 
                                       ++++lv++++y++  +++    +++s+++ ++        v v++l++ +++ +
  gi|344210209|ref|YP_004786385.1| 153 SIGMLVGYVAYFA--VLFggeRNVGSWIMAMIasslanaLVMVFVLAISRYREY 204
                                       3566677777777..455669999999999994444332222444455455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1625.18
//
Query:       gi|344210210|ref|YP_004786386.1|  [L=338]
Description: alcohol dehydrogenase [Haloarcula hispanica ATCC 33960]
Scores for complete 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  107.7   3.3    5.8e-31  106.6   3.3    1.6  1  ADH_N         Alcohol dehydrogenase GroES-like domain
      4e-21   75.4   0.3    8.1e-21   74.4   0.3    1.5  1  ADH_zinc_N    Zinc-binding dehydrogenase
    5.7e-06   27.4   0.6    1.1e-05   26.6   0.1    1.8  2  ADH_zinc_N_2  Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.082   12.8   0.0       0.42   10.5   0.0    2.0  2  ADH_N_2       N-terminal domain of oxidoreductase
       0.11   12.6   1.5       0.42   10.8   0.0    2.1  2  DUF2318       Predicted membrane protein (DUF2318)
       0.99    9.6   5.2       0.56   10.4   0.3    3.0  3  TOBE_2        TOBE 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 !  106.6   3.3   1.9e-34   5.8e-31       1     108 [.      29     136 ..      29     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 1.9e-34
                                       TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE.-SSSHHHHTT CS
                             ADH_N   1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvveplis.cgeCaaCkeg 76 
                                       pgev++ v a+giC+sD+ + +g +++ v++p ++GHE++G v++vg++v+ + vGdrV v ++   c++C++C++g
  gi|344210210|ref|YP_004786386.1|  29 PGEVRVSVDACGICHSDVFTKEG-TNPVVSYPRVPGHEVAGHVDAVGDAVDAWDVGDRVGVGWHGGhCSTCEQCRQG 104
                                       689*******************9.8************************************999877********** PP

                                       -GGG-TTBEETTTSS-SSSBSEEEECGGGEEE CS
                             ADH_N  77 eenlCeeakllgvsldGgfaeyvvvpekklvk 108
                                       +   Ce+++++g+s+dGg+aey+++p++ l+k
  gi|344210210|ref|YP_004786386.1| 105 NFLQCENGEITGLSYDGGYAEYMTAPSEALAK 136
                                       **************************999887 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.3   2.7e-24   8.1e-21       1     127 [.     178     300 ..     178     302 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 2.7e-24
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalk 77 
                                       g+G+++vq+A+a+G+e+ a+++++ek  lak+lGad++in+ + d  +r++el    g+dvv+ ++ s +++++ ++
  gi|344210210|ref|YP_004786386.1| 178 GLGHLGVQYAHAAGFETAAISRTPEKESLAKELGADHFINAADVDAGQRLQELG---GADVVLATAPSSDAISSIVS 251
                                       89***************************************555**********...9******************* PP

                                       CEEEEEEEEECSCTSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHH CS
                        ADH_zinc_N  78 llkpgGrlvvvGggkgeeefdlrnlllkeksilGsllgslreefkealdl 127
                                        +  +G +vvvG+++++ e+++++l+  +  + G   g+  ++ ++ l++
  gi|344210210|ref|YP_004786386.1| 252 GIGVDGSVVVVGVPGEPVEVSAQQLVQSRGGVEGWASGH-ARDSQDTLEF 300
                                       **********************************99999.7777776665 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 ?   -2.7   0.1         4   1.2e+04      18      31 ..      66      78 ..      51      95 .. 0.65
   2 !   26.6   0.1   3.5e-09   1.1e-05       1     128 [.     210     331 ..     210     336 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4
                                      H-TT-EEEEEES-H CS
                      ADH_zinc_N_2 18 tggegvDvvldtvg 31
                                      +  ++vD+v d+v+
  gi|344210210|ref|YP_004786386.1| 66 V-AGHVDAVGDAVD 78
                                      3.345888888887 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 3.5e-09
                                       TT-SEEEETTSTTHH.HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE- CS
                      ADH_zinc_N_2   1 lGAdevidyrtedfe.aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkye 76 
                                       lGAd++i+  + d+  +  + +g Dvvl t+ + ++++ +++ +   G +v++g p  + +++++++ +++++v   
  gi|344210210|ref|YP_004786386.1| 210 LGADHFINAADVDAGqRLQELGGADVVLATAPSSDAISSIVSGIGVDGSVVVVGVPGEPVEVSAQQLVQSRGGVEGW 286
                                       8******99988888533334889********888889999989555***999987788888888887766655554 PP

                                       -GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--S CS
                      ADH_zinc_N_2  77 flfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrar 128
                                               + +d  ++ +++ +   + p ++ ++ple+++eA+ ++  + ar
  gi|344210210|ref|YP_004786386.1| 287 ASG-----HARD-SQDTLEFSSLRDIAPEIE-TYPLEDVNEAYGRMIDNEAR 331
                                       444.....3556.8999*************8.9**********999887765 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 ?   10.5   0.0   0.00014      0.42      16      37 ..      15      36 ..       6      42 .. 0.89
   2 ?   -1.2   0.0      0.62   1.8e+03      66      90 ..     149     173 ..     132     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                           ADH_N_2 16 sdfeleeeelpelkdGevlvra 37
                                       dfe++e ++pe+++Gev+v +
  gi|344210210|ref|YP_004786386.1| 15 ADFEVVERDVPEPDPGEVRVSV 36
                                      69*****************987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.62
                           ADH_N_2  66 mrggavgeVveSknpdfkvGdlVvg 90 
                                       +  ++v    + +n+d +vGdlV+ 
  gi|344210210|ref|YP_004786386.1| 149 LLCAGVTTFNALRNSDANVGDLVAV 173
                                       5566677777889999999999976 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00014      0.42      26      50 ..      28      52 ..      13      57 .. 0.87
   2 ?   -0.2   0.8      0.36   1.1e+03      35      49 ..      96     110 ..      89     115 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                           DUF2318 26 sdgklrvaldaCevCekkgYvqege 50
                                        g++rv +daC +C+++ +++eg 
  gi|344210210|ref|YP_004786386.1| 28 DPGEVRVSVDACGICHSDVFTKEGT 52
                                      5689****************99986 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.36
                           DUF2318  35 daCevCekkgYvqeg 49 
                                       ++Ce C++  + q +
  gi|344210210|ref|YP_004786386.1|  96 STCEQCRQGNFLQCE 110
                                       678888877777654 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       0.5   1.5e+03      35      70 ..       7      38 ..       3      41 .. 0.73
   2 ?   10.4   0.3   0.00019      0.56      53      73 ..      75      95 ..      59      97 .. 0.78
   3 ?   -1.9   0.1       1.3   3.8e+03      60      62 ..     265     267 ..     229     276 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.5
                            TOBE_2 35 yvvelaggqlvvvrqpnadrdsalapGdtVelswdp 70
                                        v  ++g++++v+  + +    ++pG+ V++s+d+
  gi|344210210|ref|YP_004786386.1|  7 AAVVPEAGADFEVVERDVP---EPDPGE-VRVSVDA 38
                                      5556678888888888888...899996.7777765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00019
                            TOBE_2 53 drdsalapGdtVelswdpdda 73
                                      d+ +a+++Gd+V+++w+  ++
  gi|344210210|ref|YP_004786386.1| 75 DAVDAWDVGDRVGVGWHGGHC 95
                                      33369************9999 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.3
                            TOBE_2  60 pGd 62 
                                       pG+
  gi|344210210|ref|YP_004786386.1| 265 PGE 267
                                       344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 2017.27
//
Query:       gi|344210211|ref|YP_004786387.1|  [L=444]
Description: putative phosphoesterase [Haloarcula hispanica ATCC 33960]
Scores for complete 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   47.0   0.0      1e-05   25.8   0.0    2.2  2  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    3.3e-10   40.8   0.5    2.4e-08   34.7   0.3    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 !   19.0   0.0   1.4e-07    0.0012       4     110 ..      11     152 ..       9     168 .. 0.74
   2 !   25.8   0.0   1.2e-09     1e-05      99     149 ..     309     358 ..     284     369 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.4e-07
                     Metallophos_2   4 aiiSDlH.......snldaleav......lealkevgvdaiihaGD.................l.eeeepevleell 49 
                                        +iSDlH       + ++ l+++      le  +e+    ++  GD                 + ee+ p+  e+l+
  gi|344210211|ref|YP_004786387.1|  11 YVISDLHiggdeqlEDVEFLDELldflgrLETTDEH--AELLINGDafglweftgmsglekfdAlEETYPSLFEQLR 85 
                                       69*****99987774555555557777778888899..888999**9999999999998886634666667777777 PP

                     Metallophos_2  50 ela...pvlaVrGNnDeev.veedvlreaaelgtdlpeeaele..lagekvlliHgdplgvkdalae 110
                                       +     +++ ++GN+D e  + ++  +++a ++ dl +++ ++  ++++ + l Hg ++  ++++++
  gi|344210211|ref|YP_004786387.1|  86 KTGeniQITLIPGNHDHELaAYDEYVERFAAYNVDLVQSKSITrpVGDQAIHLEHGNQQDPNNRIED 152
                                       766888**********4446777788888888888854444441269999******98766666554 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 1.2e-09
                     Metallophos_2  99 gdplgvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgep 149
                                       +++  +k+a +e+++e +e++ v+++GHtH+p+v+  ++ lvvn G    +
  gi|344210211|ref|YP_004786387.1| 309 DTQTPYKEAAREVFDE-KEDVVVFCYGHTHRPSVQSVDDGLVVNSGTWLKR 358
                                       4444677777777777.55555***********************986555 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.3   2.6e-12   2.4e-08       4     153 ..      11     187 ..       9     232 .. 0.62
   2 !    4.3   0.0    0.0057        51     181     204 .]     315     339 ..     284     339 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2.6e-12
                                       EEEESBTB.....TTCCTHHHHHHHHHHHHHHHTTESEEEEEST...SSSSS............HHHHHHHHHHHHH CS
                       Metallophos   4 lvigDlHl.....algggqlddllkllddllreekpdlvllaGD...lvdrg............dlekellellaal 60 
                                        vi+DlH+      + ++ ld+ll++l +l    ++  +l++GD   l                 le+ +  l+++l
  gi|344210211|ref|YP_004786387.1|  11 YVISDLHIggdeqLEDVEFLDELLDFLGRLETTDEHAELLINGDafgL---WeftgmsglekfdALEETYPSLFEQL 84 
                                       69*****88888877778888888888888777888999999**5551...44445578877775555455556666 PP

                                       HHH..TSEEEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE..EEEEEEESE..CEEE.... CS
                       Metallophos  61 vky..pipvylllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgs..lkvlllhGg..spel.... 127
                                        k   +i++ l++GNH+   +el    +y ++f++ + + ++ +++            + ++l hG+  +       
  gi|344210211|ref|YP_004786387.1|  85 RKTgeNIQITLIPGNHD---HELAAYDEYVERFAAYNVDLVQSKSITRP------VgdQAIHLEHGNqqD--Pnnri 150
                                       666889***********...34444433333333333333222222222......233489999999551..33354 PP

                                       ....THHHHHHHHHHHSCHHHHCC.......HHHHHH CS
                       Metallophos 128 ....lvsldklgslnleleapepg.......dewlkd 153
                                           ++++++lg +   l +++ g       ++wlkd
  gi|344210211|ref|YP_004786387.1| 151 edwgDTNVTPLGYYYNTLVTSRAGqlsdrgrYNWLKD 187
                                       5445444444444444444444448999999****** PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0057
                                       HHHHHHH.HHHTTESEEEEESSSSE CS
                       Metallophos 181 dealedl.lkkygvdlvisGHtHvy 204
                                        ea++++  +k +v + ++GHtH++
  gi|344210211|ref|YP_004786387.1| 315 KEAAREVfDEKEDVVVFCYGHTHRP 339
                                       4555555388888999999****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 2505.55
//
Query:       gi|344210212|ref|YP_004786388.1|  [L=189]
Description: hypothetical protein HAH_5271 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-06   27.2   0.1    4.8e-06   26.6   0.1    1.3  1  HTH_20    Helix-turn-helix domain
     0.0029   17.4   0.0     0.0054   16.5   0.0    1.5  1  HTH_IclR  IclR helix-turn-helix domain
     0.0082   16.0   0.1      0.017   15.0   0.1    1.6  1  MarR_2    MarR family
     0.0093   15.9   0.0      0.015   15.2   0.0    1.3  1  HTH_11    HTH domain
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.023   14.8   0.0    1.5  1  HTH_17    Helix-turn-helix domain
      0.036   13.9   0.0       0.06   13.2   0.0    1.3  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 !   26.6   0.1   1.6e-09   4.8e-06      19      60 ..      29      74 ..      23      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.6e-09
                                      H....STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 19 L....araegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      +     +a++lta++++++l++s++t+++ L+vL+e g +e++++g
  gi|344210212|ref|YP_004786388.1| 29 FrdrtDQAKPLTATDVMDALGCSRKTAHNKLEVLVERGELETRKVG 74
                                      455557899*********************************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 !   16.5   0.0   1.8e-06    0.0054      14      50 ..      34      70 ..      23      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.8e-06
                                      TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 14 eapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                       ++ +lt +++ +++g ++ t+h+ L  Lve+G +e+
  gi|344210212|ref|YP_004786388.1| 34 DQAKPLTATDVMDALGCSRKTAHNKLEVLVERGELET 70
                                      34556****************************8875 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   5.8e-06     0.017      10      56 ..      25      73 ..      19      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.8e-06
                                      HHHHHHCTTTS..EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 10 vLaaLgrrpgr..dltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      vL + ++r ++  +lt++++ ++lg s+ ++++ l+ Lv++G +e+r+ 
  gi|344210212|ref|YP_004786388.1| 25 VLSVFRDRTDQakPLTATDVMDALGCSRKTAHNKLEVLVERGELETRKV 73
                                      555555555556669*******************************975 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.1e-06     0.015      14      43 ..      37      66 ..      32      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.1e-06
                            HTH_11 14 gpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      +p+++ + ++ L++Sr+t ++ ++ L e g
  gi|344210212|ref|YP_004786388.1| 37 KPLTATDVMDALGCSRKTAHNKLEVLVERG 66
                                      57*********************9997766 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   7.8e-06     0.023       2      37 ..      39      78 ..      38      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.8e-06
                            HTH_17  2 ltveEaAelLgvsrstvyrli....rrgelpaakiGrrwr 37
                                      lt  ++++ Lg+sr+t+++ +     rgel   k+G r r
  gi|344210212|ref|YP_004786388.1| 39 LTATDVMDALGCSRKTAHNKLevlvERGELETRKVGARSR 78
                                      899***************99955556****7778887733 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     2e-05      0.06      21      57 ..      37      73 ..      35      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      +p+ta+++  +lg +r ++ + L+ L+++G  e++k 
  gi|344210212|ref|YP_004786388.1| 37 KPLTATDVMDALGCSRKTAHNKLEVLVERGELETRKV 73
                                      799***************************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1200.45
//
Query:       gi|344210213|ref|YP_004786389.1|  [L=584]
Description: hypothetical protein HAH_5272 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); 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:                         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: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3663.29
//
Query:       gi|344210214|ref|YP_004786390.1|  [L=145]
Description: hypothetical protein HAH_5273 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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 0.24s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 986.10
//
Query:       gi|344210215|ref|YP_004786391.1|  [L=1014]
Description: putative oxidoreductase [Haloarcula hispanica ATCC 33960]
Scores for 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-67  226.5   0.1    9.1e-67  225.3   0.1    1.6  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    8.6e-39  132.4   0.2    1.9e-38  131.4   0.2    1.6  1  FAD_binding_4  FAD binding domain
    7.3e-09   36.1   3.6    1.4e-08   35.1   3.6    1.5  1  Fer4_17        4Fe-4S dicluster domain
      6e-08   33.0   4.8    1.3e-07   32.0   4.8    1.6  1  Fer4_8         4Fe-4S dicluster domain
    2.9e-06   27.4   0.0    0.00087   19.5   0.0    2.7  2  CCG            Cysteine-rich domain
    0.00016   21.7   3.3     0.0045   17.1   0.2    2.4  2  Fer4_10        4Fe-4S dicluster domain
    0.00095   19.3   2.2      0.025   14.8   0.2    2.4  2  Fer4_9         4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.07   12.5   0.0       0.13   11.6   0.0    1.4  1  Cytokin-bind   Cytokinin dehydrogenase 1, FAD and cytokinin b
        0.3   11.7   7.4        2.3    8.9   7.7    2.3  2  Fer4_7         4Fe-4S dicluster domain
       0.31   11.2   5.5       0.32   11.2   0.5    2.6  2  Fer4_21        4Fe-4S dicluster domain
        5.5    7.0  12.3        0.2   11.5   3.4    2.5  2  Fer4           4Fe-4S binding domain
        7.9    6.7  10.4        0.6   10.3   2.2    2.4  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 !  225.3   0.1   6.1e-70   9.1e-67       2     250 .]     299     566 ..     298     566 .. 0.97

  Alignments for each domain:
  == domain 1  score: 225.3 bits;  conditional E-value: 6.1e-70
                                       -SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SS...TTS-TTT-EEEEEEEEE-HHHH CS
                     FAD-oxidase_C   2 pearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgak...kglpdeeealllvefegddeee 75 
                                       p+a+ava+++++++ +a++ v+ i ++  +p+a+e+md++ ldl+++t +++     lp+e++++llvef++d+++ 
  gi|344210215|ref|YP_004786391.1| 299 PQATAVAMLTYDDILSAMRDVAPILDH--DPSAVEVMDDVLLDLAAETPEFAdvvGMLPEETDSTLLVEFYADSADD 373
                                       99*************************..*************************9*******************999 PP

                                       HHHHHHHHHHHTTT-EEEEE............................ETGGGGGGGGHHHHHHHHHCTTEEEEEEE CS
                     FAD-oxidase_C  76 aeeelealveaileatgaad..................vlvaqdeaeaealwkaRkaalpylrdallkagvavlseD 134
                                         +++++l+++ l +  a +                  +l a+d+++++++wk+Rka lp+l +++++ ++++++eD
  gi|344210215|ref|YP_004786391.1| 374 GAQKVADLLADRLPDYDAREspsegaaavtdapvnavdALEAYDADRQAKFWKMRKAGLPILLSRTGDDKHWPFVED 450
                                       999999977777766666666************999777************************************** PP

                                       EEEEHHHHHHHHHHHHHHHHHHHEEEEEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-------- CS
                     FAD-oxidase_C 135 tsvPvsrladlvrdikalldkyglevvlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHG 211
                                       t+vP ++l+++v+di++l+d++++ +++++Hag+g+lh+++l++l++ +  e++e+++d ++dl+v+++Gs+sgEHG
  gi|344210215|ref|YP_004786391.1| 451 TAVPAENLPEYVADIRELFDEHDTFASYYAHAGPGVLHIRPLLNLKSGDGIETMEAISDAITDLVVQYDGSVSGEHG 527
                                       ***************************************************************************** PP

                                       ---------------THHHHHHHHHHHH-TT--BSTT-- CS
                     FAD-oxidase_C 212 vGldkkaylerekgeeglalmrriKaalDPkgiLNPgkv 250
                                        G+++ ++ ++ +g+++++++r +K a+DP++ LNPg++
  gi|344210215|ref|YP_004786391.1| 528 DGRARTQWNRKLYGDDLWETFRDLKTAFDPDWRLNPGNI 566
                                       *************************************85 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.4   0.2   1.3e-41   1.9e-38       1     138 [.      66     203 ..      66     204 .. 0.98

  Alignments for each domain:
  == domain 1  score: 131.4 bits;  conditional E-value: 1.3e-41
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETT.S--EEEEETTTTEEEEETTSBHHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsr.lnrileideeegtatveaGvtlgd 76 
                                       p +vv p s+++v++++++++e+g+pvl+rGgG+sl+gqav +++vvld++r ++  l++d+e+g+a+++aG+t+++
  gi|344210215|ref|YP_004786391.1|  66 PIGVVSPVSTDDVVTVMEYCAEQGIPVLPRGGGTSLAGQAV-NEAVVLDFKRhMDETLSVDPEAGRARAQAGITIAR 141
                                       668*************************************9.********999************************ PP

                                       HHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                     FAD_binding_4  77 lvealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                       l+ +l+++gl + ++p+ g+ +++GGai +n+ G +s kyG++  ++++ evvladG+  ++
  gi|344210215|ref|YP_004786391.1| 142 LNDRLEPHGLKFAPDPAWGDKSVLGGAIGNNTTGAHSLKYGKTDAYIEECEVVLADGTQTTF 203
                                       **********************************************************9876 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   3.6   9.6e-12   1.4e-08       2      61 .]     607     685 ..     606     685 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 9.6e-12
                           Fer4_17   2 CiqCgyClp........eCpsyeaydnepkkllraakl.......glleeaeke....ekaslCieCgeCerkCPqg 59 
                                       C++C+ C+         +Cp+y+a ++e  +++ +a++        l e+  +e    e+ +lCi+C++C+++CP+g
  gi|344210215|ref|YP_004786391.1| 607 CHGCAGCTVhqettggvMCPTYRAAEEEITSTRGRANMlrsamdgDLPEDPTDEefvtEVLDLCIGCKGCKKDCPSG 683
                                       ************************999988888888777765554222332333677789****************9 PP

                           Fer4_17  60 ld 61 
                                       +d
  gi|344210215|ref|YP_004786391.1| 684 VD 685
                                       97 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   4.8   8.4e-11   1.3e-07       3      65 .]     605     684 ..     603     684 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 8.4e-11
                            Fer4_8   3 ekCieCgaCq........saCpvlrrtkkhlldargeaae.......dvqeeqvlee..........eealwsCttc 54 
                                       e C++C  C+         +Cp++r+  +++ ++rg+a+        d                    e l+ C +c
  gi|344210215|ref|YP_004786391.1| 605 ELCHGCAGCTvhqettggVMCPTYRAAEEEITSTRGRANMlrsamdgD--------LpedptdeefvTEVLDLCIGC 673
                                       67********9999999999*****************99944443331........2556667778899******** PP

                            Fer4_8  55 gaCtevCpvgi 65 
                                       + C++ Cp g+
  gi|344210215|ref|YP_004786391.1| 674 KGCKKDCPSGV 684
                                       ********986 PP

>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.018        27      11      65 ..     790     844 ..     787     859 .. 0.84
   2 !   19.5   0.0   5.8e-07   0.00087       2      85 .]     911     993 ..     910     993 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.018
                               CCG  11 raaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnveta 65 
                                       ++++p+v+ka  ++lea+gv+++++++ +  G +++ +++ + a++ a+ nv+ +
  gi|344210215|ref|YP_004786391.1| 790 NYSHPDVGKAAVEVLEAAGVHVVVPDGVTDSGRPAFSKSMLDHARETARANVDVL 844
                                       67799*******************9998888888888888888888888887765 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 5.8e-07
                               CCG   2 ayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkee...laealakrnvetaeetgadaivt 75 
                                       ay+  Ch   +++ + ++    +l+++g  +++l ++ CCG +g +  + e    +e +a+  + ++++  a+ +v+
  gi|344210215|ref|YP_004786391.1| 911 AYHGHCH---QKATKKDHHAVGVLRRAGYAVDPL-DSGCCGMAGSFGYEAEhysMSEGIADLLLGQIDDSPAERVVA 983
                                       6888884...444444555566789*******99.***********99988899999******************** PP

                               CCG  76 acpgCllqlk 85 
                                       + ++C  q++
  gi|344210215|ref|YP_004786391.1| 984 PGASCRSQID 993
                                       ******9986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3      0.02        30       7      28 ..     605     630 ..     602     652 .. 0.73
   2 !   17.1   0.2     3e-06    0.0045       6      31 ..     667     692 ..     662     706 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.02
                           Fer4_10   7 dtCirCgkCvk........aCPadltsvga 28 
                                       + C +C+ C+         +CP++     a
  gi|344210215|ref|YP_004786391.1| 605 ELCHGCAGCTVhqettggvMCPTYR----A 630
                                       67********9999999988**943....2 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 3e-06
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvgakge 31 
                                        d Ci+C+ C+k CP+ +++ + k+e
  gi|344210215|ref|YP_004786391.1| 667 LDLCIGCKGCKKDCPSGVDMAKLKAE 692
                                       689*************5543333333 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.046        69      33      43 ..     596     614 ..     563     618 .. 0.70
   2 !   14.8   0.2   1.6e-05     0.025       2      24 ..     670     692 ..     624     706 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.046
                            Fer4_9  33 e........eaCigCgaCv 43 
                                       +        e C+gC  C+
  gi|344210215|ref|YP_004786391.1| 596 NengfqgmvELCHGCAGCT 614
                                       04556666788*******8 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.6e-05
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaer 24 
                                       C+gC+ C + Cp+gv + + +++
  gi|344210215|ref|YP_004786391.1| 670 CIGCKGCKKDCPSGVDMAKLKAE 692
                                       77777777777776666666555 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 ?   11.6   0.0   8.6e-05      0.13     246     278 ..     531     565 ..     489     567 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.6e-05
                                       SHHHH.HHHHGHH.HHHHHHHHHHH-TT--B-GGG CS
                      Cytokin-bind 246 sqeeW.kkhfGak.WerfverKakyDPkaiLspGq 278
                                       ++++W +k +G++ We+f + K+++DP   L pG+
  gi|344210215|ref|YP_004786391.1| 531 ARTQWnRKLYGDDlWETFRDLKTAFDPDWRLNPGN 565
                                       6789*667799555**************9999995 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   2.0       1.7   2.5e+03      32      45 ..     601     614 ..     565     628 .. 0.55
   2 ?    8.9   7.7    0.0015       2.3       2      52 .]     607     684 ..     606     684 .. 0.53

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.7
                            Fer4_7  32 eidpekClgCgaCv 45 
                                       ++  e C gC  C 
  gi|344210215|ref|YP_004786391.1| 601 QGMVELCHGCAGCT 614
                                       44455677777765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0015
                            Fer4_7   2 CigCgaCv........aaCpvkaieldeeenekgtekv...................eidpekClgCgaCvavCPtg 51 
                                       C gC  C+        ++Cp++    +e ++ +g++ +                   + + + C+gC+ C + CP+g
  gi|344210215|ref|YP_004786391.1| 607 CHGCAGCTvhqettggVMCPTYRAAEEEITSTRGRANMlrsamdgdlpedptdeefvTEVLDLCIGCKGCKKDCPSG 683
                                       77777776333333334566555444443344433222222233333333333333388899*************99 PP

                            Fer4_7  52 a 52 
                                       +
  gi|344210215|ref|YP_004786391.1| 684 V 684
                                       6 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.5      0.26   3.9e+02      29      48 ..     595     614 ..     589     626 .. 0.79
   2 ?   11.2   0.5   0.00021      0.32      36      52 ..     665     681 ..     656     701 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.26
                           Fer4_21  29 daktvlkvvedeCvGCnlCs 48 
                                       d+++ ++ + + C GC+ C+
  gi|344210215|ref|YP_004786391.1| 595 DNENGFQGMVELCHGCAGCT 614
                                       55666667778999999996 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00021
                           Fer4_21  36 vvedeCvGCnlCssvCP 52 
                                        v d C+GC+ C + CP
  gi|344210215|ref|YP_004786391.1| 665 EVLDLCIGCKGCKKDCP 681
                                       45677777777777777 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   1.6      0.68     1e+03       6      14 ..     605     613 ..     603     615 .. 0.86
   2 ?   11.5   3.4   0.00014       0.2       5      21 ..     667     683 ..     663     684 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.68
                                       TTSSS-THH CS
                              Fer4   6 ekCigCGaC 14 
                                       e+C gC  C
  gi|344210215|ref|YP_004786391.1| 605 ELCHGCAGC 613
                                       89****988 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00014
                                       TTTSSS-THHHHHSTTT CS
                              Fer4   5 eekCigCGaCvevCPvg 21 
                                        ++CigC+ C + CP g
  gi|344210215|ref|YP_004786391.1| 667 LDLCIGCKGCKKDCPSG 683
                                       599************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 ?    0.4   1.3      0.55   8.2e+02       7      17 ..     605     615 ..     604     628 .. 0.86
   2 ?   10.3   2.2    0.0004       0.6       7      22 ..     668     683 ..     663     686 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.55
                            Fer4_6   7 dkCigCgdCvr 17 
                                       ++C gC  C++
  gi|344210215|ref|YP_004786391.1| 605 ELCHGCAGCTV 615
                                       69****99976 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0004
                            Fer4_6   7 dkCigCgdCvrvCPeg 22 
                                       d+CigC  C + CP g
  gi|344210215|ref|YP_004786391.1| 668 DLCIGCKGCKKDCPSG 683
                                       89************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1014 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); 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: 0.80u 0.34s 00:00:01.14 Elapsed: 00:00:00.52
# Mc/sec: 5879.24
//
Query:       gi|344210216|ref|YP_004786392.1|  [L=592]
Description: L-lactate permease [Haloarcula hispanica ATCC 33960]
Scores for 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-102  342.2  42.9    1.6e-53  182.3  22.7    2.1  2  Lactate_perm  L-lactate permease


Domain annotation for each model (and alignments):
>> Lactate_perm  L-lactate permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.3  22.7   8.8e-58   1.6e-53       4     263 ..       8     296 ..       6     304 .. 0.93
   2 !  165.7  12.2   9.1e-53   1.6e-48     262     521 ..     329     582 ..     322     583 .. 0.95

  Alignments for each domain:
  == domain 1  score: 182.3 bits;  conditional E-value: 8.8e-58
                      Lactate_perm   4 lvalvPIlllllalavlklkgykaallslavsviiallvykmpvekvlaavlkgalsgllpialviiaavflyklsv 80 
                                       l+al+P+  + ++++ l   +   +++ +av+ i a   ++m+++ ++aa + gal+ +  i++++++a++l +  +
  gi|344210216|ref|YP_004786392.1|   8 LLALLPLATIAVLMVGLYQPATRTMPIAWAVAAIAAFVGWQMSPTLIAAASIRGALT-ATRILVIVFGAILLLYTLK 83 
                                       89******************************************************9.899**************** PP

                      Lactate_perm  81 ksgafeiirksilsispdrriqvlligfafgaflEGaaGfGtpvAIsaalLvglGfkPlyaaglcLIantapvafGa 157
                                       +sgafe+i    +sis+drr+qv+l+ f++g+f+EGaaGfGtp+AI+++lLvglGf+Pl a  ++L  n  +++fGa
  gi|344210216|ref|YP_004786392.1|  84 QSGAFEVINAGFSSISDDRRVQVILLVFLMGSFIEGAAGFGTPAAIVGPLLVGLGFPPLAAVVVALTGNILAITFGA 160
                                       ***************************************************************************** PP

                      Lactate_perm 158 vGiPitagagatkls.....................aleisslvgiilvlislliplllvilldgv....kdik... 206
                                       vG+P + g+  +                        + +i+   ++i+ ++ + ip++ v+++ ++    + ik   
  gi|344210216|ref|YP_004786392.1| 161 VGTPLIIGLRDVVFAegtgasqqvlqqggfesvgayVAQIGVWAAVIHAIVGIAIPFIGVAMMTRFfgeeRSIKpal 237
                                       ****99988877777799999**************9999*******************9999987423333444333 PP

                      Lactate_perm 207 etfpavlvsglsfaiaqflisnvlGpelpsilgalvslvilalflka..fqpkeifrfa 263
                                       e++p+ l +  sfai+++ ++ +lGp +p++lga+v+l++++ +l+a  f p   ++f 
  gi|344210216|ref|YP_004786392.1| 238 EVLPLCLFAWASFAIPYVATAYFLGPTFPALLGAMVGLLVVTTTLRAgyFLPDDEWDFG 296
                                       78899999*************************************98878888888876 PP

  == domain 2  score: 165.7 bits;  conditional E-value: 9.1e-53
                      Lactate_perm 262 fagkeeskekselkaakilkAlsPfvllvavivltsipllkalfeeggllatkllsleleelsklilkikpiveeat 338
                                        +g +++ e+s+ + ++   A+ P++l+ a +v+t+  ++  ++e   +l+t+            +l  ++i++   
  gi|344210216|ref|YP_004786392.1| 329 ADGGTATFEESHSQDMSLGMAWLPYLLVAALLVVTR--VVSPIQE---FLSTN-----------GVLLWSNILG--- 386
                                       5666778888888999********************..8888888...88777...........6899999*99... PP

                      Lactate_perm 339 alevvfkfkllsspgtiillaavlsiavlklsskdalkvlketlkelklpilaiilvlalanlmnvsG......... 406
                                        ++ +  ++l++ pg +++l+av+++a+  + +   +++  e+l++++++++a+ +++a + +m+ +G         
  gi|344210216|ref|YP_004786392.1| 387 -TPFSEGVELFYLPGSLFVLVAVITYALHGMDTDGIKASWSEALRNIAPAVVALWFAVATVMIMQRTGsavvleaap 462
                                       .77799*********************************************************************** PP

                      Lactate_perm 407 ....lsktlalalae.tGsaftlfspllGalGvfltGSdtvsNllFgslQletaeqiglsevlllaantvGgvvgkm 478
                                           ++  l+   a+ tG++f++fs ++Ga G+f++GS+tvs +lFg +Q+++a+qig+++++++aa++vGg++g++
  gi|344210216|ref|YP_004786392.1| 463 insgMLGLLSEITANgTGQMFPFFSGFIGAFGAFIAGSNTVSDILFGLFQFQAAQQIGAPTQIVVAAQAVGGAIGNL 539
                                       ***************************************************************************** PP

                      Lactate_perm 479 ispqsiaiacaavglvgkEsdllrktviysliyliivgvvall 521
                                       i+++++++a ++vgl+g E+ ++r  +i+ l+y + +g+++l+
  gi|344210216|ref|YP_004786392.1| 540 IAIHNVVAALTVVGLIGEEGRVIRLELIPVLYYGVFTGILTLI 582
                                       ****************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 3594.29
//
Query:       gi|344210217|ref|YP_004786393.1|  [L=259]
Description: trehalose utilization protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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-34  119.1   0.3    3.5e-34  118.9   0.3    1.1  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 !  118.9   0.3   1.9e-38   3.5e-34       1     210 []      16     231 ..      16     231 .. 0.82

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 1.9e-38
                                       EEEEEE-..-.SHHHH-...HHHHHH-............HHHT-EE.EEETTS.G...--HHHHHT-SEEEEE-G.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxx.xxxxxxxx...xxxxxxxxxxxxxxxxx.x RF
                              ThuA   1 rVLvfsgtagerhdsieaaieaieklg............kengfev.datedaav...fteenLaqydvvvflst.e 60 
                                       rV+v+++   ++h++++   ea+++l+            +e+gf+  +at+++ +   +te++La++dv+ ++++  
  gi|344210217|ref|YP_004786393.1|  16 RVTVWNE---YVHEQEH---EAVADLYpdgihgtiasalEERGFDTeTATLQE-PehgLTEDVLAETDVLTWWGHaA 85 
                                       89*****...69**999...88999999999*******99999*996666644.3368****************534 PP

                                       .GS-HHHHHH.HHHHHHTT-EEEEEGGGGS.....HHHH.HH-S....EEEEET............TSGGGTT--.S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThuA  61 gevldaaqeaalqryveaGgGfvglhsAadaeerskwfsgLiGa....rfvghppvqeatvkvedrshpateglpee 133
                                        + +d+++ + ++++v +G+G+++lhs+      sk f++L+G+    +++++   ++ ++ v+++ hp++ g++e 
  gi|344210217|ref|YP_004786393.1|  86 HDQVDDEVVSRVKERVLDGMGLIVLHSGHY----SKIFRELMGTtcslKWREA--AETERLWVVEPGHPIADGVDEY 156
                                       46666666666*****************66....598888****776555544..3567777999*********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+   +++++ ++   + g+ +    c +  g+Gr+Fy+++Gh+++ +y++++++++l++
  gi|344210217|ref|YP_004786393.1| 157 IELPeTEMYGerFdIPAPDT--LVFNSWFE---G-GEVFRSGCCYRR-GAGRIFYFRPGHETYpIYHNEAIQQVLAN 226
                                       **********7446666666..99999444...3.444444455545.99*************************** PP

                                       HHHHC CS
                                       xxxxx RF
                              ThuA 206 glkWa 210
                                       + +Wa
  gi|344210217|ref|YP_004786393.1| 227 ACEWA 231
                                       ****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1464.77
//
Query:       gi|344210218|ref|YP_004786394.1|  [L=189]
Description: hypothetical protein HAH_5277 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       325  (0.0181271); 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:                         0  (0); expected 0.2 (1e-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 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1225.85
//
Query:       gi|344210219|ref|YP_004786395.1|  [L=205]
Description: putative pyridine nucleotide-disulfide oxidoreductase [Haloarcula hispanica ATCC 33960]
Scores for 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   67.6   9.8    3.1e-12   46.3   0.5    2.1  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    2.5e-12   46.7   0.3    9.4e-07   28.4   0.0    2.3  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    6.5e-10   38.3   0.0    8.6e-05   21.4   0.0    2.3  2  HI0933_like    HI0933-like protein
    5.1e-09   35.8   1.0    1.4e-05   24.6   0.0    2.1  2  FAD_binding_3  FAD binding domain
    2.5e-08   33.9   0.6     0.0012   18.6   0.0    2.2  2  DAO            FAD dependent oxidoreductase
    3.1e-07   29.8   1.1    2.9e-06   26.6   0.1    2.1  2  FAD_binding_2  FAD binding domain
    3.3e-05   24.0   0.0    7.7e-05   22.8   0.0    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    5.7e-05   22.4   0.7    0.00031   20.0   0.1    2.1  2  GIDA           Glucose inhibited division protein A
    0.00014   21.4   0.0    0.00014   21.4   0.0    2.1  2  FAD_oxidored   FAD dependent oxidoreductase
    0.00046   19.5   0.0     0.0008   18.7   0.0    1.4  1  Thi4           Thi4 family
     0.0011   19.0   0.2       0.87    9.6   0.1    2.4  2  NAD_binding_9  FAD-NAD(P)-binding
     0.0023   17.3   0.2     0.0034   16.7   0.2    1.5  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
     0.0053   15.8   0.3      0.031   13.3   0.1    1.9  2  Lycopene_cycl  Lycopene cyclase protein
  ------ inclusion threshold ------
      0.012   16.1   0.1      0.057   14.0   0.0    2.0  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.052   12.7   0.1        5.3    6.1   0.0    2.1  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
       0.11   12.9   0.1       0.24   11.9   0.1    1.7  1  NAD_binding_7  Putative 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 !   46.3   0.5   2.8e-15   3.1e-12       2     110 ..      16     121 ..      15     124 .. 0.81
   2 !   32.2   3.1   5.5e-11   6.2e-08     184     293 ..      68     169 ..      60     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 2.8e-15
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH...HHHHCHHHHCCCCHCCTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias...evvkklnqgielllgeev 75 
                                       dv+v+GgGpAGl+aal+ +++g+++t+++ +gt+++   l  +  +g+++    ++    +v++++  +++  g+ev
  gi|344210219|ref|YP_004786395.1|  16 DVLVVGGGPAGLSAALFTQKNGLETTVFDTDGTWMHKAHLFNYLGVGSQDGSAFMEtarTQVDSFG--VDRKQGTEV 90 
                                       8****************************9999999988887766666666655557777777776..556666679 PP

                                       EEEEESCEEEEETEEECTCEEEEEESEEEE---EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  76 vkidpgkkkvklekkkegdeekiaydklvlAtGss 110
                                       +++ +  + +++ ++  +   ++++ +l+lAtG++
  gi|344210219|ref|YP_004786395.1|  91 TDVGQTDAGFEVATE--D--DTYEASYLILATGAN 121
                                       999988888888543..3..49***********96 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 5.5e-11
                                       HHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 184 elsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklglelderggivv 260
                                       ++ ++++ ++   Gv+ k gt+v+++ + +   ev +ed + ++a+++++a+G   +++l+ e+lg+ ++  + + v
  gi|344210219|ref|YP_004786395.1|  68 AFMETARTQVDSFGVDRKQGTEVTDVGQTDAGFEVATEDDT-YEASYLILATGA--NRDLA-ETLGCDMTAEDVVDV 140
                                       5566777777888*************999998887777766.8*********96..55588.*************** PP

                                       -TTSBESSTTEEE-GGGCTECCSS--HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 261 deflrtnvpgiyaiGDvaggkggpelaqaAvqq 293
                                       d +++t+v++ ya G ++    ++e +qa +++
  gi|344210219|ref|YP_004786395.1| 141 DVTMETSVDDAYATGGMV----RVEEWQAVISA 169
                                       ****************99....66666665554 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   0.0   3.8e-06    0.0043       1      26 [.      18      42 ..      18      48 .. 0.87
   2 !   28.4   0.0   8.4e-10   9.4e-07      84     134 ..      70     120 ..      56     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.8e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledyli 26
                                      +++G+GPaGl+aa+  +k+gle+ ++
  gi|344210219|ref|YP_004786395.1| 18 LVVGGGPAGLSAALFTQKNGLET-TV 42
                                      69*******************64.55 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 8.4e-10
                       Pyr_redox_3  84 leYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGe 134
                                       +e  r+ ++sf ++ k+ +eV++v ++d gfev t+ +tyeA+++i+AtG 
  gi|344210219|ref|YP_004786395.1|  70 METARTQVDSFGVDRKQGTEVTDVGQTDAGFEVATEDDTYEASYLILATGA 120
                                       566778899999999***********************************6 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   7.7e-08   8.6e-05       2      38 ..      16      52 ..      15      56 .. 0.90
   2 !   14.5   0.0   9.8e-06     0.011     112     164 ..      70     120 ..      62     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7.7e-08
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                      dv+v+GgG+AGl aA+  +k+g ++++++   +  +K
  gi|344210219|ref|YP_004786395.1| 16 DVLVVGGGPAGLSAALFTQKNGLETTVFDTDGTWMHK 52
                                      89***************************98776665 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 9.8e-06
                                       HHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 112 vdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       +++  +++++ gv+ +  tev++v +++ g f+v+t +++++ea++l+lAtG 
  gi|344210219|ref|YP_004786395.1|  70 METARTQVDSFGVDRKQGTEVTDVGQTDAG-FEVAT-EDDTYEASYLILATGA 120
                                       56667889999*************998888.*****.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 !   24.6   0.0   1.2e-08   1.4e-05       2      33 ..      15      46 ..      14      57 .. 0.90
   2 !   10.0   0.6   0.00033      0.37     116     199 ..      78     151 ..      68     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.2e-08
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      tdVl+VG+GpaGl++al+ ++ G ++++ +  
  gi|344210219|ref|YP_004786395.1| 15 TDVLVVGGGPAGLSAALFTQKNGLETTVFDTD 46
                                      89************************998865 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00033
                                       HHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEE CS
                     FAD_binding_3 116 eerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgiefegeetvyeagvldvlf 192
                                        + g++ +++tev+ + q++ g +         e+ t +a Yl+ a G++   ++tlg ++++e+ v     +dv++
  gi|344210219|ref|YP_004786395.1|  78 DSFGVDRKQGTEVTDVGQTDAGFEVAT------EDDTYEASYLILATGANRDLAETLGCDMTAEDVV----DVDVTM 144
                                       467788888888887777777744433......444889**********************999955....666666 PP

                                       EC-SCCC CS
                     FAD_binding_3 193 dadlsdi 199
                                       ++ ++d 
  gi|344210219|ref|YP_004786395.1| 145 ETSVDDA 151
                                       6666554 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     1e-06    0.0012       1      29 [.      16      46 ..      16      53 .. 0.93
   2 !   14.1   0.1   2.4e-05     0.027     141     213 ..      62     128 ..      46     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                      dv+++GGG +Gls+A++ ++ g  +t+++ +
  gi|344210219|ref|YP_004786395.1| 16 DVLVVGGGPAGLSAALFTQKNGleTTVFDTD 46
                                      8*****************9999*****9976 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.4e-05
                                       EEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTTCTT CS
                               DAO 141 gqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdllgllkel 213
                                       g  d  +++   + ++ + Gv+  +gtevt++ ++d  + +v  +t+  +  +a ++++a+Ga  dl+   ++l
  gi|344210219|ref|YP_004786395.1|  62 GSQDGSAFMETARTQVDSFGVDRKQGTEVTDVGQTD-AGFEV--ATEdDT-YEASYLILATGANRDLA---ETL 128
                                       5557788899999999999************96654.45777..554343.35688*******97776...444 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   2.6e-09   2.9e-06       1      30 [.      16      45 ..      16      55 .. 0.93
   2 ?    2.6   0.1     0.051        57     138     223 ..      64     141 ..      45     185 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.6e-09
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvek 30
                                      Dv+V+G+G AGL+AAl  +++Gl+++v + 
  gi|344210219|ref|YP_004786395.1| 16 DVLVVGGGPAGLSAALFTQKNGLETTVFDT 45
                                      9************************99875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.051
                                       .HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG.......... CS
                     FAD_binding_2 138 vtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaa 214
                                        +g a +++  +++++ gvd    te++++ +      G +v+     ++ +++a  ++latg+   +l+++l   +
  gi|344210219|ref|YP_004786395.1|  64 QDGSAFMETARTQVDSFGVDRKQGTEVTDVGQ---TDAGFEVA----TEDDTYEASYLILATGANR-DLAETLGCDM 132
                                       47888888888999888999999999999844...44566666....6677889999999999888.5666655555 PP

                                       GSSSBSSGT CS
                     FAD_binding_2 215 aeaettnap 223
                                        +++++ + 
  gi|344210219|ref|YP_004786395.1| 133 TAEDVVDVD 141
                                       555555444 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 !   22.8   0.0   6.9e-08   7.7e-05       1      28 [.      19      46 ..      19      57 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 6.9e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      +vG+G +Gl+aA + +k+g++ +++++ 
  gi|344210219|ref|YP_004786395.1| 19 VVGGGPAGLSAALFTQKNGLETTVFDTD 46
                                      8*************************85 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   2.7e-07   0.00031       1      29 [.      16      50 ..      16      81 .. 0.83
   2 ?    0.8   0.0      0.18   2.1e+02     132     150 ..     102     120 ..      63     135 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.7e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE......E CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi......t 29
                                      dv V+GgG AG+ AAl + + G++++ +       
  gi|344210219|ref|YP_004786395.1| 16 DVLVVGGGPAGLSAALFTQKNGLETTVFdtdgtwM 50
                                      79************************996666552 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.18
                                       EETTS-EEEECEEEE--TT CS
                              GIDA 132 vtedgetikakavviatGt 150
                                       v +++ t++a+  ++atG+
  gi|344210219|ref|YP_004786395.1| 102 VATEDDTYEASYLILATGA 120
                                       44566789999*******8 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.3e-07   0.00014       1      31 [.      16      46 ..      16      49 .. 0.92
   2 ?   -1.0   1.7      0.78   8.8e+02     131     158 ..     106     134 ..      63     196 .. 0.56

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.3e-07
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                      Dv+VvGGgpaG+ AA+   ++G ++ + +++
  gi|344210219|ref|YP_004786395.1| 16 DVLVVGGGPAGLSAALFTQKNGLETTVFDTD 46
                                      9************************988765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.78
                      FAD_oxidored 131 rktirAkvfiDATgdG.dlaalaGvpyrv 158
                                       + t++A++ i ATg   dla++ G+ ++ 
  gi|344210219|ref|YP_004786395.1| 106 DDTYEASYLILATGANrDLAETLGCDMTA 134
                                       55666666666665322555555554444 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   7.1e-07    0.0008      18      49 ..      15      45 ..       8      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.1e-07
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailer 49
                                      +Dv++vG+G++GL+aa    k+ +l++++++ 
  gi|344210219|ref|YP_004786395.1| 15 TDVLVVGGGPAGLSAALFTQKN-GLETTVFDT 45
                                      7****************99999.999999875 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 !    7.3   0.0    0.0039       4.3       2      37 ..      19      49 ..      18      56 .. 0.77
   2 !    9.6   0.1   0.00078      0.87     113     155 ..      78     120 ..      66     121 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0039
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsepg 37
                                      +vG+Gp+Gl+++  L  +   k+ le t+fd ++++
  gi|344210219|ref|YP_004786395.1| 19 VVGGGPAGLSAA--LFTQ---KNGLETTVFDTDGTW 49
                                      8********987..4555...467888888887776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00078
                     NAD_binding_9 113 egvtvevhra.evvdleeradgqavlladgaslaadaVvLAlGh 155
                                       +++ v+  ++ ev+d+ ++++g++v  +++++++a +++LA+G 
  gi|344210219|ref|YP_004786395.1|  78 DSFGVDRKQGtEVTDVGQTDAGFEV-ATEDDTYEASYLILATGA 120
                                       445666665449***********99.5566799*********95 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 !   16.7   0.2   3.1e-06    0.0034      29      66 ..      15      52 ..       1     107 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.1e-06
                                      -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHH CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleq 66
                                        vlv+GgG aGl+A+   ++ g ++tv+D++ + +++
  gi|344210219|ref|YP_004786395.1| 15 TDVLVVGGGPAGLSAALFTQKNGLETTVFDTDGTWMHK 52
                                      48****************************98776655 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   2.8e-05     0.031       1      32 [.      16      45 ..      16      56 .. 0.85
   2 ?    0.3   0.0      0.25   2.8e+02     131     173 ..      72     115 ..      61     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.8e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                      Dv+v+G+GpAgls A     +k gl+ ++ ++
  gi|344210219|ref|YP_004786395.1| 16 DVLVVGGGPAGLSAALFT--QKNGLETTVFDT 45
                                      9************99888..899988877765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.25
                     Lycopene_cycl 131 rarlvvdarglaslk.karrlglQtfyGvevevdnppfdldkmv 173
                                        ar+ vd+ g+ +++  + +   Qt  G ev ++ + ++ +  +
  gi|344210219|ref|YP_004786395.1|  72 TARTQVDSFGVDRKQgTEVTDVGQTDAGFEVATEDDTYEASYLI 115
                                       58899999997666654555667************999987665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.1e-05     0.057       2      32 ..      17      47 ..      16      56 .. 0.90
   2 ?   -1.2   0.0       2.8   3.2e+03      54      74 ..      81     101 ..      61     107 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.1e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversd 32
                                      v+vvGgG  gl +A + ++ g ++tv++   
  gi|344210219|ref|YP_004786395.1| 17 VLVVGGGPAGLSAALFTQKNGLETTVFDTDG 47
                                      89************************98765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.8
                                       TEEEECSEEEEEEEEETTSEE CS
                         Pyr_redox  54 gievllntkveeiegsedgve 74 
                                       g++   +t+v+ + +++ g+e
  gi|344210219|ref|YP_004786395.1|  81 GVDRKQGTEVTDVGQTDAGFE 101
                                       777777777777777776643 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0047       5.3       3      41 ..      15      49 ..      13      58 .. 0.82
   2 ?    5.0   0.0      0.01        11     114     185 ..      85     147 ..      67     190 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0047
                       K_oxygenase  3 lDligiGiGpsnLsLailleevkkelkalflerqpefaW 41
                                       D+  +G Gp+ Ls a+ ++++   l++ +++   +  W
  gi|344210219|ref|YP_004786395.1| 15 TDVLVVGGGPAGLSAALFTQKNG--LETTVFD--TDGTW 49
                                      799***********999998888..9999999..45555 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.01
                       K_oxygenase 114 rfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerk 185
                                       + g+ev++v + ++     ++v +     e +++ea  l+l++G ++ + e+l    + e+vv  + ++e+ 
  gi|344210219|ref|YP_004786395.1|  85 KQGTEVTDVGQTDA----GFEVAT-----EDDTYEASYLILATGANRDLAETLGCDMTAEDVVDVDVTMETS 147
                                       45666777666665....488887.....6789************999998887666667777666555544 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 ?   11.9   0.1   0.00021      0.24       9      58 ..      16     107 ..      13     202 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                     NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapevkeele................................elvklaee 53 
                                        vlvvGgG+ +++ +    ++g + tv + + +  ++                                +       
  gi|344210219|ref|YP_004786395.1|  16 DVLVVGGGPAGLSAALFTQKNGLETTVFDTDGTWMHKahlfnylgvgsqdgsafmetartqvdsfgvdrK------- 85 
                                       69*************************9999755555555666666666555555444433333333330....... PP

                     NAD_binding_7  54 e.................lekd 58 
                                       +                  e+d
  gi|344210219|ref|YP_004786395.1|  86 QgtevtdvgqtdagfevaTEDD 107
                                       1333333444444444332333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); 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 0.35s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1196.13
//
Query:       gi|344210220|ref|YP_004786396.1|  [L=346]
Description: alcohol dehydrogenase [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      6e-27   93.7   0.9      6e-27   93.7   0.9    1.8  2  ADH_N         Alcohol dehydrogenase GroES-like domain
    2.7e-23   82.4   1.3      5e-23   81.5   1.3    1.4  1  ADH_zinc_N    Zinc-binding dehydrogenase
    2.1e-07   30.6   0.4    3.2e-07   30.0   0.4    1.3  1  Glu_dehyd_C   Glucose dehydrogenase C-terminus
    3.1e-05   23.8   0.1    3.1e-05   23.8   0.1    1.8  2  ADH_N_assoc   Alcohol dehydrogenase GroES-associated
    0.00031   21.8   0.1    0.00066   20.7   0.1    1.5  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.047   13.0   2.0      0.072   12.4   2.0    1.2  1  AlaDh_PNT_C   Alanine dehydrogenase/PNT, C-terminal 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 !   93.7   0.9     2e-30     6e-27       2     103 ..      26     125 ..      25     132 .. 0.96
   2 ?   -3.7   0.1       3.8   1.1e+04      66      89 ..     242     265 ..     235     270 .. 0.57

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 2e-30
                                       TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-G CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegee 78 
                                       ++++++v+ +++CgsDl++++g  ++ ++ +  +GHE +G+veevg++v++++ GdrV+++++iscg+C+ C++g +
  gi|344210220|ref|YP_004786396.1|  26 TDAIVRVTHTAVCGSDLWFYRG--QSDREEGSRVGHEPMGIVEEVGDDVRSVEPGDRVFAPFVISCGRCEFCRKGLH 100
                                       6899*****************9..7999************************************************* PP

                                       GG-TTBEETTTSS-SSSBSEEEECG CS
                             ADH_N  79 nlCeeakllgvsldGgfaeyvvvpe 103
                                       + C +++ +g +  Gg+ eyv + e
  gi|344210220|ref|YP_004786396.1| 101 TSCVNGDSWGGDNGGGQGEYVRATE 125
                                       *********************9876 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.8
                                       E-SSSHHHHTT-GGG-TTBEETTT CS
                             ADH_N  66 scgeCaaCkegeenlCeeakllgv 89 
                                       +c  +a+  e + ++C+ ++++g+
  gi|344210220|ref|YP_004786396.1| 242 ECVGAASAMETAIDVCRPGGTVGY 265
                                       455555555555555655555554 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   1.3   1.7e-26     5e-23       1     111 [.     179     291 ..     179     307 .. 0.92

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 1.7e-26
                                       HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykea.dlverikeltggegvdvvfecvGsgatleaa 75 
                                       +vGl++v +A+ lGa ++ia+ + e++lela+++Ga+e+i + +  d v++  +lt+g g++ v+ecvG+ +++e+a
  gi|344210220|ref|YP_004786396.1| 179 AVGLCGVLAARRLGAeRIIAMGHHEDRLELAESFGATETIAA-RGqDAVDAADDLTNG-GANHVLECVGAASAMETA 253
                                       69****************************************.555**********87.****************** PP

                                       HHCEEEEEEEEECSCTSSEEE..EEHHHHHHTT-EEEE CS
                        ADH_zinc_N  76 lkllkpgGrlvvvGggkgeee..fdlrnlllkeksilG 111
                                       +++++pgG++ +vG+++g ++  +d++ l+  ++ + G
  gi|344210220|ref|YP_004786396.1| 254 IDVCRPGGTVGYVGVPHGVDDsgLDVFSLFGDNIALNG 291
                                       ***************88877788999999988887776 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 !   30.0   0.4   1.1e-10   3.2e-07      30     211 ..     168     345 ..     155     346 .] 0.76

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.1e-10
                       Glu_dehyd_C  30 epesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYv..dsretpvdeipeas.eemdl 103
                                       e +s +v+G G++GL    +l+a++ g er+  +g ++    +++l e+ Gat       ++ vd   + +    + 
  gi|344210220|ref|YP_004786396.1| 168 EGDSCIVVGDGAVGLCG--VLAARRLGAERIIAMGHHE---DRLELAESFGATETiaARGQDAVDAADDLTnGGANH 239
                                       66899**********99..77777899****9999654...47999******864114446789988876515799* PP

                       Glu_dehyd_C 104 vvEaTGsakhafeaiealapnGvaaLlGvpeds.evevdggelhrelvleNkalvGsvNanrrhfeaavdtLaalpe 179
                                       v+E+ G+a ++  ai+  +p G +  +Gvp++  +  +d+ +l      +N al G v   +r+++   + La + +
  gi|344210220|ref|YP_004786396.1| 240 VLECVGAASAMETAIDVCRPGGTVGYVGVPHGVdDSGLDVFSLFG----DNIALNGGVA-PVRAYA--DELLADVLQ 309
                                       ******************************997456666666555....5999999995.555553..345555555 PP

                       Glu_dehyd_C 180 sl..ldelvtkvvdldeleeAfe..dddetiKtvve 211
                                            + + tk vdld + e ++  d+ e iK+ v+
  gi|344210220|ref|YP_004786396.1| 310 GTldPSPIFTKTVDLDGVPEGYRamDEREAIKVLVK 345
                                       441245789999999999999973355578999887 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 !   23.8   0.1     1e-08   3.1e-05       1      23 []       1      23 [.       1      23 [. 0.98
   2 ?   -3.2   0.2         3   8.8e+03      14      19 ..      65      70 ..      65      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1e-08
                       ADH_N_assoc  1 MKAVTyqGpkdVrVeeVPDPkIe 23
                                      M+A  y Gp +++VeeVP P+Ie
  gi|344210220|ref|YP_004786396.1|  1 MRAAIYRGPGEIAVEEVPRPEIE 23
                                      9999******************8 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3
                       ADH_N_assoc 14 VeeVPD 19
                                      VeeV D
  gi|344210220|ref|YP_004786396.1| 65 VEEVGD 70
                                      9***87 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 !   20.7   0.1   2.2e-07   0.00066       2     124 ..     213     336 ..     212     340 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.2e-07
                                       T-SEEEETT.STTHH..HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE CS
                      ADH_zinc_N_2   2 GAdevidyr.tedfe..aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvky 75 
                                       GA+e i  r ++++   +++ ++g ++vl++vg ++++e +++v+++gG++  +g p   ++ +   +   g ++ +
  gi|344210220|ref|YP_004786396.1| 213 GATETIAARgQDAVDaaDDLTNGGANHVLECVGAASAMETAIDVCRPGGTVGYVGVPHGVDDSGLDVFSLFGDNIAL 289
                                       99****888555555885555788*********88888*******88799966554333444444444455555555 PP

                                       --GGG...-.-HHHHHHHHHHHHHHH--..--EEEEEEGGGHHHHHHHHHS CS
                      ADH_zinc_N_2  76 eflfsmkasaqadileelaalieeGklr..pvvdrvfpleeaaeAhryles 124
                                       +  +   +  +a   +el+a + +G+l   p  +++ +l+ ++e +r++ +
  gi|344210220|ref|YP_004786396.1| 290 NGGV--APV-RAY-ADELLADVLQGTLDpsPIFTKTVDLDGVPEGYRAMDE 336
                                       5544..344.444.5566666666776532444566666666666666655 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   2.0   2.4e-05     0.072      21      78 ..     161     218 ..     151     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                                       CEETCB---.EEEEESTSHHHHHHHHHHHHTT-E.EEEEESSHHHHHHHHHTTTCECEEH CS
                       AlaDh_PNT_C  21 Ggvpgvepa.kvlviGgGvaGlqAiatakglgak.VtvlDvrparleqleslgakfvevl 78 
                                       +   gv+++   +v+G G +Gl  + +a++lga+ + ++   ++rle  es+ga+  e++
  gi|344210220|ref|YP_004786396.1| 161 AVSAGVSEGdSCIVVGDGAVGLCGVLAARRLGAErIIAMGHHEDRLELAESFGAT--ETI 218
                                       445556565257899*****************964889999**********9998..443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 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:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2178.53
//
Query:       gi|344210221|ref|YP_004786397.1|  [L=403]
Description: ferrichrome-binding protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   67.3   0.0    1.9e-18   66.9   0.0    1.1  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 !   66.9   0.0   1.1e-22   1.9e-18       9     232 ..      87     339 ..      84     345 .. 0.89

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 1.1e-22
                                       HHHHHHTT-GGGEEEB-GGG--GGGGGGT.........TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHHH CS
                      Peripla_BP_2   9 teillalGatdkvvgvdtttsdpldadklee.......aivevgadgeidvEklaalkPDlvilskglgltdedeel 78 
                                       +++ lalG  d v++  + ++++   ++  e       + + + +++ ++ Ekl +l+ D+ ++++ +   +++++ 
  gi|344210221|ref|YP_004786397.1|  87 ADMALALGRGDTVTAMHAPDYYSGLWNQFVErlpgvslDWTGLYSSWKPSKEKLYELDSDIHLADPAW--IAKQDNW 161
                                       677888888887777777777776666666666667777799999999999*****************..9999999 PP

                                       HHHHS-EEE----TTS....................HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT CS
                      Peripla_BP_2  79 lksgiptvivessntg....................eslkeqiralgellgledeaeklvaeidsklaaaksaidse 135
                                       ++++ + ++ + s+++                    + l eq++ ++e++++++++e+l+a +d+    + + ++ e
  gi|344210221|ref|YP_004786397.1| 162 DREDFEEIATNVSPWFgnslsdrhaeppsgwgdyeyYTLWEQFELVAEAFQEQARYEALAAVHDEMRSTIDANLPPE 238
                                       99999999999999999999***************99999************************************* PP

                                       ...-EEEEEEEETTE..EEEE-TTSTTTHHHHT.S--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH..HHHT- CS
                      Peripla_BP_2 136 ..kpkpvlvfggadeggyvvagsnsyigdllda.lgieniaaeskkseyeeisaEqilasdpdvifvsgr..aeadn 207
                                          p++vl+ + + + +y ++ +n+++   +    g++++++ s  + ++ +++E++la+dpdvi+  g   +  + 
  gi|344210221|ref|YP_004786397.1| 239 seRPSAVLLAAADLDEIYAYTLDNPGFLTAHTRpFGARDAFEGS-VETNSVVDFETLLAADPDVILHLGGfePNTSL 314
                                       6555555555555559*********999999999**********.**************************9***** PP

                                       S--HHHHT-SHHHHTSHHHHTT-EE CS
                      Peripla_BP_2 208 ktgleflkenpllaelpAvkngrVy 232
                                        ++ e++k++p+ +e++Av+n r+y
  gi|344210221|ref|YP_004786397.1| 315 PERREAFKSDPVGSEITAVQNDRIY 339
                                       ************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2622.63
//
Query:       gi|344210222|ref|YP_004786398.1|  [L=310]
Description: ferrichrome ABC transporter ATP-binding protein [Haloarcula hispanica ATCC 33960]
Scores for 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-30  104.2   0.0    1.2e-29  103.6   0.0    1.3  1  ABC_tran        ABC transporter
    5.3e-12   46.2   4.0    2.1e-05   24.5   0.3    2.2  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    2.2e-11   43.6   0.0    5.7e-06   25.9   0.0    2.1  2  SMC_N           RecF/RecN/SMC N terminal domain
    1.4e-05   24.7   0.0    2.6e-05   23.8   0.0    1.4  1  AAA_29          P-loop containing region of AAA domain
      6e-05   23.3   1.8    0.00098   19.4   1.8    2.2  1  AAA_22          AAA domain
    0.00017   21.4   0.1    0.00028   20.7   0.1    1.5  1  AAA_30          AAA domain
    0.00021   21.5   0.1      0.001   19.3   0.0    1.9  2  AAA_33          AAA domain
    0.00043   19.2   0.7       0.48    9.2   0.0    2.9  2  ABC_ATPase      Predicted ATPase of the ABC class
    0.00049   20.5   0.4    0.00089   19.7   0.4    1.7  1  AAA_16          AAA ATPase domain
    0.00072   20.1   0.0     0.0013   19.3   0.0    1.3  1  AAA_23          AAA domain
     0.0021   17.8   0.0     0.0035   17.1   0.0    1.3  1  AAA_15          AAA ATPase domain
     0.0032   17.1   0.1     0.0067   16.1   0.1    1.5  1  SRP54           SRP54-type protein, GTPase domain
     0.0043   16.3   0.0     0.0079   15.5   0.0    1.4  1  Zeta_toxin      Zeta toxin
     0.0073   16.2   0.4      0.013   15.4   0.1    1.6  1  RsgA_GTPase     RsgA GTPase
     0.0095   15.9   0.1       0.02   14.8   0.0    1.6  1  NACHT           NACHT domain
  ------ inclusion threshold ------
      0.016   15.2   0.3      0.071   13.2   0.3    2.0  1  MMR_HSR1        50S ribosome-binding GTPase
      0.017   15.6   0.2      0.042   14.3   0.1    2.0  1  AAA             ATPase family associated with various cellula
      0.018   14.4   0.2       0.43    9.9   0.2    2.1  2  TniB            Bacterial TniB protein
      0.022   14.5   0.1        1.6    8.4   0.0    2.1  2  ATP_bind_1      Conserved hypothetical ATP binding protein
      0.025   14.4   0.3       0.52   10.1   0.1    2.4  2  MukB            MukB N-terminal
      0.031   13.9   0.9      0.087   12.4   0.0    2.1  2  AAA_25          AAA domain
      0.035   14.2   0.0      0.087   12.9   0.0    1.6  1  AAA_14          AAA domain
      0.035   13.7   0.5      0.064   12.8   0.1    1.6  2  cobW            CobW/HypB/UreG, nucleotide-binding domain
       0.04   13.6   0.1       0.39   10.4   0.0    2.0  2  AAA_24          AAA domain
      0.051   13.5   0.0      0.078   12.9   0.0    1.4  1  ATPase_2        ATPase domain predominantly from Archaea
      0.054   12.9   0.1       0.28   10.6   0.0    2.0  2  Mg_chelatase    Magnesium chelatase, subunit ChlI
      0.055   13.2   0.1       0.12   12.1   0.1    1.7  1  Cytidylate_kin  Cytidylate kinase
      0.055   13.9   0.0      0.097   13.1   0.0    1.5  1  RNA_helicase    RNA helicase
      0.058   13.3   0.8        1.8    8.5   0.0    2.2  2  NTPase_1        NTPase
      0.065   13.8   0.3       0.23   12.0   0.1    2.0  2  AAA_18          AAA domain
      0.069   13.1   0.1        0.2   11.6   0.0    1.7  1  TsaE            Threonylcarbamoyl adenosine biosynthesis prot
      0.081   13.2   0.1       0.18   12.0   0.1    1.6  1  AAA_28          AAA domain
      0.095   12.6   0.0       0.17   11.8   0.0    1.4  1  APS_kinase      Adenylylsulphate kinase
       0.16   11.5   0.0       0.25   10.8   0.0    1.2  1  AAA_7           P-loop containing dynein motor region
       0.22   10.7   0.6       0.92    8.7   0.6    1.8  1  KAP_NTPase      KAP family P-loop domain
       0.24   11.3   0.4       0.61   10.0   0.0    1.7  2  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 !  103.6   0.0   2.4e-32   1.2e-29       5     136 ..      51     195 ..      47     196 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 2.4e-32
                                       EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                          ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                       s++ ++g ++a+vG+nG+GKStLlk la++l+p++G++lldg+d+++ e++   +++g l+qe++  + ++v++   
  gi|344210222|ref|YP_004786398.1|  51 SITAEPGAVTALVGPNGSGKSTLLKGLANQLEPEAGSVLLDGQDIQTLETKAIARKLGLLSQESTSPNSISVEDLvy 127
                                       78999**********************************************************999999999999** PP

                                       ...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                      e+++ +e+a++  g  +l ++ v     sLSgGqkq   +a++l+++ ++lllDEpt
  gi|344210222|ref|YP_004786398.1| 128 hgryphrgffdsvteEDEAAVERAIDLAGCGHLCEREV----GSLSGGQKQLAWIAMVLAQDTDVLLLDEPT 195
                                       ************99888888************999999....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.3   4.2e-08   2.1e-05       1      20 [.      59      78 ..      59     141 .. 0.86
   2 !   23.4   0.3     9e-08   4.5e-05     232     294 ..     163     223 ..     127     229 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.2e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdald 20
                                      +++l+GpNgsGKS+LL+ l 
  gi|344210222|ref|YP_004786398.1| 59 VTALVGPNGSGKSTLLKGLA 78
                                      69****************94 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 9e-08
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell...kelsrngaQvil 294
                                       + + +lS G+k+l a ++++l+++   ++ll+DEp ++L+ + + +++e++   +++s+  + +++
  gi|344210222|ref|YP_004786398.1| 163 REVGSLSGGQKQL-AWIAMVLAQDT--DVLLLDEPTTFLDLHHQLEVMEIIetlRDESD--ITIVV 223
                                       667899*******.********998..9************9888666666622255554..77766 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 !   15.8   0.1   1.4e-05    0.0072      25      44 ..      58      77 ..      48      84 .. 0.83
   2 !   25.9   0.0   1.2e-08   5.7e-06     110     205 ..      87     232 ..      78     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-05
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                       +ta+vGpNGSGKs ll  +
  gi|344210222|ref|YP_004786398.1| 58 AVTALVGPNGSGKSTLLKGL 77
                                      589************99765 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 1.2e-08
                                       EEEETTEEE-HHHHHHHHHCTT-STT................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                             SMC_N 110 eykingkevtkkevsellesagiske................................................... 135
                                       ++ ++g++++  e + + ++ g+ ++                                                   
  gi|344210222|ref|YP_004786398.1|  87 SVLLDGQDIQTLETKAIARKLGLLSQestspnsisvedlvyhgryphrgffdsvteedeaaveraidlagcghlcer 163
                                       56788888888888888888888777899999999999999999999999999999999999999999999999999 PP

                                       ...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 ...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemleka 205
                                          +LSgG+k+L+ +a+++A    + + + llDe    LD ++  +v e++++ ++++ + ++ + +++ + a
  gi|344210222|ref|YP_004786398.1| 164 evgSLSGGQKQLAWIAMVLA----QDTDVLLLDEPTTFLDLHHQLEVMEIIETLRDESDITIVVVLHDIEQAA 232
                                       999***************98....567899**********************999998876655544443333 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 !   23.8   0.0   5.3e-08   2.6e-05      12      48 ..      47      83 ..      43      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.3e-08
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiqalLvp 48
                                      +dg++i+ ++  +t l+Gp+GsGKSTll  ++  L p
  gi|344210222|ref|YP_004786398.1| 47 IDGESITAEPGAVTALVGPNGSGKSTLLKGLANQLEP 83
                                      578889999877***************9887776666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.8     2e-06   0.00098       6     128 ..      58     224 ..      54     233 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2e-06
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl.lrellralglelka........... 70 
                                        +++++G+ G+GK+tll+ l++ql         +pe  +v l ++   ++l  ++++r+lgl   +           
  gi|344210222|ref|YP_004786398.1|  58 AVTALVGPNGSGKSTLLKGLANQL---------EPEAGSVLLDGQD-IQTLeTKAIARKLGLLSQEstspnsisved 124
                                       5789********************.........6666666666666.333334444444444333344446777777 PP

                            AAA_22  71 .......................................erlsseellealeqalrarav.....ielliiDEaqh. 102
                                                                              e +s++   ++l+  +    +     + +l++DE    
  gi|344210222|ref|YP_004786398.1| 125 lvyhgryphrgffdsvteedeaaveraidlagcghlcerEVGSLSGGQKQLAWIA----MvlaqdTDVLLLDEPTTf 197
                                       7777777777777777777777777555555555554442233333333333222....133335678888887775 PP

                            AAA_22 103 lr...seealeeLrsllnlsrkgvqliLv 128
                                       l+   + e++e + +l +  ++++++++v
  gi|344210222|ref|YP_004786398.1| 198 LDlhhQLEVMEIIETLRD--ESDITIVVV 224
                                       657544666666666677..666766665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   5.6e-07   0.00028      12      63 ..      51     108 ..      49     232 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.6e-07
                            AAA_30  12 alltsgdrvavltGpAGtGKttalkalreaweaa.g.....grviglAptgkaAkvLa 63 
                                       ++++++  v++l+Gp G+GK+t+lk+l++ +e + g     g+ i    t++ A++L+
  gi|344210222|ref|YP_004786398.1|  51 SITAEPGAVTALVGPNGSGKSTLLKGLANQLEPEaGsvlldGQDIQTLETKAIARKLG 108
                                       67888999********************999999445555533333445555566655 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     2e-06     0.001       1      32 [.      59      94 ..      59     148 .. 0.78
   2 ?   -0.2   0.0       2.1     1e+03      68     118 ..     183     237 ..     170     259 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2e-06
                            AAA_33  1 lvllvGlpGsGKstlaerllkklg....avllssdt 32
                                      ++ lvG++GsGKstl+++l+++l      vll+  +
  gi|344210222|ref|YP_004786398.1| 59 VTALVGPNGSGKSTLLKGLANQLEpeagSVLLDGQD 94
                                      5679****************9998787766666544 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.1
                            AAA_33  68 sagrnvil...datnlsrrerarflklar..rlgvpvrivvvetdeetlkeRlakR 118
                                       ++  +v+l     t+l+ +++ +++++ +  r ++ ++ivvv  d e+ ++Rla R
  gi|344210222|ref|YP_004786398.1| 183 AQDTDVLLldePTTFLDLHHQLEVMEIIEtlRDESDITIVVVLHDIEQ-AARLADR 237
                                       444554444334557776666666666552223334555555555544.4455555 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 !    9.2   0.0   0.00096      0.48     245     265 ..      57      78 ..      44      84 .. 0.85
   2 !    6.3   0.3     0.007       3.5     324     413 ..     169     243 ..     164     266 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00096
                                       S.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 245 G.vtlIvGggfhGKsTLLeAle 265
                                       G vt++vG++  GKsTLL+ l+
  gi|344210222|ref|YP_004786398.1|  57 GaVTALVGPNGSGKSTLLKGLA 78 
                                       449****************986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.007
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GC CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsgd 400
                                       SG   q a+i+  l  ++++lL+DE t+   l ++ e               +++ ++ l+++ ++++++v   +++
  gi|344210222|ref|YP_004786398.1| 169 SGGQKQLAWIAMVLAQDTDVLLLDEPTTFLDLHHQLE---------------VMEIIETLRDESDITIVVVLHDIEQ 230
                                       7888888999999999999999999887555555222...............3455666667777777777777777 PP

                                       CTTT-SEEEEEET CS
                        ABC_ATPase 401 yldvAdtvilmee 413
                                         ++Ad+++++++
  gi|344210222|ref|YP_004786398.1| 231 AARLADRMVALKD 243
                                       7777777777665 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   0.4   1.8e-06   0.00089      25      88 ..      58     116 ..      47     256 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.8e-06
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrqllde 88 
                                        ++ l+G+ G+GKs+l++ l+++le + g + l g+  q    ++  a+a+ l   +ll q+ + 
  gi|344210222|ref|YP_004786398.1|  58 AVTALVGPNGSGKSTLLKGLANQLEPEAGSVlLDGQDIQT---LETKAIARKL---GLLSQESTS 116
                                       56789**********************6444377777766...4444566666...566666555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.6e-06    0.0013      21      39 ..      59      77 ..      43      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.6e-06
                            AAA_23 21 ltlItGpNGaGKTTildAi 39
                                      +t+++GpNG+GK+T+l  +
  gi|344210222|ref|YP_004786398.1| 59 VTALVGPNGSGKSTLLKGL 77
                                      89*************9876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   7.1e-06    0.0035      25      43 ..      59      77 ..      47     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.1e-06
                            AAA_15 25 ltvliGkNnsGKSsileal 43
                                      +t l+G+N+sGKS++l+ l
  gi|344210222|ref|YP_004786398.1| 59 VTALVGPNGSGKSTLLKGL 77
                                      8***************998 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.3e-05    0.0067       3      39 ..      59      95 ..      57     112 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      v++lvG++G+GK t l  La++l+ e+ +vll   D+
  gi|344210222|ref|YP_004786398.1| 59 VTALVGPNGSGKSTLLKGLANQLEPEAGSVLLDGQDI 95
                                      789***************************9988886 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   1.6e-05    0.0079      19      57 ..      60      98 ..      50     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-05
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57
                                        l+G  G+GKs+l++ l+++le++ + v ld+ d+++l
  gi|344210222|ref|YP_004786398.1| 60 TALVGPNGSGKSTLLKGLANQLEPEAGSVLLDGQDIQTL 98
                                      5699******************************99987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.5e-05     0.013     100     130 ..      58      88 ..      36     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-05
                                       SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelktgev 130
                                        +++lvG+ G GKStL++ l+++le + g+v
  gi|344210222|ref|YP_004786398.1|  58 AVTALVGPNGSGKSTLLKGLANQLEPEAGSV 88 
                                       789**************99999965555444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     4e-05      0.02       2      24 ..      59      81 ..      58      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4e-05
                                      CEEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                      + +l G++GsGK+tLl++la ++
  gi|344210222|ref|YP_004786398.1| 59 VTALVGPNGSGKSTLLKGLANQL 81
                                      5689***************9987 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   0.00014     0.071       3      55 ..      61     156 ..      59     258 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
                                       EEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEE...ETTEE............................ CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvk...lkgke............................ 47 
                                       a+vG   +GKStL++ l ++ + ++++     +di++ + k       +                            
  gi|344210222|ref|YP_004786398.1|  61 ALVGPNGSGKSTLLKGLANQlEPEAGSVLLDGQDIQTLETKaiaR---Klgllsqestspnsisvedlvyhgryphr 134
                                       89*****************87667777776666666665553220...12333334455556666666666666666 PP

                                       ..............EEEEECGG CS
                          MMR_HSR1  48 ..............ielvDtpG 55 
                                                      + +D++G
  gi|344210222|ref|YP_004786398.1| 135 gffdsvteedeaavERAIDLAG 156
                                       6666666666666633444444 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 ?   14.3   0.1   8.5e-05     0.042       3      25 ..      62      84 ..      60     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.5e-05
                                      EESSTTSSHHHHHHHHHHHHTHE CS
                               AAA  3 lyGppGtGKTllakavakelgve 25
                                      l+Gp G GK++l k +a++l+ e
  gi|344210222|ref|YP_004786398.1| 62 LVGPNGSGKSTLLKGLANQLEPE 84
                                      89*****************9532 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.21     1e+02      39      60 ..      61      82 ..      55      99 .. 0.84
   2 ?    9.9   0.2   0.00087      0.43     110     160 ..     176     224 ..     163     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.21
                              TniB 39 llvGdsnnGKtmivekFarlhp 60
                                       lvG+   GK+++++  a++ +
  gi|344210222|ref|YP_004786398.1| 61 ALVGPNGSGKSTLLKGLANQLE 82
                                      69***********998876655 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00087
                              TniB 110 qvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                       + +++  + ++ vL++DE   +l    ++q e+++++ +L +e +i+iv+v
  gi|344210222|ref|YP_004786398.1| 176 AWIAMVLAQDTDVLLLDEPTTFL--DLHHQLEVMEIIETLRDESDITIVVV 224
                                       556677788999***********..8999*******************987 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 ?    8.4   0.0    0.0032       1.6       2      21 ..      63      82 ..      62      91 .. 0.84
   2 ?    4.0   0.1     0.072        36      75     137 ..     171     233 ..     162     244 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0032
                        ATP_bind_1  2 vGpaGsGKttfvgalseile 21
                                      vGp GsGK+t+ + l++ le
  gi|344210222|ref|YP_004786398.1| 63 VGPNGSGKSTLLKGLANQLE 82
                                      8***********99987765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.072
                        ATP_bind_1  75 lresldwldeelekeeddyllfDtPGQielfthseslakiveeLes.efalvvvyLvDsqrltd 137
                                       ++++l w++  l  +++d ll+D P       h  +  +i+e+L   +  ++vv+L D + ++ 
  gi|344210222|ref|YP_004786398.1| 171 GQKQLAWIAMVL-AQDTDVLLLDEPTTFLDLHHQLEVMEIIETLRDeSDITIVVVLHDIEQAAR 233
                                       567788999888.67889999999976544445555556******9878889999999876655 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.42   2.1e+02      61      78 ..      15      32 ..      10      42 .. 0.89
   2 ?   10.1   0.1     0.001      0.52      27      54 ..      58      85 ..      56     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.42
                                      ----------------GG CS
                              MukB 61 ntteaGatsgsrdkGlyG 78
                                      n t aG++s+ rd+ l G
  gi|344210222|ref|YP_004786398.1| 15 NDTAAGSQSSHRDRPLVG 32
                                      889***********9988 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.001
                                      HHHHHHS--SHHHHHHHHHHHHHHS--T CS
                              MukB 27 lvttlsGgnGaGksttmaafvtaliPdl 54
                                       vt+l G nG+Gkst + ++   l P+ 
  gi|344210222|ref|YP_004786398.1| 58 AVTALVGPNGSGKSTLLKGLANQLEPEA 85
                                      59***************99999988875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00017     0.087      32      54 ..      56      78 ..      45      88 .. 0.90
   2 ?   -1.1   0.1       2.3   1.2e+03     169     186 ..     207     224 ..     141     241 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                            AAA_25 32 agelallaGapgtGKttlaldla 54
                                       g++++l+G+ g+GK+tl+  la
  gi|344210222|ref|YP_004786398.1| 56 PGAVTALVGPNGSGKSTLLKGLA 78
                                      699***************97776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.3
                            AAA_25 169 vealeriarrtgaavllv 186
                                       +e +e ++++ ++++++v
  gi|344210222|ref|YP_004786398.1| 207 MEIIETLRDESDITIVVV 224
                                       333334444444444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00017     0.087       4      47 ..      59     101 ..      57     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00017
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla 47 
                                       + +++G+  +GK+tllk l+++l  ++   + ++ +d ++ + +
  gi|344210222|ref|YP_004786398.1|  59 VTALVGPNGSGKSTLLKGLANQLE-PEAGSVLLDGQDIQTLETK 101
                                       6789****************8887.7777777777777775544 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 ?   12.8   0.1   0.00013     0.064       2      33 ..      59      90 ..      58     115 .. 0.80
   2 ?   -2.7   0.0       7.5   3.8e+03      26      37 ..     218     229 ..     195     257 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                                      EEEEEESTTCCHHHHHHHHHCT--SS-EEEEE CS
                              cobW  2 vtvltGflGsGKTtLlnhllenraglklaviv 33
                                      vt l+G+ GsGK+tLl+ l ++ + +   v++
  gi|344210222|ref|YP_004786398.1| 59 VTALVGPNGSGKSTLLKGLANQLEPEAGSVLL 90
                                      899**************999776666666655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.5
                                       SS-EEEEESS-S CS
                              cobW  26 glklavivNefg 37 
                                       +  + v++ ++ 
  gi|344210222|ref|YP_004786398.1| 218 DITIVVVLHDIE 229
                                       333333333333 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   0.00077      0.39       4      43 ..      59      95 ..      57     126 .. 0.75
   2 ?    0.9   0.0      0.64   3.2e+02      51      91 ..     205     245 ..     181     256 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00077
                            AAA_24  4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadkf 43
                                        +++Gp+g+GK+tl+k l  +   +  e+G+  ld+ ++
  gi|344210222|ref|YP_004786398.1| 59 VTALVGPNGSGKSTLLKGL-AN--QLEPEAGSVLLDGQDI 95
                                      5789*************99.33..3445555555555555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.64
                            AAA_24  51 dfldevvelaaeladyktlviDtideleelclaevirqnek 91 
                                       ++++ +++l++e +   ++v+  i+++ +l++++v  +++ 
  gi|344210222|ref|YP_004786398.1| 205 EVMEIIETLRDESDITIVVVLHDIEQAARLADRMVALKDGE 245
                                       34555556677777777777777777777777777766665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00016     0.078      16      46 ..      53      83 ..      49     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                          ATPase_2 16 erepneiyfiYGpegsGKtaLlkeiienled 46
                                        ep  +  + Gp gsGK++Llk ++++le 
  gi|344210222|ref|YP_004786398.1| 53 TAEPGAVTALVGPNGSGKSTLLKGLANQLEP 83
                                      56788899999***************99964 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   0.00056      0.28      26      97 ..      61     132 ..      49     140 .. 0.77
   2 ?   -0.3   0.0       1.2   5.8e+02      89     119 ..     167     198 ..     159     235 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00056
                      Mg_chelatase  26 llvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekllkrrpfraphhsaskaalvGggskp 97 
                                        lvGp GsGK+ l k l++ l p   +  l+ + i+++ +k  ++kl       +  +s+s   lv  g+ p
  gi|344210222|ref|YP_004786398.1|  61 ALVGPNGSGKSTLLKGLANQLEPEAGSVLLDGQDIQTLETKAIARKLGLLSQESTSPNSISVEDLVYHGRYP 132
                                       699******************999999999999999999877766665555445555666666666666655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                      Mg_chelatase  89 alvGggskpkpGeislah.nGvLfLDElpefk 119
                                       +l Gg+++    ++ la+ + vL+LDE + f 
  gi|344210222|ref|YP_004786398.1| 167 SLSGGQKQLAWIAMVLAQdTDVLLLDEPTTFL 198
                                       56677777777777777625699999987773 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00024      0.12       2      23 ..      61      82 ..      60     152 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                                      EEE-STTSSHHHHHHHHHHHHT CS
                    Cytidylate_kin  2 aiDGPagsGKssvaralaeklg 23
                                      a+ GP gsGKs++ + la++l+
  gi|344210222|ref|YP_004786398.1| 61 ALVGPNGSGKSTLLKGLANQLE 82
                                      678****************997 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   0.00019     0.097       3      24 ..      62      83 ..      60     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00019
                      RNA_helicase  3 lyGpsgeGKStlakeLakallk 24
                                      l+Gp+g GKStl k La++l+ 
  gi|344210222|ref|YP_004786398.1| 62 LVGPNGSGKSTLLKGLANQLEP 83
                                      79****************9984 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0036       1.8       4      25 ..      62      83 ..      59     107 .. 0.88
   2 ?    3.3   0.2      0.13        67      94     152 ..     184     246 ..     167     259 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0036
                                      EE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellks 25
                                      + Gp G+GK+Tl+k ++++l+ 
  gi|344210222|ref|YP_004786398.1| 62 LVGPNGSGKSTLLKGLANQLEP 83
                                      78***************99975 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.13
                                       HHH-EEEE--.-STTGGG-HHHHHHHHHHHT..TTSEEEEE--SS-.-SHHHHHHHT-TT-EE CS
                          NTPase_1  94 seadviviDE.iGkmElkskkfkeaveevLk..sekpvlavihrrk.dlalveeirerkdvkv 152
                                       +++dv+++DE    + l  +    ++ e+L+  s+  +++v+h  +   +l +++   kd+++
  gi|344210222|ref|YP_004786398.1| 184 QDTDVLLLDEpTTFLDLHHQLEVMEIIETLRdeSDITIVVVLHDIEqAARLADRMVALKDGEI 246
                                       667788888833456777765555555556546677777778877667778888888777765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00047      0.23       3      22 ..      62      81 ..      61     153 .. 0.84
   2 ?   -0.9   0.0       4.4   2.2e+03      96     113 ..     214     237 ..     176     249 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00047
                            AAA_18  3 ltGtpGvGKttlakeLskrl 22
                                      l G+ G+GK+tl k L++ l
  gi|344210222|ref|YP_004786398.1| 62 LVGPNGSGKSTLLKGLANQL 81
                                      89**************9886 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 4.4
                            AAA_18  96 k......vvLtaspeelleRlekR 113
                                       +      +v+ +++ e + Rl++R
  gi|344210222|ref|YP_004786398.1| 214 RdesditIVVVLHDIEQAARLADR 237
                                       133334488888999999999988 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00041       0.2      14      44 ..      52      82 ..      45      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00041
                                      HHHCHTEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE 14 lakalgdvilLeGdLGaGKTtlvrglakalg 44
                                      ++++ g+v +L G+ G+GK+tl +gla++l+
  gi|344210222|ref|YP_004786398.1| 52 ITAEPGAVTALVGPNGSGKSTLLKGLANQLE 82
                                      444447889******************9986 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00037      0.18       3      22 ..      61      80 ..      59     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00037
                            AAA_28  3 vitGgestGKTtlleaLaar 22
                                      +++G+ ++GK+tll+ La++
  gi|344210222|ref|YP_004786398.1| 61 ALVGPNGSGKSTLLKGLANQ 80
                                      799***************86 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00034      0.17       2      43 ..      57      97 ..      56     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00034
                                      -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTT CS
                        APS_kinase  2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRh 43
                                      g+v  l G  gsGKst+ + l+++L+ +  s +lLdG+ + +
  gi|344210222|ref|YP_004786398.1| 57 GAVTALVGPNGSGKSTLLKGLANQLEPEAGS-VLLDGQDIQT 97
                                      5677899******************987655.689***9975 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    0.0005      0.25      36      61 ..      60      85 ..      52      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0005
                             AAA_7 36 vllvGptGtGKtviikdllkkldkek 61
                                      + lvGp G+GK++++k l ++l++e 
  gi|344210222|ref|YP_004786398.1| 60 TALVGPNGSGKSTLLKGLANQLEPEA 85
                                      679*******************9875 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 ?    8.7   0.6    0.0018      0.92      17      58 ..      54     122 ..      50     238 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0018
                        KAP_NTPase  17 latpivvgLygkWGsGKssllnkledelkefa...........................kpvrflfaef 58 
                                       ++++ v +L g+ GsGKs+ll+ l ++l+ +a                           ++++   +++
  gi|344210222|ref|YP_004786398.1|  54 AEPGAVTALVGPNGSGKSTLLKGLANQLEPEAgsvlldgqdiqtletkaiarklgllsqESTSPNSISV 122
                                       5678888899999**************999987777777777776666666666666663444444444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0012      0.61      39      72 ..      51      84 ..      44     116 .. 0.78
   2 ?   -1.5   0.1       4.2   2.1e+03     135     177 ..     188     230 ..     176     234 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                             Rad17 39 vLesrkkriLLisGPsGCgkstvvkvLskelgik 72
                                      ++  ++  +  + GP G gkst +k L+ +l ++
  gi|344210222|ref|YP_004786398.1| 51 SITAEPGAVTALVGPNGSGKSTLLKGLANQLEPE 84
                                      5556666677899**************9988765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.2
                             Rad17 135 lilvedlPnkfyrdsdalrev.irkylrssealplilviteies 177
                                       ++l+++ P  f    ++l+ + i + lr +  +++++v+ +ie+
  gi|344210222|ref|YP_004786398.1| 188 VLLLDE-PTTFLDLHHQLEVMeIIETLRDESDITIVVVLHDIEQ 230
                                       444544.7777655565543335566777777799999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); 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:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              36  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 1922.62
//
Query:       gi|344210223|ref|YP_004786399.1|  [L=371]
Description: ferrichrome ABC transporter permease [Haloarcula hispanica ATCC 33960]
Scores for 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-89  297.5  35.7    1.1e-88  297.2  35.7    1.1  1  FecCD     FecCD transport family
    0.00041   19.9  11.9    0.00041   19.9  11.9    2.4  2  ABC-3     ABC 3 transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.2  35.7   1.3e-92   1.1e-88       5     312 .]      40     364 ..      34     364 .. 0.94

  Alignments for each domain:
  == domain 1  score: 297.2 bits;  conditional E-value: 1.3e-92
                             FecCD   5 llllslllgavkispsevfeallgka.....dsleae..............ivlelrlprvlaallvGaaLavaGal 62 
                                       + ll +++ga+++++ e ++a+++ +     + ++++              iv+++r+prv++a+l+G++Lav+Ga+
  gi|344210223|ref|YP_004786399.1|  40 AGLLQVSFGAYSMTILEAWQAVFDPKvwfsvQAWQSFffgaelpelpkrtlIVWNIRMPRVIVAVLAGMCLAVSGAI 116
                                       567889999999999999999998888887633333366666666677777************************** PP

                             FecCD  63 lQtvtrNpLadPsilGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGia 139
                                       +Q+vtrN+La+P ilG+ssga+l ++l+l+l+  s+ +  lpl+a +g+ +a+llv+++a +++g+sp++l+LaG++
  gi|344210223|ref|YP_004786399.1| 117 FQAVTRNELASPFILGVSSGAGLTVLLTLVLF--SSLAPFLPLFAAVGGSIAFLLVYMIA-WQGGTSPVRLVLAGVI 190
                                       *******************************7..5555579*******************.**************** PP

                             FecCD 140 vsallsaltsllllll.neealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGv 215
                                       v++++++l   l +++ +   ++s+l w++Gsl g+ w+++ ++++ +l+++ll+l+ ar+l+ll lg+etA+slG+
  gi|344210223|ref|YP_004786399.1| 191 VNMVFTSLQRGLFFFAdDLGVVQSALAWITGSLTGVGWEEFRIAVIPTLAATLLALAGARQLNLLLLGEETASSLGM 267
                                       ***************9777899******************************************************* PP

                             FecCD 216 nvervrllllllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptel 292
                                       +vervr++l ++++l++++a++++G+igF GL+vPhi+rl+vg+d+r+ll+ ++++G +l+++ad+ arl+lsp+++
  gi|344210223|ref|YP_004786399.1| 268 SVERVRFMLSAVAILAASTAISVAGIIGFFGLVVPHIVRLIVGSDYRRLLIGCVFVGPALMVVADVGARLALSPAQV 344
                                       ***************************************************************************** PP

                             FecCD 293 pvgivtaliGapffiylllr 312
                                       pvg+vt ++G+p+f+yl++r
  gi|344210223|ref|YP_004786399.1| 345 PVGVVTGVVGGPYFLYLMRR 364
                                       ******************97 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   2.3      0.12   1.1e+03     216     254 ..     102     150 ..      91     154 .. 0.54
   2 !   19.9  11.9   4.5e-08   0.00041      91     226 ..     195     329 ..     161     363 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.12
                             ABC-3 216 vAillglvsvvaGlll..........SyyldlatGavivlvatllflla 254
                                       vA+l g+  +v+G+++           ++l +++Ga +++++tl+++ +
  gi|344210223|ref|YP_004786399.1| 102 VAVLAGMCLAVSGAIFqavtrnelasPFILGVSSGAGLTVLLTLVLFSS 150
                                       4555555555555444111111111034556777777777777666665 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 4.5e-08
                             ABC-3  91 svflalglvlvslikkskvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkl 167
                                        ++l  gl+++    ++ ++  +++ G++ ++  e++ + +i ++   ll+l   ++l l+ + ee+A + g+sv++
  gi|344210223|ref|YP_004786399.1| 195 FTSLQRGLFFFADDLGVVQSALAWITGSLTGVGWEEFRIAVIPTLAATLLALAGARQLNLLLLGEETASSLGMSVER 271
                                       344556888888777788899999***************************************************** PP

                             ABC-3 168 lkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvv 226
                                       ++++l a+  la ++a+ ++G+i  + l ++P ++ + ++++ ++lli  + +g   +v
  gi|344210223|ref|YP_004786399.1| 272 VRFMLSAVAILAASTAISVAGIIGFFGL-VVPHIVRLIVGSDYRRLLIGCVFVGPALMV 329
                                       ***********************99986.679999999999999999998888865554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 2107.98
//
Query:       gi|344210224|ref|YP_004786400.1|  [L=323]
Description: thioredoxin reductase [Haloarcula hispanica ATCC 33960]
Scores for 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-07   28.6   0.0    1.1e-06   28.1   0.0    1.3  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    2.7e-05   23.6   0.2      0.049   12.9   0.0    2.6  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    0.00011   21.5   1.3    0.00065   18.9   0.1    2.1  2  GIDA           Glucose inhibited division protein A
    0.00011   21.4   1.5    0.00013   21.2   0.2    1.8  2  FAD_binding_2  FAD binding domain
     0.0015   17.4   0.0     0.0086   14.8   0.0    1.9  2  HI0933_like    HI0933-like protein
      0.002   18.3   0.2     0.0047   17.1   0.2    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0023   17.4   0.8     0.0023   17.4   0.8    1.7  2  FAD_oxidored   FAD dependent oxidoreductase
     0.0028   17.0   0.0     0.0058   15.9   0.0    1.4  1  Thi4           Thi4 family
     0.0059   15.9   1.9      0.013   14.8   0.2    2.1  2  FAD_binding_3  FAD binding domain
     0.0094   15.6  14.2      0.022   14.4   0.9    3.2  3  DAO            FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.068   12.2   0.8       0.23   10.5   0.1    2.0  2  Lycopene_cycl  Lycopene cyclase protein
       0.31   11.0   5.7       0.76    9.8   0.4    2.9  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 !   28.1   0.0   7.3e-10   1.1e-06       2     107 ..      12     118 ..      11     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 7.3e-10
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH......HHHHCHHHHCCCCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias......evvkklnqgielllg 72 
                                       dv+++GgGpAG++a  + a+a ++++++ ++g   + +c + + +lg+++  ++++      ++ +  +  +   l 
  gi|344210224|ref|YP_004786400.1|  12 DVIIVGGGPAGCSAGVFTARADLDTAVY-DRGRSSLKRCAYLENYLGFPAGIDVETlydriqDHAETAGCTVVSQLV 87 
                                       8***************************.999999******999999999999888999888443333333222222 PP

                                       CTCEEEEESCEEEEETEEECTCEEEEEESEEEE-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  73 eevvkidpgkkkvklekkkegdeekiaydklvlAt 107
                                       e+  + d g+  +++   +++d+e+ +  +++ At
  gi|344210224|ref|YP_004786400.1|  88 ESLDRTDDGE-GFVV---ETQDGETATTRRVIAAT 118
                                       3455555555.3444...22567788888888777 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   0.0   3.3e-05     0.049       1      31 [.      14      43 ..      14      54 .. 0.89
   2 !    6.5   0.0    0.0028       4.2     104     132 ..      87     118 ..      81     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.3e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                      iI+G+GPaG +a++   +a+l d  + ++g+
  gi|344210224|ref|YP_004786400.1| 14 IIVGGGPAGCSAGVFTARADL-DTAVYDRGR 43
                                      8********************.678998886 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0028
                       Pyr_redox_3 104 Vesvkk..edegfevetske.tyeAkkviiAt 132
                                       Ves+++  ++egf+vet+ + t ++++vi At
  gi|344210224|ref|YP_004786400.1|  87 VESLDRtdDGEGFVVETQDGeTATTRRVIAAT 118
                                       778888324577*****997477778888777 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   4.4e-07   0.00065       1      34 [.      12      48 ..      12      62 .. 0.80
   2 ?    1.6   0.1     0.077   1.2e+02      93     148 ..      63     118 ..      54     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.4e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE...ES-GGG CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi...thkldt 34
                                      dvi++GgG AGc A + +ar+ ++++ +     +l++
  gi|344210224|ref|YP_004786400.1| 12 DVIIVGGGPAGCSAGVFTARADLDTAVYdrgRSSLKR 48
                                      8*************************99444333333 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.077
                                       -HHHHHHHHHHHHHTSTTEEEEES-EEEEEECT.TEEEEEEETTS-EEEECEEEE-- CS
                              GIDA  93 drelyskevteklenepnleiieeeveelivee.kkvkgvvtedgetikakavviat 148
                                       d e+   ++++  e+    +++++ ve+l+ ++ ++  +v t+dget +++ v+ at
  gi|344210224|ref|YP_004786400.1|  63 DVETLYDRIQDHAET-AGCTVVSQLVESLDRTDdGEGFVVETQDGETATTRRVIAAT 118
                                       555556666666665.778999999****765546667799*************999 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   8.9e-08   0.00013       1      32 [.      12      43 ..      12      49 .. 0.93
   2 ?   -1.7   0.1      0.78   1.2e+03     175     203 ..      97     122 ..      64     169 .. 0.52

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 8.9e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                      Dvi++G+G AG++A++  a+a l++av + + 
  gi|344210224|ref|YP_004786400.1| 12 DVIIVGGGPAGCSAGVFTARADLDTAVYDRGR 43
                                      9**************************98875 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.78
                                       EEEEEEETTTTCEEEEEESEEEE-----G CS
                     FAD_binding_2 175 tGavvenpesgrevrirakavvlatgGfg 203
                                        G vve  ++ +e + + ++v+ at   g
  gi|344210224|ref|YP_004786400.1|  97 EGFVVE--TQDGE-TATTRRVIAATRYDG 122
                                       444444..22222.223445554444333 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   5.8e-06    0.0086       2      37 ..      12      47 ..      11      51 .. 0.92
   2 ?    0.1   0.0      0.17   2.6e+02     107     162 ..      63     118 ..      57     119 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.8e-06
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgr 37
                                      dvi++GgG+AG  a +  a+++ ++++++++++ ++
  gi|344210224|ref|YP_004786400.1| 12 DVIIVGGGPAGCSAGVFTARADLDTAVYDRGRSSLK 47
                                      8*****************************998776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.17
                                       -CHHHHHHHHHHHHHHT-EEE-S--EEEEEC.ETTE.EEEEE.TTEEEEESEEEE-- CS
                       HI0933_like 107 kaedivdallkelkeagvklrletevksvek.eedgkfrvktkseeeleadklvlAt 162
                                       + e++ d ++ +++ ag+++  ++ v+s+++ ++++ f v+t+++e+ ++++++ At
  gi|344210224|ref|YP_004786400.1|  63 DVETLYDRIQDHAETAGCTVV-SQLVESLDRtDDGEGFVVETQDGETATTRRVIAAT 118
                                       556666666667777777664.455777755145567999**888888888888775 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 !   17.1   0.2   3.2e-06    0.0047       1      29 [.      15      43 ..      15      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.2e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                      IvG+G +G++a  + a+a++d  ++++++
  gi|344210224|ref|YP_004786400.1| 15 IVGGGPAGCSAGVFTARADLDTAVYDRGR 43
                                      9*************************986 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.8   1.5e-06    0.0023       1      30 [.      12      41 ..      12      44 .. 0.92
   2 ?   -1.7   0.3      0.92   1.4e+03     218     218 ..     177     177 ..      72     281 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.5e-06
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLvee 30
                                      Dv++vGGgpaG+ A +  ara+  +++ ++
  gi|344210224|ref|YP_004786400.1| 12 DVIIVGGGPAGCSAGVFTARADLDTAVYDR 41
                                      9***********************998776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.92
                      FAD_oxidored 218 p 218
                                        
  gi|344210224|ref|YP_004786400.1| 177 A 177
                                       0 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.9e-06    0.0058      17      49 ..      10      41 ..       5      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.9e-06
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailer 49
                                      + Dv+ivG+G++G +a+   a++ dl +a+ +r
  gi|344210224|ref|YP_004786400.1| 10 DRDVIIVGGGPAGCSAGVFTARA-DLDTAVYDR 41
                                      67********************9.***999876 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   8.5e-06     0.013       3      34 ..      12      43 ..      10      54 .. 0.85
   2 ?   -0.3   0.1      0.34     5e+02     109     152 ..      69     113 ..      57     118 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.5e-06
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                      dV+IVG+GpaG +++ + ++a  ++ + ++ +
  gi|344210224|ref|YP_004786400.1| 12 DVIIVGGGPAGCSAGVFTARADLDTAVYDRGR 43
                                      8****************999988888877765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHT.EEETCSEEEECCEECCCCCCCEEEECCTTEEEE CS
                     FAD_binding_3 109 riLvehaeerg.lqvrfktevesleqdeegvtaevrdketgeeet 152
                                         + +hae +g + v +  e +  ++d+eg   e +d et ++++
  gi|344210224|ref|YP_004786400.1|  69 DRIQDHAETAGcTVVSQLVESLDRTDDGEGFVVETQDGETATTRR 113
                                       556899999995555555565555555555555555555555555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.9   1.5e-05     0.022       1      30 [.      12      43 ..      12      48 .. 0.93
   2 !    8.7   0.2   0.00075       1.1     144     200 ..      63     118 ..      47     132 .. 0.82
   3 ?    0.1   1.9      0.31   4.7e+02      70     140 ..     217     289 ..     137     309 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgd 30
                                      dv+i+GGG +G+s+  + ar+   ++++++g+
  gi|344210224|ref|YP_004786400.1| 12 DVIIVGGGPAGCSAGVFTARADldTAVYDRGR 43
                                      9******************99899******95 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00075
                                       EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEE.TCEEEEEEECT.EEE.EEEEEEEE-- CS
                               DAO 144 dpakltaalaraaealGveilegtevtgleeed.gkvwgverttp.gen.daadavVnaa 200
                                       d + l   +++ ae++G++++ +  v++l+++d g +  v  +t+ ge+ ++ + v+ a+
  gi|344210224|ref|YP_004786400.1|  63 DVETLYDRIQDHAETAGCTVVSQ-LVESLDRTDdGEGFVV--ETQdGETaTT-RRVIAAT 118
                                       66667778999************.*****99774666666..8888998444.7799887 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.31
                                       HHHHHHSSTTSEEEEEEEEEESSH.....HHHHHHHHHHHHHHHTTTTE...EEEEHHHHHHHSTTSTTTSEEEEET CS
                               DAO  70 eleeelgididyrrtGllslaade.....eelealdkllallleaglda...elldaeevrelepalpgllgalfyp 138
                                       el++e    +  +r++ + +++d+       ++++ ++++++++a ld+   ++++++e++++    ++ l+++++p
  gi|344210224|ref|YP_004786400.1| 217 ELDDE----W-TERSTWVEYFDDRyaedaPVEPGS-DRFQRVRKAALDErrsSYITSDEIADRTETGQEALAGYLDP 287
                                       22222....2.344555555532111111112223.44444444444332235789988888886422445666666 PP

                                       TE CS
                               DAO 139 dt 140
                                       ++
  gi|344210224|ref|YP_004786400.1| 288 TA 289
                                       63 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00015      0.23       1      25 [.      12      34 ..      12      51 .. 0.73
   2 ?   -0.4   0.1      0.32   4.7e+02      89     139 ..      67     118 ..      60     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpgl 25
                                      Dv+++G+GpAg+s       a+++l
  gi|344210224|ref|YP_004786400.1| 12 DVIIVGGGPAGCSAGVFT--ARADL 34
                                      9***********965555..44444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.32
                     Lycopene_cycl  89 lkeellerlvengvklleakvesveeeeages.lvvleggrkirarlvvdar 139
                                       l  +++ +  ++g + ++  ves    ++ge  +v +++g++   r v+ a+
  gi|344210224|ref|YP_004786400.1|  67 LYDRIQDHAETAGCTVVSQLVESLDRTDDGEGfVVETQDGETATTRRVIAAT 118
                                       55566666668888999999999999999775156799999*******9986 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 ?    2.9   0.0     0.065        97       2      13 ..      15      26 ..      14      54 .. 0.77
   2 ?    9.8   0.4   0.00051      0.76     103     153 ..      67     118 ..      64     119 .. 0.80
   3 ?   -1.3   0.2       1.3   1.9e+03      72     108 ..     211     240 ..     199     279 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.065
                     NAD_binding_9  2 ivGaGprGlavl 13
                                      ivG+Gp+G ++ 
  gi|344210224|ref|YP_004786400.1| 15 IVGGGPAGCSAG 26
                                      9*******9875 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00051
                     NAD_binding_9 103 lfeellarlpegvtvevhraevvdleeradg..qavlladgaslaadaVvLAl 153
                                       l++++++ + e    +v+++ v++l++++dg  + v ++dg++ + ++V+ A+
  gi|344210224|ref|YP_004786400.1|  67 LYDRIQDHA-ETAGCTVVSQLVESLDRTDDGegFVVETQDGETATTRRVIAAT 118
                                       556666666.456899***********9988435888899**********997 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.3
                     NAD_binding_9  72 WlrergaleeaeeldpddfvpRalyGrYlrdlfeell 108
                                       W+r+r++        +d+   R+ + +Y++d+++e +
  gi|344210224|ref|YP_004786400.1| 211 WVRRRAE-------LDDEWTERSTWVEYFDDRYAEDA 240
                                       4444442.......35577788888888888877644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 1955.16
//
Query:       gi|344210225|ref|YP_004786401.1|  [L=504]
Description: beta,beta-carotene 15,15'-monooxygenase/beta-carotene dioxygenase 1 [Haloarcula hispanica ATCC 33960]
Scores for complete 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-110  370.7   0.1   1.5e-110  370.6   0.1    1.0  1  RPE65     Retinal pigment epithelial membrane protein


Domain annotation for each model (and alignments):
>> RPE65  Retinal pigment epithelial membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.6   0.1  8.5e-115  1.5e-110       2     463 .]      26     496 ..      25     496 .. 0.85

  Alignments for each domain:
  == domain 1  score: 370.6 bits;  conditional E-value: 8.5e-115
                                       S---S-EEEC--E..EEE---TT--EEEEEEEEE.ESCETTCCSSSGGGSEEEEEEEEE..CTTEEEEEEEE---HH CS
                             RPE65   2 apvreevpeplevkvieGeiPawlkGtllRnGpgkpevgedgkvshwFDGdGmlhrfef..kdgkvtyrnRfvrtda 76 
                                        ++++e+++ ++v   +G +P+wl+G+l+RnGpg +++++ ++v+hwFDG++ml rf+f  +++ v+yrnRf+rtda
  gi|344210225|ref|YP_004786401.1|  26 HSLHDETTASIPV---TGGLPDWLRGSLIRNGPGAFSFPNGSSVDHWFDGFAMLYRFTFdpDGDAVHYRNRFLRTDA 99 
                                       6778899888777...6******************************************6533889*********** PP

                                       HHHHHHHTS................--SBSTTTTSB-----SEEEEETTEEEEEETTCEEEEEETTTTEEEEE--CC CS
                             RPE65  77 ylaerkagk................slfdglpakkkknnantnvvyhggrllalteagkpyeidpetLetlgkvdld 137
                                       y+a+++ g+                ++f     +++ +n n+   ++g +++alte+++ +++dp+tLet g ++ d
  gi|344210225|ref|YP_004786401.1| 100 YEAATS-GEfeggfatgettlrsrlATF----LTDPYDNTNIIAERFGREYVALTESPRKVRFDPNTLETTGHIEHD 171
                                       *99988.665666666555544433222....34455666666669****************************996 PP

                                       C...TTS-B-SS-EEETTCEEEEEEEECCTCECEEEEEEE-.T...T-...EEEEEEEECS.S..------EEE-SS CS
                             RPE65 138 g...eseaftAHpkvdpetgelynfglslgkppsvtysvfdvaaaidk...srevkiklpgeklkpayiHdfalTen 208
                                       +    ++  +AH k+dp++g l+n+ + +g ++s +y+v+ ++   +    ++  +++ +    +p+y+H+falT++
  gi|344210225|ref|YP_004786401.1| 172 DgvpTGQLSCAHVKRDPTSGVLVNVDTAFG-RTS-QYHVTAMT---PDgtrRHVGSVDTD----QPSYMHSFALTPR 239
                                       447644556********************9.554.78888777...42221222233444....5************ PP

                                       EEEEEE--EECHC.H.....CCCTCGGCEEE-TTS-EEEEEEETT.TT--GG....EEEEE--SEEEEEEEEEEET. CS
                             RPE65 209 yvvlvelplklnlkk.....gkksggdalewdpekptrfgvipRr.gekegv.akfrwfeteaffvfHtaNayeeee 278
                                       yvvl e+pl+l++++     +++++++ +ew+p+++tr++v++R+ g   +v a+   ++  a+f fH++Na+e+++
  gi|344210225|ref|YP_004786401.1| 240 YVVLTEFPLRLDPRRflkpgRQAPFIEQFEWEPDRGTRIIVMDRTtG---TVvAEP-VID--AVFGFHHVNAFERDG 310
                                       **********9998899999999**********************66...333555.555..*************97 PP

                                       TCEEEEEEEEE.SS.--STTS-CT.T----.-...GGTGGG-EEEEEEEEETTTTTCEECE........EEEEESS- CS
                             RPE65 279 dgevvvdlcryedaevldnlylenlrsrkgeakkeekaeesqsrlrryrldlktgsateeke.......eaalsdrs 348
                                       ++e+v+dl +++da ++d lyl+nlr  ++            +r+ r+++dl tgs + +          ++l +++
  gi|344210225|ref|YP_004786401.1| 311 GRELVFDLETVPDATTIDSLYLDNLRAGEMG--------AIVGRIERFTVDLGTGSGAPRYGdvdaavsREMLYPDG 379
                                       77777********9***********865543........36789********9988888866999999999999999 PP

                                       EEEEE--GGGTTS--SEEEEEE-SSTTSS-..-.-EEEEEET-TTTE........EE--EEEE..ESTTTSSTT-EE CS
                             RPE65 349 lEfPrinpaysgrkyryvYgasasggsdkaskf.dglvkvDletkgrea...eghypgEpiFV..PragateEDdGv 419
                                         +P++ pa+ +r++ryvY+++++ + +   +    ++k+D++t   e+    g y gEp+FV  P++  ++EDdGv
  gi|344210225|ref|YP_004786401.1| 380 SALPTVSPARWCRPHRYVYAMGMDTPVT---EWaRRVLKLDTDTGAVETfddGGDYFGEPVFVsaPNG--DAEDDGV 451
                                       9**********************99854...4449*******9986655999999********55555..******* PP

                                       EEEEEEET.TTEEEEEEEETTBCCCSEEEEESS---S--BEEEEE CS
                             RPE65 420 llsvvlde.eersellvldAktltevArvelpqrvpygfHGtfvp 463
                                       +l+v+ld  ++rs llvld++t+te Ar++lp++ p++fHG ++p
  gi|344210225|ref|YP_004786401.1| 452 VLVVALDAdADRSRLLVLDGQTFTERARATLPHAAPFDFHGRYFP 496
                                       ******99**********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 3180.22
//
Query:       gi|344210226|ref|YP_004786402.1|  [L=329]
Description: hypothetical protein HAH_5285 [Haloarcula hispanica ATCC 33960]
Scores for complete 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  132.5  35.4    1.4e-20   73.8   7.9    2.0  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
      0.088   12.3   5.8       0.32   10.5   1.6    2.2  2  SLC35F    Solute carrier family 35


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 !   73.8   7.9   1.6e-24   1.4e-20       5     135 ..      10     141 ..       7     143 .. 0.94
   2 !   64.9  19.6     9e-22   8.1e-18       2     134 ..     154     289 ..     153     291 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 1.6e-24
                              EamA   5 llallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafll 81 
                                       ll+ + al+w+++fv++k +l+ v+p+ l++vr  ia+++ll +al+++++l+  ++ dw l+l+ g++ + + f l
  gi|344210226|ref|YP_004786402.1|  10 LLFAALALIWGLSFVAIKTGLEGVPPVLLAAVRHDIAAVVLLGYALWRGRSLRPQTRDDWSLILIGGTVLIGAHFAL 86 
                                       455677889*******************************************8888888****************** PP

                              EamA  82 ffyalkktsasnaslitslePvftlilsvlll.gekltlkqllgivlillGvlli 135
                                       +f +++++++s+ ++++sl+Pv+t  +++ l    +    +l+g+v++++Gv++i
  gi|344210226|ref|YP_004786402.1|  87 LFLGQQYVPSSFGAILLSLTPVVTPAFASTLIpSYRARPHELIGTVCGFIGVVII 141
                                       ************************999888887********************98 PP

  == domain 2  score: 64.9 bits;  conditional E-value: 9e-22
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl...aklslkdwllllllgllgt 75 
                                       lg+ l++ +a+ +a+++vl+ +  ++++ ++l ++++l+++ +l ++++   + +       l++++++++lg++++
  gi|344210226|ref|YP_004786402.1| 154 LGVALLISSAVAFAVGAVLTERYTSSLPLVSLQAWMTLLGAGILHAVSAGLPSERlgtVTVGLEQLAAIAYLGIVAS 230
                                       7999**********************************999999777666666655788899999************ PP

                              EamA  76 vlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvll 134
                                       +++fll+f ++++++a++ sl+++++P++t+i ++lllge+l+  ++ g+++i++G + 
  gi|344210226|ref|YP_004786402.1| 231 AIGFLLYFRLISTVGAAETSLVSYVVPAVTAISGWLLLGETLGPVTVTGFAVIVVGFAW 289
                                       ********************************************************876 PP

>> SLC35F  Solute carrier family 35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.6   3.6e-05      0.32     124     233 ..     122     227 ..      47     250 .. 0.70
   2 ?    3.9   0.1    0.0035        32     105     158 ..     251     305 ..     242     326 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.6e-05
                            SLC35F 124 ryrlvkiigvvvcilGvvllvvsdvlagrransgsnpvlGdllvlaGatlyavsnvleeylvkklslvellgllglf 200
                                       r r  ++ig v   +Gvv++  ++       ++   ++lG  l++  a  +av  vl e   + l+lv l + ++l 
  gi|344210226|ref|YP_004786402.1| 122 RARPHELIGTVCGFIGVVII--ANPTP----GAVGGRLLGVALLISSAVAFAVGAVLTERYTSSLPLVSLQAWMTLL 192
                                       55556666666666666543..33333....3445789*************************************** PP

                            SLC35F 201 Gaiisaiqlailerkel..kaihWdaeiallfvgf 233
                                       Ga i     a l  + l   ++  ++ +a+ ++g 
  gi|344210226|ref|YP_004786402.1| 193 GAGILHAVSAGLPSERLgtVTVGLEQLAAIAYLGI 227
                                       *9554433333434444003344444444555443 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0035
                            SLC35F 105 ldcfaipvvlvls.wlflkvryrlvkiigvvvcilGvvllvvsdvlag.rransgs 158
                                       l ++++p+v ++s wl+l      v + g +v ++G +  v +dvl   rr ++gs
  gi|344210226|ref|YP_004786402.1| 251 LVSYVVPAVTAISgWLLLGETLGPVTVTGFAVIVVGFAW-VKADVLRSlRRRHTGS 305
                                       66899**9998866**********************976.6889886514445665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); 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:                         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 0.32s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2023.07
//
Query:       gi|344210227|ref|YP_004786403.1|  [L=89]
Description: hypothetical protein HAH_5286 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   10.0   8.9        1.1    8.8   0.6    2.9  2  zf_Rg          Reverse gyrase zinc finger
       0.45   10.5   8.0        0.1   12.6   2.3    2.3  2  RNHCP          RNHCP domain


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 ?    8.8   0.6   0.00012       1.1       8      26 ..       2      20 ..       1      37 [. 0.89
   2 ?    2.4   4.1     0.012     1e+02       4      29 ..      39      66 ..      37      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00012
                             zf_Rg  8 klCPNCgGdisdeRlekGL 26
                                      +lC NC+ +i ++ l+k L
  gi|344210227|ref|YP_004786403.1|  2 QLCQNCQAAIDEYLLDKQL 20
                                      69***********999866 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.012
                             zf_Rg  4 avfeklCPNCgGdisdeRlekGLp..Ck 29
                                       v+   C  C+G++   R e   p  C 
  gi|344210227|ref|YP_004786403.1| 39 TVVADACVECDGAVYVPRSETAVPdcCP 66
                                      588899*******999999888775444 PP

>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.05   4.5e+02       6      15 ..       4      13 ..       1      22 [. 0.72
   2 ?   12.6   2.3   1.1e-05       0.1       5      41 ..      44      79 ..      40      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.05
                             RNHCP  6 CeeCgkevek 15
                                      C++C++++ +
  gi|344210227|ref|YP_004786403.1|  4 CQNCQAAIDE 13
                                      8888877765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.1e-05
                             RNHCP  5 tCeeCgkeveklaagsakrnHCpsCLlskHvdeepgd 41
                                      +C eC+ +v   ++++a  + Cp+C  s+H+de+  d
  gi|344210227|ref|YP_004786403.1| 44 ACVECDGAVYVPRSETAVPDCCPAC-RSEHIDETGTD 79
                                      6************************.79****98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 651.00
//
Query:       gi|344210228|ref|YP_004786404.1|  [L=205]
Description: type 11 methyltransferase [Haloarcula hispanica ATCC 33960]
Scores for complete 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   57.9   0.0    2.1e-15   57.2   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    3.4e-14   53.2   0.0    5.4e-14   52.6   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    8.9e-10   38.7   0.0    1.1e-09   38.3   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    2.5e-09   37.1   0.1    3.1e-09   36.8   0.1    1.1  1  Methyltransf_31  Methyltransferase domain
    2.7e-08   33.6   0.0      4e-08   33.1   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
    4.7e-08   33.7   0.1    7.1e-08   33.1   0.1    1.3  1  Methyltransf_12  Methyltransferase domain
    0.00024   20.6   0.0    0.00025   20.5   0.0    1.2  1  TehB             Tellurite resistance protein TehB
     0.0044   18.0   0.1      0.008   17.2   0.1    1.7  1  Methyltransf_24  Methyltransferase domain
     0.0054   16.5   0.0     0.0076   16.0   0.0    1.4  1  DUF938           Protein of unknown function (DUF938)
     0.0077   15.8   0.0     0.0096   15.5   0.0    1.2  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.017   14.1   0.0      0.022   13.7   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.017   14.2   0.0      0.021   13.9   0.0    1.1  1  Pox_MCEL         mRNA capping enzyme


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 !   57.2   0.0   1.4e-18   2.1e-15       1      92 [.      48     139 ..      48     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 1.4e-18
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG..BSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaed..lpfedgsfDlvvssgalh 75 
                                       +++lGcG+Gr++++l+++ g +++tg+Di++e  + ++e++ +   + +f++g +ed   +fed+ fD+v+s+ +l+
  gi|344210228|ref|YP_004786404.1|  48 IIELGCGSGRHLAHLQTN-GYGNLTGIDINDESFDVMAEHYPRLADSGTFHTGALEDivTEFEDDAFDVVYSVETLQ 123
                                       789*************99.68********************776559**********4447***********999** PP

                                       GSSHHHHHHHHHHHHHH CS
                   Methyltransf_25  76 hlsdedlekalkeiarv 92 
                                       h++++d + +++eiar+
  gi|344210228|ref|YP_004786404.1| 124 HIHPDD-AWVFEEIARI 139
                                       **9877.569****997 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   3.6e-17   5.4e-14       2      87 ..      50     139 ..      49     142 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 3.6e-17
                                       EET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT..SS-TT-EEEEEEES-CCC-. CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaekl..pfednsfDlvvssevlhhv. 74 
                                       ++GcG+Gr++++l+ +g ++++g+D+++e  ++  e++++   + +f+ + +e++   fed+ fD+v+s e+l+h+ 
  gi|344210228|ref|YP_004786404.1|  50 ELGCGSGRHLAHLQTNGyGNLTGIDINDESFDVMAEHYPRLADSGTFHTGALEDIvtEFEDDAFDVVYSVETLQHIh 126
                                       89************9999*********************99998899******95448******************9 PP

                                       CCHHHHHHHHHHH CS
                   Methyltransf_11  75 edpekalkeiaRv 87 
                                       +d + +++eiaR+
  gi|344210228|ref|YP_004786404.1| 127 PDDAWVFEEIARI 139
                                       99**********7 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   7.4e-13   1.1e-09       8     107 ..      29     138 ..      21     191 .. 0.70

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 7.4e-13
                   Methyltransf_23   8 elsdklerllpk.lraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiaekakkaqkdqfdeqeaae.... 78 
                                       e+s+ l  +l+     ++r++++GcG+G+ l +l++ng+ ++tg+D+++e              +fd + + +    
  gi|344210228|ref|YP_004786404.1|  29 EVSETLVNVLDHyVHDDARIIELGCGSGRHLAHLQTNGYgNLTGIDINDE--------------SFDVMAEHYprla 91 
                                       555555555543247789*****************************975..............3333333331222 PP

                   Methyltransf_23  79 .................pqgkfdlIvlrevlehvp.dppellrqiat 107
                                                        +++ fd++++ e+l h++ d + ++  ia+
  gi|344210228|ref|YP_004786404.1|  92 dsgtfhtgaledivtefEDDAFDVVYSVETLQHIHpDDAWVFEEIAR 138
                                       22333333333344444777**************9644444444444 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.1   2.1e-12   3.1e-09       2      99 ..      43     138 ..      42     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2.1e-12
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       +++ r+++lGCG+G+ +  l    +  ++++GiDi+ e+  ++ e+  +l  d  +F+ g  e++ + +ed+ fD++
  gi|344210228|ref|YP_004786404.1|  43 HDDARIIELGCGSGRHLAHLQ--TNGYGNLTGIDINDESFDVMAEHYPRLA-DSGTFHTGALEDIVTEFEDDAFDVV 116
                                       57889**********999999..667899****************877665.5699********8866********* PP

                   Methyltransf_31  79 lsnevl.naladpdkileeier 99 
                                        s e+l +  +d + ++eei r
  gi|344210228|ref|YP_004786404.1| 117 YSVETLqHIHPDDAWVFEEIAR 138
                                       ******5445677777777766 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   2.7e-11     4e-08       6     113 ..      37     151 ..      33     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.7e-11
                              MetW   6 liaelikpgsrvldlGcGdGellellkeekqvdgrGleldeegv...aec...vakGlsviqgdldkdlenfedksf 76 
                                       ++ +++++ +r+++lGcG G  l  l+ +   +  G+++++e+    ae    +a   + + g l++ +++fed++f
  gi|344210228|ref|YP_004786404.1|  37 VLDHYVHDDARIIELGCGSGRHLAHLQTNGYGNLTGIDINDESFdvmAEHyprLADSGTFHTGALEDIVTEFEDDAF 113
                                       566899********************998888888998887764111333112344556899999999********* PP

                              MetW  77 dyvvlsqtlqatrnp.kevldellrigrraivsfPnfG 113
                                       d+v    tlq ++   + v++e+ ri+   +v   n G
  gi|344210228|ref|YP_004786404.1| 114 DVVYSVETLQHIHPDdAWVFEEIARIAGDLLVIAENEG 151
                                       *************761569*******999888777766 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   4.8e-11   7.1e-08       2      91 ..      50     138 ..      49     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 4.8e-11
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhh 78 
                                       e+GcG+G+ l++l  +    ++tg+Di+ ++++  +e+  +   ++ ++ +   +d+  +++ ++fD+v++ ++l+h
  gi|344210228|ref|YP_004786404.1|  50 ELGCGSGRHLAHLQTN-GYGNLTGIDINDESFDVMAEHYPRLA-DSGTFHTGALEDIVTEFEDDAFDVVYSVETLQH 124
                                       9************988.99*************88888888877.5889999999999999999************** PP

                   Methyltransf_12  79 l.kdirevldnirk 91 
                                       + +d + v+++i++
  gi|344210228|ref|YP_004786404.1| 125 IhPDDAWVFEEIAR 138
                                       *8777677777665 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.6e-07   0.00025      30     103 ..      44     120 ..      21     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.6e-07
                                       -S-EEEEES-TTSHHHHHHHHTT-.EEEEEES-HHHHHHHHHHHHHTT-T.TE.EEEE--GGG----S-EEEEEEES CS
                              TehB  30 kpgkvldlgcgqgrnslylsllgy.dvtawdknensiafleeikekenlk.ni.stalydineaklderydfilstv 103
                                       + +++++lgcg+gr   +l+ +gy ++t +d n++s   + e   + + + +  + al di +   d+ +d + s  
  gi|344210228|ref|YP_004786404.1|  44 DDARIIELGCGSGRHLAHLQTNGYgNLTGIDINDESFDVMAEHYPRLADSgTFhTGALEDIVTEFEDDAFDVVYSVE 120
                                       56899*******************779*********99987765443322023034566666666666677666655 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   5.4e-06     0.008       1      74 [.      49     117 ..      49     204 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.4e-06
                   Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalare..aglddrvrlikadseealaslaagsiDllf 74 
                                       +E+G+ sG+     l+ l+ ng g+l+ +d +    e   +++e    l+d  +++ + +e+ +++++++ +D+++
  gi|344210228|ref|YP_004786404.1|  49 IELGCGSGR----HLAHLQTNGYGNLTGIDIND---ESFDVMAEhyPRLADSGTFHTGALEDIVTEFEDDAFDVVY 117
                                       589988888....4456789***********99...4444555548899999****************9****997 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   5.1e-06    0.0076      11      45 ..      31      64 ..      25     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.1e-06
                            DUF938 11 repilevLksylakttervLEiasGtGqHAvffAp 45
                                      +e++++vL +y+ +  + ++E++ G+G+H +++ +
  gi|344210228|ref|YP_004786404.1| 31 SETLVNVLDHYVHDDAR-IIELGCGSGRHLAHLQT 64
                                      68999*********995.*************9976 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.4e-06    0.0096      18     103 ..      29     118 ..      16     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.4e-06
                                       HHHHHHHHHCHCC..TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC...EEEEE-ST CS
                               MTS  18 kGsklLletlpke..lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle...vevvasdv 89 
                                         s+ L++ l++    + +++ lGcG G   a+l+  +   ++t +d++ ++ ++  e + + + +    +   +d+
  gi|344210228|ref|YP_004786404.1|  29 EVSETLVNVLDHYvhDDARIIELGCGSGRHLAHLQT-NGYGNLTGIDINDESFDVMAEHYPRLADSgtfHTGALEDI 104
                                       5689999999998777788*********97666665.4455788888888888888877766665522244456899 PP

                                       TTTSTTS-EEEEEE CS
                               MTS  90 leeveekkfdlivs 103
                                       + e+e++ fd++ s
  gi|344210228|ref|YP_004786404.1| 105 VTEFEDDAFDVVYS 118
                                       99999999999865 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.5e-05     0.022     116     195 ..      45     125 ..      33     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                                       T-EEEEET-TTSHHHHHHHHCT-SEEEEE---H.HHHHHHHHHHCCTTTTSSEEEE---GGGS-T...---EEEEEE CS
                    Methyltransf_9 116 grtildvGcgnGyhlwrmvgegaklvvGidPse.lfliqfeavrkllgedqrahllplgieqlpe...leafdtvfs 188
                                       + +i+++Gcg+G hl  + ++g     Gid +   f +  e   +l ++ +  +    ++e++ +    +afd+v+s
  gi|344210228|ref|YP_004786404.1|  45 DARIIELGCGSGRHLAHLQTNGYGNLTGIDINDeSFDVMAEHYPRLADSGTFHT---GALEDIVTefeDDAFDVVYS 118
                                       66899*************************875156677788888874443332...3456654333379******* PP

                                       ES-GGG- CS
                    Methyltransf_9 189 mGvlyhr 195
                                       +  l h 
  gi|344210228|ref|YP_004786404.1| 119 VETLQHI 125
                                       9999985 PP

>> Pox_MCEL  mRNA capping enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.4e-05     0.021      64     109 ..      44      90 ..      28     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.4e-05
                          Pox_MCEL  64 nklkvLdldcgkGgDLeKyekgeIsklvatDiaeesieeckeRY.nk 109
                                       ++ ++++l+cg G  L   +  +  +l ++Di++es +   e Y + 
  gi|344210228|ref|YP_004786404.1|  44 DDARIIELGCGSGRHLAHLQTNGYGNLTGIDINDESFDVMAEHYpRL 90 
                                       67899*********************************999999433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1378.88
//
Query:       gi|344210229|ref|YP_004786405.1|  [L=70]
Description: hypothetical protein HAH_5288 [Haloarcula hispanica ATCC 33960]
Scores for 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-07   28.5   1.9    1.2e-06   28.1   1.9    1.2  1  SHOCT     Short C-terminal domain
    0.00027   21.2   0.3    0.00032   20.9   0.3    1.1  1  DUF4381   Domain of unknown function (DUF4381)
     0.0015   18.4   0.0     0.0016   18.4   0.0    1.2  1  FtsL      Cell division protein FtsL
     0.0016   18.4   0.6     0.0023   17.9   0.6    1.3  1  GvpG      Gas vesicle protein G
     0.0042   17.1   0.6      0.006   16.6   0.6    1.3  1  DUF1707   Domain of unknown function (DUF1707)
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.013   15.4   0.0    1.0  1  PIG-P     PIG-P
      0.026   14.4   0.6      0.036   13.9   0.6    1.3  1  VbhA      Antitoxin VbhA
      0.031   14.1   0.1      0.036   13.9   0.1    1.1  1  CdvA      CdvA-like coiled-coil domain
       0.04   14.3   0.1      0.048   14.1   0.1    1.1  1  DUF2681   Protein of unknown function (DUF2681)
       0.12   12.5   0.0       0.13   12.3   0.0    1.1  1  TssO      Type VI secretion system, TssO
       0.13   12.1   0.0       0.14   11.9   0.0    1.1  1  DUF4307   Domain of unknown function (DUF4307)
       0.13   12.5   0.2       0.17   12.2   0.2    1.2  1  DUF3135   Protein of unknown function (DUF3135)


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 !   28.1   1.9   7.9e-10   1.2e-06       1      28 []      39      66 ..      39      66 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 7.9e-10
                             SHOCT  1 daLekLkeLyarGeIteEEFeakKakLL 28
                                      d Le+Lk+ ya+GeI+e+E e++ ++LL
  gi|344210229|ref|YP_004786405.1| 39 DSLETLKQQYASGEIDEAELETRADRLL 66
                                      679********************99998 PP

>> DUF4381  Domain of unknown function (DUF4381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.3   2.2e-07   0.00032      20      65 ..       7      55 ..       4      68 .. 0.56

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.2e-07
                           DUF4381 20 Gwwlllaalll..llllvlalwllrrrkrnrreAlreLaalr.adeada 65
                                      Gwwlllaa ++  +++ vl++++l+r+ ++  + l+ L++   ++e d+
  gi|344210229|ref|YP_004786405.1|  7 GWWLLLAAFIIavVAIGVLLYVQLQREATAEPDSLETLKQQYaSGEIDE 55
                                      9*****7766655555555555555555555555555555444333333 PP

>> FtsL  Cell division protein FtsL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.1e-06    0.0016       9      53 ..       3      47 ..       1      68 [. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                              FtsL  9 llsvgkvlllllllvlvsavavvlithqtRqlvselekllserdk 53
                                      ++s g++lll ++++ v a++v+l+++  R++++e ++l   +++
  gi|344210229|ref|YP_004786405.1|  3 MASGGWWLLLAAFIIAVVAIGVLLYVQLQREATAEPDSLETLKQQ 47
                                      678899999999999********************7777655554 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.6   1.5e-06    0.0023      36      63 ..      40      67 ..      24      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.5e-06
                              GvpG 36 eLaaLqqeLdaGeIdeeeFdrrEeelLd 63
                                       L +L+q+  +GeIde+e + r ++lL+
  gi|344210229|ref|YP_004786405.1| 40 SLETLKQQYASGEIDEAELETRADRLLQ 67
                                      6899**********************96 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.6     4e-06     0.006      12      37 ..      41      66 ..      30      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4e-06
                           DUF1707 12 velLrealaeGrLtldEfdeRleaal 37
                                      +e L++ +a G ++ +E+++R ++ l
  gi|344210229|ref|YP_004786405.1| 41 LETLKQQYASGEIDEAELETRADRLL 66
                                      689*******************9987 PP

>> PIG-P  PIG-P
   #    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      44      92 ..       8      55 ..       4      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9e-06
                             PIG-P 44 WalavpayllmlvlyiyvalaslnlevltppldsletivDeaakveeee 92
                                      W l++ a+++++v++ +++++ l+   +t++ dslet+  ++a+ e +e
  gi|344210229|ref|YP_004786405.1|  8 WWLLLAAFIIAVVAIGVLLYVQLQR-EATAEPDSLETLKQQYASGEIDE 55
                                      889999******************9.899*************9753333 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   2.4e-05     0.036      23      45 ..      41      63 ..      32      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
                              VbhA 23 tvadleayvrGeIdadElvrrvr 45
                                      ++ + ++y+ GeId +El  r++
  gi|344210229|ref|YP_004786405.1| 41 LETLKQQYASGEIDEAELETRAD 63
                                      67789*************88876 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.4e-05     0.036      62      87 ..      40      65 ..      28      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
                              CdvA 62 alanlkisyasGEidEeaYksaieai 87
                                      +l +lk +yasGEidE + ++  + +
  gi|344210229|ref|YP_004786405.1| 40 SLETLKQQYASGEIDEAELETRADRL 65
                                      57789************999887765 PP

>> DUF2681  Protein of unknown function (DUF2681)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   3.2e-05     0.048       6      42 ..      11      48 ..       9      66 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                           DUF2681  6 llvgliaavlllvaylswqlkkar....kknaklqaekqql 42
                                      ll+++i+av+++  +l+ ql+++     +    l++ kqq 
  gi|344210229|ref|YP_004786405.1| 11 LLAAFIIAVVAIGVLLYVQLQREAtaepD---SLETLKQQY 48
                                      7899****************999864443...444444443 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.9e-05      0.13      10      51 ..       8      48 ..       5      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.9e-05
                              TssO 10 flyflllFlvtvlllflivffffkssplqekeillkelerkk 51
                                       +++l+ F+++v+ ++++++ + ++  + e + l + l+++ 
  gi|344210229|ref|YP_004786405.1|  8 WWLLLAAFIIAVVAIGVLLYVQLQREATAEPDSL-ETLKQQY 48
                                      699*********************9999999888.5555443 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.7e-05      0.14       3      32 ..       8      38 ..       6      64 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.7e-05
                           DUF4307  3 rllvillvvlvvvalalvawigysq.gsadv 32
                                       +l++++ +++vva++++ ++ +++ ++a+ 
  gi|344210229|ref|YP_004786405.1|  8 WWLLLAAFIIAVVAIGVLLYVQLQReATAEP 38
                                      5777888888888888888888888744333 PP

>> DUF3135  Protein of unknown function (DUF3135)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00011      0.17      12      40 ..      34      62 ..      26      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                           DUF3135 12 akedPealealrqelieelIesapeemqr 40
                                      a ++P+ le+l+q+     I++a+ e+++
  gi|344210229|ref|YP_004786405.1| 34 ATAEPDSLETLKQQYASGEIDEAELETRA 62
                                      789********************877663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1158  (0.0645881); expected 358.6 (0.02)
Passed bias filter:                      835  (0.0465726); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); 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 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 456.11
//
Query:       gi|344210230|ref|YP_004786406.1|  [L=144]
Description: pyridoxamine 5'-phosphate oxidase-like FMN-binding protein [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-14   53.8   0.2    2.3e-14   53.6   0.2    1.0  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    0.00057   20.0   0.0    0.00084   19.5   0.0    1.2  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
        0.1   12.3   0.0       0.13   12.0   0.0    1.3  1  FMN_bind_2      Putative FMN-binding 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 !   53.6   0.2   3.8e-18   2.3e-14       2     139 ..       6     138 ..       5     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 3.8e-18
                                       HHHHHHHHHC-SEEEEEEEE..TTEEEEEEEEEEEE..TTEEEEEEET..TSHCCHCCC.T--ECEEEEEEEEEEE- CS
                      Pyridox_ox_2   2 reeilalLdegevgrlafvd..dgepvilPvnyvvd..gdslyfhgak..gsrlaaalr.gapvcvvvtevdglvla 71 
                                       +e++ ++L ++++g+la++   +++p+ +Pv++++d   dsl fh ++  +s+++++l+ +a v ++v+e  +  ++
  gi|344210230|ref|YP_004786406.1|   6 DETVVDVLTDNGIGVLALSSpmEAAPYPVPVAFGYDpaTDSLAFHLSEsdESQKHRYLTaDATVGFTVYEETE--PK 80 
                                       578999*************977777***********99999****8887899999999966669999999443..44 PP

                                       SEGGEEEEEEEEEEEEEEEE--HHHHHHHCCCHHHHH..STTT..GGCSB---CCCCCTEEEEEEEEEEEEE CS
                      Pyridox_ox_2  72 rsfnslnyrSVvvrGraeevtdeeekaealellveki..vpgr..wenlrpptrkelkatsvlrlkieevsg 139
                                       +      +rSVvv+G++ e  + +e + al +l+ +   +p+   w+++         +t+ ++l+i++  g
  gi|344210230|ref|YP_004786406.1|  81 SV-----WRSVVVTGELVEA-TYDEVEPALASLASNTqfAPNPvsWDDTS--------TTTPYELRIDDWYG 138
                                       44.....*********8888.44444444444444332377667788666........56666666666555 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.4e-07   0.00084       3      80 ..       7      91 ..       5      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.4e-07
                                      HHHHHHHHHSSEEEEEEEE.TTSEEEEEEEEEEEETTT..TEEEEEEETTSHHHHHHHHH-EEEEEEEETT....GSEE CS
                    Putative_PNPOx  3 eelreflaeskavvlATvd.edGrPnvspvllkagdgr..dgivfatnadsrklrnleenprvallfldde....lgrg 74
                                      e ++++l +  ++vlA  +  +  P+ +pv + +++++    + ++ + +s+k+r l ++  v+++++++       r+
  gi|344210230|ref|YP_004786406.1|  7 ETVVDVLTDNGIGVLALSSpMEAAPYPVPVAFGYDPATdsLAFHLSESDESQKHRYLTADATVGFTVYEETepksVWRS 85
                                      566788888999999987756899**************665666689999********************998777777 PP

                                      EEEEEE CS
                    Putative_PNPOx 75 vrieGt 80
                                      v + G+
  gi|344210230|ref|YP_004786406.1| 86 VVVTGE 91
                                      777765 PP

>> FMN_bind_2  Putative FMN-binding domain
   #    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       9      78 ..       3      71 ..       1     111 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.1e-05
                                      X--HCHHHHHHHHS-EEEEEEEETTEEEEEEEE-EE...-TTSSEEEEEEETTSGGGGGT.TTS-EEEEE CS
                        FMN_bind_2  9 eedleelrqlirenplgtLvtaiesglqashiPflldeeekgkgkLrgHlaraNpqakaleeeeevlvvf 78
                                      e + e++ +++ +n++g+L  +++ +     +P+ +   +  ++ L +Hl+++++  k+   +++++v f
  gi|344210230|ref|YP_004786406.1|  3 ELRDETVVDVLTDNGIGVLALSSPMEAAPYPVPVAF-GYDPATDSLAFHLSESDESQKHRYLTADATVGF 71
                                      56788999*****************99999***999.77888889*******999887763333344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 936.20
//
Query:       gi|344210231|ref|YP_004786407.1|  [L=611]
Description: putative long-chain-fatty-acid-CoA ligase [Haloarcula hispanica ATCC 33960]
Scores for complete 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  164.5   0.0    4.2e-48  164.0   0.0    1.2  1  AMP-binding      AMP-binding enzyme
    5.5e-09   36.7   6.6    5.5e-09   36.7   6.6    2.1  3  Hemerythrin      Hemerythrin HHE cation binding domain
  ------ inclusion threshold ------
      0.071   13.3   0.0       0.69   10.1   0.0    2.4  2  AsnC_trans_reg2  AsnC-like ligand binding 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 !  164.0   0.0   7.1e-52   4.2e-48       1     411 [.     202     608 ..     202     610 .. 0.84

  Alignments for each domain:
  == domain 1  score: 164.0 bits;  conditional E-value: 7.1e-52
                                       HHHHHHHSTTSEEEEE..CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEE CS
                       AMP-binding   1 leeqaaktpdkvalvd..sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvv 75 
                                       +e+ +  + d++a     +ge    +++e+ er++++A gL+s  +++gdr ai ++  +ew v++la+  aG+v+v
  gi|344210231|ref|YP_004786407.1| 202 FEDIVSDHGDRTAALVrdDGEFVERSFEEMAERAKAVAGGLLSTELRPGDRLAIRAQSQYEWSVLDLACHFAGLVPV 278
                                       567778889888875558999*********************99********************************* PP

                                       EEETTS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSC CS
                       AMP-binding  76 plnptltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpee 152
                                        l+p+ ++++ a+i+e ++a+ l+          + ++a++l + ++++vld ++l+++      e   ++   p  
  gi|344210231|ref|YP_004786407.1| 279 ALYPSASNDRAAQIIERTGATGLV--A-------AGDEAGDL-SMAVETVLDFEALPTA------EA--RVL--P-- 333
                                       ************************..2.......22333433.5666778886554433......31..222..2.. PP

                                       CCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT- CS
                       AMP-binding 153 eeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGa 229
                                         +++ d++a++ +      +  G+ l+hrnl+a++ sl   +   ++++ +  + lplahi++  +++++  + G+
  gi|344210231|ref|YP_004786407.1| 334 GLQTDGDEVATVAFDVAAPAEKAGCALTHRNLLAAAESLR--EGLPTGPGATGTCSLPLAHIYQR-VATYYLWATGS 407
                                       336799********************************74..44556678899***********6.*********** PP

                                       EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHH.............HHCCCHHCHHHHC............. CS
                       AMP-binding 230 tvvllpkdaaldpklllelieklkvtviagvPrvleal.............lesgalkaakkak............. 280
                                       +v +l+ +++      +e++++ k+ v++gvP ++++l             +         k+k             
  gi|344210231|ref|YP_004786407.1| 408 AVAYLEAEEF------VEQLAAVKPDVLVGVPKMYQQLygtiqdrlgdmgwM---------KRKvggrvasygqgiv 469
                                       ****997766......799999****************98855444443331.........4444455566666777 PP

                                       ........................CGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTC CS
                       AMP-binding 281 ........................dlsslrlvllggeplspellrffralfgeevlegYGlTEttgvvtvlpleedk 333
                                                                ls l ++l+g ++l  +ll ffr l+ + + e+YG   ttgv + l++  + 
  gi|344210231|ref|YP_004786407.1| 470 egrgtplkyraakrlvykplrretGLSNLTYALSGTGRLDDHLLYFFRGLGVP-ICELYGSVGTTGVGA-LNPAAS- 543
                                       7777777777777888888888878888999*******************875.**************9.775555. PP

                                       TSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEE CS
                       AMP-binding 334 kklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyl 410
                                        +  s+G p+pgve+++ +             e+lvrgp+v  g+l  ++  a+++   ++w++TG +g++ +dG+l
  gi|344210231|ref|YP_004786407.1| 544 FVEESIGDPMPGVEIAVSESR-----------EILVRGPTVLGGFLDGDQTGAQTLR--DDWYHTGEVGEVGPDGEL 607
                                       67889************8887...........9*************99899999997..57**************98 PP

                                       E CS
                       AMP-binding 411 e 411
                                        
  gi|344210231|ref|YP_004786407.1| 608 S 608
                                       6 PP

>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   6.6   9.2e-13   5.5e-09       2     122 ..      20     131 ..      19     136 .. 0.85
   2 ?   -3.1   0.1       1.9   1.1e+04      68      96 ..     208     237 ..     202     249 .. 0.57
   3 ?   -2.8   0.0       1.5     9e+03      10      31 ..     362     383 ..     359     400 .. 0.58

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 9.2e-13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHCCHHHHHHHHHHHHHHHHHHHHHHC..HHHHH.CCC.HHHHHHH CS
                       Hemerythrin   2 ivealdeeHralrallerlraladaaaevhgalrklaelldelvdeleaHhaaEEell..fPlledrpggravldvl 76 
                                        +e++de+H++l+ ll++l++++++  +     +++ ++l+el++++e H+ +EEe +    +   + +  + +  +
  gi|344210231|ref|YP_004786407.1|  20 NIERFDEQHKRLFGLLNDLHTAMNEGHS----EEEVGDILRELERYTEYHFGDEEEFMqnCGY---AMDCSDCFYNH 89 
                                       5899***************999998444....369**********************855333...44789****** PP

                                       HHHHHHHHHHHHHHHHHCHTCGGSTCHHHHHHHHHHHHHHHHHHHH CS
                       Hemerythrin  77 ereHdeirelleelrellkgleepsaaafaelleeladllreHiak 122
                                       ++ H+e++ +++elre  ++ e      + e l++ +d+l+ Hia 
  gi|344210231|ref|YP_004786407.1|  90 REMHEEFAGKVQELREKHENGE----YVTMEVLTVARDWLDAHIAA 131
                                       ***************5555555....47777*************86 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.9
                                       C.HHHHHHHHHHHHHHH.HHHHHHHHHCHT CS
                       Hemerythrin  68 ggravldvlereHdeir.elleelrellkg 96 
                                       ++ +++++l r+  e+  + +ee++e +k 
  gi|344210231|ref|YP_004786407.1| 208 DHGDRTAALVRDDGEFVeRSFEEMAERAKA 237
                                       556666666666666664333444433333 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHHHHHHHHHC CS
                       Hemerythrin  10 Hralrallerlraladaaaevh 31 
                                       Hr+l+a +e lr+ + + +++ 
  gi|344210231|ref|YP_004786407.1| 362 HRNLLAAAESLREGLPTGPGAT 383
                                       6666666666666555544444 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 ?   -0.7   0.0      0.28   1.7e+03      47      69 ..      42      64 ..      41      71 .. 0.85
   2 ?   10.1   0.0   0.00012      0.69      33      65 ..     391     423 ..     388     433 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.28
                   AsnC_trans_reg2 47 mvharseeeveevlaeiaaatgl 69
                                      m  ++seeev  +l+e+++ t+ 
  gi|344210231|ref|YP_004786407.1| 42 MNEGHSEEEVGDILRELERYTEY 64
                                      677899**********9998865 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00012
                   AsnC_trans_reg2  33 tHcYeRewpynlyfmvharseeeveevlaeiaa 65 
                                       +H+Y+R  +y l+++ +a    e ee+++++aa
  gi|344210231|ref|YP_004786407.1| 391 AHIYQRVATYYLWATGSAVAYLEAEEFVEQLAA 423
                                       7**************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 4237.48
//
Query:       gi|344210232|ref|YP_004786408.1|  [L=76]
Description: hypothetical protein HAH_5291 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   11.3   7.5       0.29   11.2   7.5    1.1  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 ?   11.2   7.5   1.6e-05      0.29      35      80 ..      13      72 ..       4      76 .] 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.6e-05
                   Phage_holin_3_6 35 sgagllgaagvlallalllllvala................lalaalwlaalivaavllvla 80
                                      s ++ ++aa+vl +l+++++++ ++                +a+  +++a+l+v + l++l+
  gi|344210232|ref|YP_004786408.1| 13 SILATVVAAAVLYILMVGFFVFVVLprsrlpsariaairrdWAI--SAAAYLVVLVPLVALG 72
                                      55777888888888999988888878999999777544444444..6777777766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 514.72
//
Query:       gi|344210233|ref|YP_004786409.1|  [L=256]
Description: hypothetical protein HAH_5292 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   0.8       0.19   11.8   0.8    1.4  1  DZR            Double zinc ribbon
       0.23   11.5   1.6       0.57   10.2   1.6    1.6  1  Zn_Tnp_IS1595  Transposase 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 ?   11.8   0.8   2.1e-05      0.19       8      39 ..     221     253 ..     215     256 .] 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.1e-05
                               DZR   8 lppdarfCseCgtk.lkavaaedrCpsCgekvd 39 
                                        + d + C++Cg++ ++ va++ +C +C++++ 
  gi|344210233|ref|YP_004786409.1| 221 YDTDHHRCPHCGSTdVNWVAESVVCLRCSRPTA 253
                                       6778889*****887998999*******99864 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   1.6   6.4e-05      0.57      17      40 ..     224     248 ..     222     250 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6.4e-05
                     Zn_Tnp_IS1595  17 ngfvCPhCgsr.kayriktrglfqC 40 
                                       ++++CPhCgs+   +  ++   ++C
  gi|344210233|ref|YP_004786409.1| 224 DHHRCPHCGSTdVNWVAESVVCLRC 248
                                       5689******944444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1938.85
//
Query:       gi|344210234|ref|YP_004786410.1|  [L=282]
Description: hypothetical protein HAH_5293 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2163.42
//
Query:       gi|344210235|ref|YP_004786411.1|  [L=308]
Description: hypothetical protein HAH_5294 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   14.4   0.2       0.11   12.9   0.2    1.8  1  Rrf2      Transcriptional regulator
       0.12   12.2   1.6          1    9.2   1.3    2.8  3  HTH_IclR  IclR helix-turn-helix domain
       0.19   11.5   3.3        1.4    8.8   1.1    2.7  2  HTH_DeoR  DeoR-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   1.8e-05      0.11      14      56 ..     243     284 ..     241     287 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                                       HHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2  14 llyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56 
                                       +++La+  +++  s++e+ +r ++s+++++++l++L   +lv+
  gi|344210235|ref|YP_004786411.1| 243 VADLAQTVTQS-TSLDEVTQRLDLSQTHARRLLSELDLLDLVT 284
                                       67888888877.************************9999987 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 ?   -1.4   0.0      0.35   2.1e+03       7      19 ..      12      24 ..      11      29 .. 0.82
   2 ?   -3.9   0.0       2.1   1.2e+04      17      28 ..      95     106 ..      93     109 .. 0.71
   3 ?    9.2   1.3   0.00017         1      17      48 ..     252     283 ..     216     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.35
                                      HHHCT-CTTBSS- CS
                          HTH_IclR  7 aiLdalaeapqel 19
                                      ++L++l + + e+
  gi|344210235|ref|YP_004786411.1| 12 QVLECLDSSDTEV 24
                                      89****9998876 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.1
                                       SS-BHHHHHHHH CS
                          HTH_IclR  17 qeltlselArrt 28 
                                       q+ t  elA+ +
  gi|344210235|ref|YP_004786411.1|  95 QGGTSNELAETL 106
                                       667788898865 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00017
                                       SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  17 qeltlselArrtglpkStvhRlLqtLvelGyv 48 
                                       q  +l e+ +r++l+ + ++RlL+ L  l +v
  gi|344210235|ref|YP_004786411.1| 252 QSTSLDEVTQRLDLSQTHARRLLSELDLLDLV 283
                                       556999******************99766666 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 ?    1.7   0.0     0.036   2.2e+02      25      33 ..     141     149 ..     133     156 .. 0.84
   2 ?    8.8   1.1   0.00023       1.4      13      44 ..     252     283 ..     242     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.036
                          HTH_DeoR  25 gvSeaTiRR 33 
                                       +v+ +T+RR
  gi|344210235|ref|YP_004786411.1| 141 DVTSETVRR 149
                                       79******9 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00023
                          HTH_DeoR  13 gklsveelvellgvSeaTiRRDLneLeeqgll 44 
                                       ++ s++e++++l+ S++ +RR L+eL+  +l+
  gi|344210235|ref|YP_004786411.1| 252 QSTSLDEVTQRLDLSQTHARRLLSELDLLDLV 283
                                       46689*******************99877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); 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:                         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 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2053.04
//
Query:       gi|344210236|ref|YP_004786412.1|  [L=432]
Description: N-ethylammeline chlorohydrolase [Haloarcula hispanica ATCC 33960]
Scores for 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-49  166.7   0.1    9.9e-49  166.5   0.1    1.1  1  Amidohydro_1  Amidohydrolase family
      3e-19   69.9   2.6      6e-14   52.4   0.6    2.2  2  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
      0.014   14.8   0.1      0.023   14.1   0.1    1.3  1  TatD_DNase    TatD related DNase


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 !  166.5   0.1   1.7e-52   9.9e-49       1     344 []      50     403 ..      50     403 .. 0.89

  Alignments for each domain:
  == domain 1  score: 166.5 bits;  conditional E-value: 1.7e-52
                                       EEEE-EEEEEEECETTECSSS.......GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSST CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga.......tledwl..........vppetaaealesgiktalksGtttvadmgatts 60 
                                       +v+PGl++ H+H +  ++rga        + + l           ++++a+  +   ++++l+sG+tt++d +    
  gi|344210236|ref|YP_004786412.1|  50 VVIPGLVNCHTHMYALPIRGAplaaspeSFYEALvdiwwnvdeaFTERDARLSALGSCAEMLQSGVTTFCDNYSGPN 126
                                       69*******************99997774444447888999*********************************777 PP

                                       H...HHHHHHHHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHH CS
                      Amidohydro_1  61 t...giealleaaeelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeel 134
                                       t   g++a++  + ++   +r ++++   +r s+++ ++ + +  + ++et+     + v+ +   h  ++++++ +
  gi|344210236|ref|YP_004786412.1| 127 TlpgGLDAVAAGVAQT--PIRGMIAFETTARNSESQARDGIAENQRFIDETEE--RYDTVSGHYCLHTLFTNTEDIV 199
                                       7999999999999998..89999999999995556666666666566655554..4567889*************** PP

                                       HHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHH CS
                      Amidohydro_1 135 kealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlk 211
                                       +e+++ a ++d p++iH+ e   +v +++a++g   ++  ++  +e+ g++d   +i+ah+vh t +e+e+l+e+  
  gi|344210236|ref|YP_004786412.1| 200 EECVDRATDHDRPIQIHLEEGLVDVHESIADYG---KR--PVPALEDMGFFDA-EVIAAHCVHSTESEIEILAEN-- 268
                                       *********************************...88..*************.*********************.. PP

                                       HHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHH CS
                      Amidohydro_1 212 eagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrm 288
                                       +++vah p sn + + g+++++ +  + + +glg D    g  ++++e++r a+ +++++ + ++ g ++ + al++
  gi|344210236|ref|YP_004786412.1| 269 DVNVAHNPYSNINNAVGIADVETMQANEMTIGLGDD----GWDPDMFETMRSAVGIHKLKQR-NPSG-FDMATALEW 339
                                       ************************************....9*************99994444.6666.********* PP

                                       HTHHHHHHTT-TTTSSSS-TTSB--EEEECC..CT......CGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 289 aTingAkalglddkvGsievGkdADlvvvdl..di......laafvglkkdgnvkkvivkGklv 344
                                       aTi+ A +lg+dd vGsievGk+ D+v +dl  ++         +v  ++   v+++i++G++v
  gi|344210236|ref|YP_004786412.1| 340 ATIGSAAVLGMDDAVGSIEVGKRGDFVTLDLgpNPvldgsaPYYVVSAASRADVTRTIIDGETV 403
                                       *******************************653378887433445566778899999999987 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   3.2e-07    0.0019       1      23 [.      42      64 ..      42      85 .. 0.84
   2 !   52.4   0.6     1e-17     6e-14     248     473 .]     187     404 ..      89     404 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.2e-07
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlag 23
                                      +viDa+  +v+PG+v  HtH+++
  gi|344210236|ref|YP_004786412.1| 42 DVIDATDEVVIPGLVNCHTHMYA 64
                                      69******************876 PP

  == domain 2  score: 52.4 bits;  conditional E-value: 1e-17
                      Amidohydro_3 248 lltepyftgwpdfedealaelvaaadergldvaihaigdaavd..dvldafeaa....aekngnqdrrrlehaegv. 317
                                       +l+        + +++ ++e+v++a++++ ++ ih  +    d  + ++ + ++     e++g+ d  +++ a  v 
  gi|344210236|ref|YP_004786412.1| 187 CLHT-----LFTNTEDIVEECVDRATDHDRPIQIHLEEGLV-DvhESIADYGKRpvpaLEDMGFFDA-EVIAAHCVh 256
                                       3333.....22344445******************976554.4369999999999999999999999.555555555 PP

                      Amidohydro_3 318 .tesqiervaalqvaagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsDapvgpfdpwprigaavmr 393
                                        tes+ie +a+  v  +  p +n+           ++a g++ v ++ ++ +++ lg+D  +  +d + ++++av  
  gi|344210236|ref|YP_004786412.1| 257 sTESEIEILAENDVNVAHNPYSNI-----------NNAVGIADVETMQANEMTIGLGDD--GWDPDMFETMRSAVGI 320
                                       6******************99999...........899*********************..7777777788888876 PP

                      Amidohydro_3 394 ktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld..........adpldvdppelaea 460
                                        + ++    r    +++ +al   T g+A++lg++d  G++evG+++D+v ld          a    v ++ +a+ 
  gi|344210236|ref|YP_004786412.1| 321 HKLKQ----RNPSGFDMATALEWATIGSAAVLGMDDAVGSIEVGKRGDFVTLDlgpnpvldgsAPYYVVSAASRAD- 392
                                       67655....5788***********************99****************9877766644444444443333. PP

                      Amidohydro_3 461 rvrltvvdGrvvy 473
                                        v  t++dG++vy
  gi|344210236|ref|YP_004786412.1| 393 -VTRTIIDGETVY 404
                                       .***********8 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   3.9e-06     0.023     107     174 ..     193     272 ..     180     297 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.9e-06
                                       HHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCS............EEEETT--S-HHHHHHHHHTT CS
                        TatD_DNase 107 eaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeaka............kvvlHsfsgsaeeakkflklg 171
                                          e++ ee+++ A ++++p++iHl++   d+ e++ +++++++             +  H+  +++ e++ +++ +
  gi|344210236|ref|YP_004786412.1| 193 TNTEDIVEECVDRATDHDRPIQIHLEEGLVDVHESIADYGKRPVpaledmgffdaeVIAAHCVHSTESEIEILAEND 269
                                       5678999********************99999999977776666667777777777555666666666666665555 PP

                                       EEE CS
                        TatD_DNase 172 yyi 174
                                       + +
  gi|344210236|ref|YP_004786412.1| 270 VNV 272
                                       555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3016.67
//
Query:       gi|344210237|ref|YP_004786413.1|  [L=447]
Description: dihydroorotase [Haloarcula hispanica ATCC 33960]
Scores for complete 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   63.4   0.0      4e-17   62.5   0.0    1.4  1  Amidohydro_1  Amidohydrolase family
    7.4e-06   25.7  11.8      0.012   15.1   3.5    3.1  3  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
       0.13   12.6   0.4       0.44   10.9   0.4    1.9  1  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 !   62.5   0.0   6.7e-21     4e-17       2     344 .]      55     427 ..      54     427 .. 0.73

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 6.7e-21
                                       EEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH....HHHHHHHHHHT.S CS
                      Amidohydro_1   2 vlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst....giealleaaee.l 73 
                                        lPG ID+H+H  +++l    + d           ++s ++ a+ +G+ttv++ ++ t+     +++  + a+++ +
  gi|344210237|ref|YP_004786413.1|  55 ALPGAIDVHTHMHDDEL----FPDG--------IDFASQTASAVAGGVTTVIELPTQTPVttpeAMQEKAAACSAlA 119
                                       69**********98875....3333........34444455566666666666666443354448888888999998 PP

                                       SSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEE CS
                      Amidohydro_1  74 plglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvai 150
                                        +++++++g       +++++++++  ++ag a+++ ++           + ++ +sd+ ++ +++ + +++  v +
  gi|344210237|ref|YP_004786413.1| 120 HVDFGLVAG------NVQDPDIDVAGIVDAGTADFKTFT-----------ADPYLASDASIARLMRRVGDAGGTVRV 179
                                       889999999......9***************98888866...........6788899******************** PP

                                       EETSSCHHHHHHHHHHTTTEEEETTTTSTCC.............HHTTTHCCEEEHCTCEEE.HHHHHHHHHHHHHH CS
                      Amidohydro_1 151 Haletkgevedaeaafgetiehgthlevaes.............lglldeiklilahgvhlt.pteaellkerlkea 213
                                       H+ et+g   da+ a++++  +     v+++             +g + e+  +  h vh++  + a+  ++ + +a
  gi|344210237|ref|YP_004786413.1| 180 HC-ETQGLLDDARSAIDGDEPE-----VYMDsrpleaeldaisrAGYFAEYADCPLHVVHISsGSGAREGDRFKSRA 250
                                       **.**************55555.....44444444466666666333333333345555555533333333333334 PP

                                       CEE.......................HHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECT...............TSS CS
                      Amidohydro_1 214 gva.......................hcpfsnsilrsgrealrkaldeGvkvglgtDga...............asg 252
                                       +v+                       +   ++++++ +re+l++a+++G++  +gtD+                   
  gi|344210237|ref|YP_004786413.1| 251 NVPvtletcpqylafskgdvaehgpfLKVNPSLKSDAERERLWDAVQDGTIDLIGTDHFptyretrdvgwddiwE-- 325
                                       4445566666666566666667666666668888***********************887776655555544440.. PP

                                       CCGGHHHH......HHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC..CT CS
                      Amidohydro_1 253 nslnllee......lrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl..di 321
                                                     +  ++   +++  ++ e+ +s+ ++ ++++  +A+  g++ k+Gs++vG dAD  +v +  + 
  gi|344210237|ref|YP_004786413.1| 326 -------PyaglpgVETMV--EFLVSEGVHEDRISWPRLRELVCAAPAQNAGIYPKKGSLQVGTDADVMLVRTeeYE 393
                                       .......344444333343..444455577788**************************************997622 PP

                                       ...........CGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 322 ...........laafvglkkdgnvkkvivkGklv 344
                                                   ++++g+  +  v++v+ +G++v
  gi|344210237|ref|YP_004786413.1| 394 vtadgltfvggWTPYEGQQWSARVDTVVAGGEVV 427
                                       67788899999999999999999*****999987 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   3.5   2.1e-06     0.012       2      21 ..      47      66 ..      46      95 .. 0.88
   2 !    4.5   0.2    0.0032        19     242     310 ..     146     209 ..      80     227 .. 0.79
   3 !   10.9   0.1   3.7e-05      0.22     407     472 ..     349     427 ..     310     428 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-06
                      Amidohydro_3  2 viDakGrlvlPGFvDsHtHl 21
                                      viDa+G++ lPG +D+HtH+
  gi|344210237|ref|YP_004786413.1| 47 VIDADGMVALPGAIDVHTHM 66
                                      9******************6 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0032
                      Amidohydro_3 242 lgsrtalltepyftgwpdfedea.laelvaaadergldvaihaigdaavddvldafeaaaekngnqdrr.r 310
                                        + +t++++       p + ++a +a+l++++ ++g  v++h+ +++ +dd+  a++   ++  +  r+ +
  gi|344210237|ref|YP_004786413.1| 146 ADFKTFTAD-------PYLASDAsIARLMRRVGDAGGTVRVHCETQGLLDDARSAIDGDEPEVYMDSRPlE 209
                                       444444444.......44467777*************************9999999988888777777554 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 3.7e-05
                      Amidohydro_3 407 elsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaear.............vrltvvdGr 470
                                       ++s+  +  l+ + pA+  g   +kG+L+vG dAD+++ +++  +v+++ l  ++             v  +v +G+
  gi|344210237|ref|YP_004786413.1| 349 RISWPRLRELVCAAPAQNAGIYPKKGSLQVGTDADVMLVRTEEYEVTADGLTFVGgwtpyegqqwsarVDTVVAGGE 425
                                       6677777777888999999999999***************9999999986666669999999999998999999999 PP

                      Amidohydro_3 471 vv 472
                                       vv
  gi|344210237|ref|YP_004786413.1| 426 VV 427
                                       88 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 ?   10.9   0.4   7.3e-05      0.44      66     101 ..       2      37 ..       1      54 [. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.3e-05
                      Urease_alpha  66 lDlvitnavilDatgivkadigikdgrivaiGkagn 101
                                       +D+ i +a ++ a+gi + +i+i dg+i a G a  
  gi|344210237|ref|YP_004786413.1|   2 TDIHIKDAQVVTASGIQHGEIAISDGTIDAAGPASS 37 
                                       68999*************************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3094.06
//
Query:       gi|344210238|ref|YP_004786414.1|  [L=404]
Description: threonine synthase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-71  239.9   0.8    4.6e-71  239.6   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 !  239.6   0.8   2.6e-75   4.6e-71       2     294 .]      63     364 ..      62     364 .. 0.96

  Alignments for each domain:
  == domain 1  score: 239.6 bits;  conditional E-value: 2.6e-75
                                       GGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT CS
                              PALP   2 tlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallG 78 
                                       tl +g+T l ++p+ls++lgv+ ++K+++ nptg fKdR+ + +++++k + g++ +++as+GN++++l+ +aa+ G
  gi|344210238|ref|YP_004786414.1|  63 TLNEGGTDLFDAPNLSDALGVETLVKDDGRNPTGCFKDRASAIAVTKAKHA-GRDIITCASTGNAAASLSGYAARGG 138
                                       7899***********************************************.************************* PP

                                       -EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTT CS
                              PALP  79 lkvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlg 155
                                       ++++i+vp da+++k+a+   +Ga+v  v+g+ydea ++  e++++ +g+y+ +   np  +eg  t+g E+++q  
  gi|344210238|ref|YP_004786414.1| 139 MDCRIFVPGDAPTGKLAQPLVYGADVLAVNGSYDEAYDLSVEVTEK-YGWYNRNAAINPFQVEGKRTVGHELADQSI 214
                                       **********************************************.*************************74433 PP

                                       ...TTEEEEEEE-SSSHHHHHHHHHHHH......HSTT..-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCST CS
                              PALP 156 ...gkpdavvvpvGgGgliaGiaaglke......rrpd..vrvigvepegsdalarslragrrvtvpvsdtiadgla 221
                                          ++pd+vv ++G G +iaG ++g+ke         d  ++++gv+++g++a+++++ + + +  + ++t+ad++a
  gi|344210238|ref|YP_004786414.1| 215 argHVPDWVVFSMGDGCTIAGAWKGFKEfydlgyV--DdhPQMLGVQADGASAIHDAF-HDHDDIDDIAETLADSIA 288
                                       678*************************9988644..246******************.8888888888******** PP

                                       CS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 222 vg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                       vg  +++ +a ++l++++++ v vsd+e+l+a +ll ++egi  ep++aa +a++ +++++g ++++++vvv+ tg
  gi|344210238|ref|YP_004786414.1| 289 VGrpRNTLKACRALEQSGGTSVLVSDDEILAAEKLLGSTEGIYSEPAGAAPIAGVqTALDRGIIEQDETVVVVSTG 364
                                       **9999999999*************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2857.90
//
Query:       gi|344210239|ref|YP_004786415.1|  [L=344]
Description: F420-dependent N5,N10-methylene-tetrahydromethanopterin reductase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-59  200.9   0.0    3.8e-59  200.7   0.0    1.0  1  Bac_luciferase  Luciferase-like monooxygenase
  ------ inclusion threshold ------
      0.039   14.3   0.3       0.56   10.6   0.0    2.5  2  DUF3243         Protein of unknown function (DUF3243)


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 !  200.7   0.0   4.2e-63   3.8e-59      17     312 ..      19     320 ..       6     322 .. 0.89

  Alignments for each domain:
  == domain 1  score: 200.7 bits;  conditional E-value: 4.2e-63
                    Bac_luciferase  17 aasaslrylvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatL 93 
                                       ++ +sl+++vel++ aEe G d +w ae+ +     +da+++l+a aa+T+ i+lgt+v + +tr+ a++Aq+  tL
  gi|344210239|ref|YP_004786415.1|  19 DK-HSLEENVELVQYAEEQGIDEIWQAESRLA----RDAVSPLGAYAAVTDDIKLGTGVINNWTRNAALIAQSMSTL 90 
                                       33.49**************************9....***************************************** PP

                    Bac_luciferase  94 dhlsg.GRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgp... 166
                                       ++l+g  R+ +g+g+++++   ++ G+d++  ++ +rE vev + l+  e v+++Gef++++++ l    g+++   
  gi|344210239|ref|YP_004786415.1|  91 EELAGpDRIMCGIGAWWDPLA-EKVGIDRSGALRAMRECVEVTQDLLDMENVTYDGEFVQMRDVELDVVHGDDGprt 166
                                       ****989*************9.888**********************88888*******996665555554444568 PP

                    Bac_luciferase 167 iPvyvaaaspaglelaarhadglllag.eppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraear 242
                                       +Pvyv++++ ++lel++ +adg ll+   +pe  +++++ l+ ga++ +r+ +di+    + +++++++e+A+++ar
  gi|344210239|ref|YP_004786415.1| 167 VPVYVGGTGFKMLELTGHFADGALLNYlVSPEYNEKALDALKTGAERGDRSLDDIDRPQLVVCSMDHDQEKALDNAR 243
                                       9**************************************************************************** PP

                    Bac_luciferase 243 aliagld......fyaldsegagreaeaa.eiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagv 312
                                       +li ++       ++a+  +    ++ ++   + + d+ + ++ ++++pd++v+++++ Gtpeq++e++++yae+g 
  gi|344210239|ref|YP_004786415.1| 244 ELITQYLgqqphiMKASGVSQDLIDEVGEtIGGWPADKDDIEEGMHLIPDDVVHKLTASGTPEQCREKVREYAETGC 320
                                       ***88879888853333333333333333355*******************************************96 PP

>> DUF3243  Protein of unknown function (DUF3243)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2     0.065   5.8e+02      47      64 ..      30      47 ..       1      56 [. 0.56
   2 ?   10.6   0.0   6.2e-05      0.56      10      44 ..     247     281 ..     242     287 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.065
                                      --SHHHHHHHHHHHC--H CS
                           DUF3243 47 pknkeerlLkeLWkvade 64
                                       + +ee+ + e+W++ + 
  gi|344210239|ref|YP_004786415.1| 30 VQYAEEQGIDEIWQAESR 47
                                      345677788888877655 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 6.2e-05
                                       HHHHHHHHHHHHHHHHHTT----HHHHHHHHHHT- CS
                           DUF3243  10 kkfLgdrveqaeklGlseetieklAyevGdyLaek 44 
                                       +++Lg++ + +++ G+s++ i+++ +++G++ a+k
  gi|344210239|ref|YP_004786415.1| 247 TQYLGQQPHIMKASGVSQDLIDEVGETIGGWPADK 281
                                       589***************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2630.26
//
Query:       gi|344210240|ref|YP_004786416.1|  [L=330]
Description: sugar ABC transporter permease [Haloarcula hispanica ATCC 33960]
Scores for 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-38  130.4  28.9    6.6e-38  130.4  28.9    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 !  130.4  28.9   3.7e-42   6.6e-38       4     245 ..      11     258 ..       8     286 .. 0.89
   2 ?   -2.6   0.0      0.13   2.4e+03      68      87 ..     298     317 ..     290     320 .. 0.79

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 3.7e-42
                      BPD_transp_2   4 nlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrl 80 
                                        ++  a++l++a++G  l+  +aGv+nlg++g+m++Ga   ++  +  +s  +l++ v++l+g++++l+ ++l++ l
  gi|344210240|ref|YP_004786416.1|  11 ATVQAATVLLLAGMGELLSE-RAGVLNLGVEGMMLVGALGGFITTVVTGS-HWLGFGVGILLGMVLALVHAFLCITL 85 
                                       56778999************.*****************************.************************** PP

                      BPD_transp_2  81 kvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv.................llall 140
                                       k +++i++++l+++  glt           +g+ +v e ++ ++++   l++++                  +lal 
  gi|344210240|ref|YP_004786416.1|  86 KSNQVISGVMLTLLGGGLTT---------FFGSGWVEESIDGFPQMTLPLVGQYLvdipvigeaffrstatdYLALG 153
                                       *******************9.........4444444444444444444444444444555557889*********** PP

                      BPD_transp_2 141 lvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfna 216
                                       l+++v+++l+++++G+ + avge++e+a+ +G++v+r++ l+++i+g++Ag aGa+l+l +   ++  +  g g+ a
  gi|344210240|ref|YP_004786416.1| 154 LLVVVWYFLHHSNLGLEMIAVGEDPEMADTMGVSVFRLRYLAVLIGGGFAGAAGAHLSLAFSQLWVpGMTAGRGWIA 230
                                       ************************************************************9999999********** PP

                      BPD_transp_2 217 iaavvlGgagsllgtviGaliigvvksll 245
                                       +a v+ + + +++  ++Ga+++g++++l 
  gi|344210240|ref|YP_004786416.1| 231 VALVIFAQW-RPRRMLVGAYLFGLLDALR 258
                                       *********.***************9964 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.13
                      BPD_transp_2  68 avglllgllvlrlkvdelii 87 
                                       a  l+l+++v+r+k d+l++
  gi|344210240|ref|YP_004786416.1| 298 ATILVLAYAVIRTKSDQLAV 317
                                       56678888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2016.00
//
Query:       gi|344210241|ref|YP_004786417.1|  [L=366]
Description: sugar ABC transporter permease [Haloarcula hispanica ATCC 33960]
Scores for complete 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-34  119.1  32.7    1.8e-34  119.1  32.7    1.7  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 ?   -0.9   0.3     0.041   7.4e+02     228     246 ..      22      40 ..      10      57 .. 0.52
   2 !  119.1  32.7     1e-38   1.8e-34       2     267 ..      62     335 ..      61     336 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.041
                      BPD_transp_2 228 llgtviGaliigvvkslll 246
                                       ++ tv++al++++v  + l
  gi|344210241|ref|YP_004786417.1|  22 PVFTVLAALAVSAVALVVL 40 
                                       3334444444443333333 PP

  == domain 2  score: 119.1 bits;  conditional E-value: 1e-38
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl....lllallvallvgaavglllg 74 
                                       + ++lt+a +l++++l+++l   +aG++n+g++g+++ Ga + +++  ++  +    ++l++++a ++g++++ + +
  gi|344210241|ref|YP_004786417.1|  62 LTETLTKAVPLILTGLAVYLPL-KAGLFNIGAEGQLVAGALAGTWIGLNVSLPglalVPLMFVAAAVAGGIWAGIPA 137
                                       6689******************.****************888777776666666999******************** PP

                      BPD_transp_2  75 llvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv..llalllvlavllll 149
                                       +l +++ v+e+i++lll++v++ +  +ll+g+ +g +g+  ++e +  a ++   +s+v +  l+a+ +v++ ++l+
  gi|344210241|ref|YP_004786417.1| 138 YLRAKWDVNEIITSLLLTFVALEIQSYLLRGPMQGGTGNFPQSERFSEAATIPELVSGVHAglLVAVCMVVVTYVLM 214
                                       ********************************************999999999999999989777777888889999 PP

                      BPD_transp_2 150 rrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGga 225
                                       +rtr+G+ +  vg+n  aa+ +G++ + v ll+fv++ga+A++ G+  ++  ++ +   + +g+gf+ai +++lG +
  gi|344210241|ref|YP_004786417.1| 215 TRTRLGFEITFVGSNDAAAQQAGMSKFYVYLLVFVVGGAFAAMGGISEIAGAQGRYRaGFEPGYGFTAIPIALLGRN 291
                                       *************************************************999999988******************* PP

                      BPD_transp_2 226 gsllgtviGaliigvvksllltllgi....ptelarvllgallilv 267
                                        s+l +++++l ++v+   ++++  +    p +l  +++ ++++++
  gi|344210241|ref|YP_004786417.1| 292 -SALKVLLAGLFFAVLFVGGSSME-VafgvPAALVEIIQALVILFL 335
                                       .***************99555554.4477799******99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); 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:                         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 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2436.79
//
Query:       gi|344210242|ref|YP_004786418.1|  [L=554]
Description: ribose ABC transporter ATP-binding protein RbsA [Haloarcula hispanica ATCC 33960]
Scores for complete 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  160.9   0.0      5e-29  101.6   0.0    2.2  2  ABC_tran     ABC transporter
    7.4e-10   39.1   0.9    0.00054   19.9   0.0    2.6  3  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
  ------ inclusion threshold ------
      0.012   15.4   0.6       0.03   14.0   0.0    1.9  3  AAA_29       P-loop containing region of AAA domain
      0.013   15.5   0.1       0.39   10.6   0.0    2.3  2  RsgA_GTPase  RsgA GTPase
       0.03   13.9   0.0      0.056   13.0   0.0    1.4  1  AAA_27       AAA domain
      0.038   13.7   0.0       0.22   11.2   0.0    1.9  2  AAA_15       AAA ATPase domain
      0.039   13.7   0.1        1.2    8.8   0.0    2.2  2  AAA_30       AAA domain
      0.064   13.8   0.0       0.11   12.9   0.0    1.3  1  AAA_23       AAA domain
       0.19   11.5   0.1       0.36   10.6   0.1    1.4  1  Bac_DnaA     Bacterial dnaA  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 !  101.6   0.0   2.5e-32     5e-29       2     137 .]      23     198 ..      22     198 .. 0.93
   2 !   57.4   0.0   1.1e-18   2.1e-15       1     136 [.     302     460 ..     302     461 .. 0.89

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 2.5e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                       ++v+l++++ge+++++GenGaGKStL+k+l+gl++++ G+i ldg+ l+   +    ++ ig+++q+  l p+ltv+
  gi|344210242|ref|YP_004786418.1|  23 DHVNLSVERGEIHGLLGENGAGKSTLMKILYGLYSQDHGDIYLDGERLDLeSPQDAIDAGIGMVHQHFMLIPRLTVA 99 
                                       689*******************************************9998789999********************* PP

                                       HH...........................................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-H CS
                                       xx...........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en...........................................esdeeiekalsklglkelkdtvvksspssLSg 111
                                       en                                             +++i+++++++g + +   ++     +L  
  gi|344210242|ref|YP_004786418.1| 100 ENvvlgerepatafrsdaedswlpaavrnnslvqslagqfslgldVPEQRIQDLADQYGFDIDVSAKI----WELDV 172
                                       *****************999999999999999998888888888888888999999999877666665....9**** PP

                                       HHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 112 GqkqrvalarallkkpkllllDEpta 137
                                       Gq+qrv++ +al ++ +ll+lDEpta
  gi|344210242|ref|YP_004786418.1| 173 GQQQRVEILKALYRDVDLLILDEPTA 198
                                       ************************97 PP

  == domain 2  score: 57.4 bits;  conditional E-value: 1.1e-18
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS...--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx...xxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqe...pqlfpe 73 
                                       l+ ++l++++ge+v+i G +G G   L+++lag  + t+Ge+ ++g+d++  ++++++++ ++++p++       ++
  gi|344210242|ref|YP_004786418.1| 302 LSGIDLTVRQGEIVGIAGVSGNGQKELAEVLAGIRDVTAGELVVNGEDITGaKPKTFVDSGVSFVPEDrlqYGCAED 378
                                       57899*********************************************999***************555455566 PP

                                       SBHHHH....................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEE CS
                                       xxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren....................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkll 130
                                       l+v  n                    e ++ +e+++++++  +   +v ++++  LSgG  q++ lar + ++p+ll
  gi|344210242|ref|YP_004786418.1| 379 LSVMHNatmkdfrdgrfgdrpfldygELRKYAETLVEEFDVRG-VSDVTETNAGDLSGGNLQKLILAREIYRDPDLL 454
                                       6666669999999999999999988877777*********999.556667999************************ PP

                                       EEESTT CS
                                       xxxxxx RF
                          ABC_tran 131 llDEpt 136
                                       ++  pt
  gi|344210242|ref|YP_004786418.1| 455 IANQPT 460
                                       *99998 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.7e-07   0.00054       2      56 ..      35      77 ..      34      91 .. 0.73
   2 !   16.9   0.3   2.2e-06    0.0043     243     299 ..     177     229 ..     173     233 .. 0.89
   3 ?   -2.3   0.0       1.5     3e+03     228     284 ..     424     477 ..     400     489 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.7e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpei 56
                                       +l G Ng+GKS+L+++l++l +            +++g+i  +  +ldl +p  
  gi|344210242|ref|YP_004786418.1| 35 HGLLGENGAGKSTLMKILYGLYS------------QDHGDIYLDGERLDLESPQD 77
                                      689******************75............55555555555555555555 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.2e-06
                            AAA_21 243 rllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                       r+  +l al+r+    +ll++DEp + L P   +rl++ l++l+++g  +i+ TH  
  gi|344210242|ref|YP_004786418.1| 177 RV-EILKALYRDV---DLLILDEPTAVLTPTEAERLFDSLERLTDEGLSIIFITHKL 229
                                       55.7788889888...9**************************************65 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.5
                            AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellke 284
                                       d  e++a +lS G ++ l l+  ++r++   +ll+   p  g +  +++ + e l e
  gi|344210242|ref|YP_004786418.1| 424 DVTETNAGDLSGGNLQKLILAREIYRDP---DLLIANQPTRGVDVGAIEFIRETLLE 477
                                       6678899999999999988877777777...77887777777777777777766544 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.5e-05      0.03      16      39 ..      26      49 ..      20      58 .. 0.80
   2 ?   -3.6   0.0       4.8   9.6e+03      38      50 ..     192     204 ..     192     207 .. 0.82
   3 ?   -3.7   0.1       5.4   1.1e+04      23      34 ..     312     324 ..     305     325 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                       +++++ +++ l G++G+GKSTl+
  gi|344210242|ref|YP_004786418.1| 26 NLSVERGEIHGLLGENGAGKSTLM 49
                                      56666555899************8 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.8
                            AAA_29  38 llDAiqalLvpak 50 
                                       +lD  +a+L+p++
  gi|344210242|ref|YP_004786418.1| 192 ILDEPTAVLTPTE 204
                                       6888899***987 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 5.4
                            AAA_29  23 g.atlltGpsGsG 34 
                                       g ++ ++G sG+G
  gi|344210242|ref|YP_004786418.1| 312 GeIVGIAGVSGNG 324
                                       4477899999998 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      0.39      99     130 ..      32      63 ..      21      69 .. 0.81
   2 ?    2.5   0.0     0.063   1.2e+02      53     129 ..     256     342 ..     219     350 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                                       TSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelktgev 130
                                       +++  l+G+ G+GKStL++ l +  ++  g++
  gi|344210242|ref|YP_004786418.1|  32 GEIHGLLGENGAGKSTLMKILYGLYSQDHGDI 63 
                                       578889*************9998777766665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.063
                                       EE-GGG--HHH...HHHHHHHHHHHTTSEEE...E--TTTHTTHHHHH...HHCTT.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  53 lnKiDlleeee...eleelkeelealgyevl...lvsaktkegleelk...ellkd.ktsvlvGqSGvGKStLinal 119
                                       ++++Dl+e +     l e+  +  +lg +vl    v+a++++++e+l+     +++ +++ ++G SG G   L ++l
  gi|344210242|ref|YP_004786418.1| 256 VSRADLAEMMVgreVLFEIDRDAVDLGEPVLrarGVEATDNRDIEALSgidLTVRQgEIVGIAGVSGNGQKELAEVL 332
                                       5556665555444434444555555555554111344445555555432114555559999**********999999 PP

                                       CTT-----S- CS
                       RsgA_GTPase 120 lpelelktge 129
                                       ++  ++  ge
  gi|344210242|ref|YP_004786418.1| 333 AGIRDVTAGE 342
                                       9876666555 PP

>> AAA_27  AAA 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      12      57 ..      18      59 ..      12      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                            AAA_27 12 GkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGipert 57
                                      G +++ ++++s e+ ++h ++G N AGKst+++    +l+G+  + 
  gi|344210242|ref|YP_004786418.1| 18 GVVANDHVNLSVERGEIHGLLGENGAGKSTLMK----ILYGLYSQD 59
                                      7788999***********************986....566665555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.22      28      50 ..      37      59 ..      23      88 .. 0.78
   2 ?   -0.1   0.0      0.31   6.1e+02     323     364 ..     187     227 ..     178     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                            AAA_15 28 liGkNnsGKSsilealdlFlnnk 50
                                      l G+N++GKS+++++l+ + +++
  gi|344210242|ref|YP_004786418.1| 37 LLGENGAGKSTLMKILYGLYSQD 59
                                      78***************998876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.31
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       + ++l+++EP a L p   + l+++l +l +++   +i+ TH
  gi|344210242|ref|YP_004786418.1| 187 DVDLLILDEPTAVLTPTEAERLFDSLERLTDEGL-SIIFITH 227
                                       56899*************************9997.8888888 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    0.0006       1.2      19      48 ..      33      62 ..      23      76 .. 0.84
   2 ?    2.3   0.2      0.06   1.2e+02      61     133 ..     152     234 ..     129     270 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0006
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggr 48
                                       ++ l G  G+GK+t++k l  ++ ++ g+
  gi|344210242|ref|YP_004786418.1| 33 EIHGLLGENGAGKSTLMKILYGLYSQDHGD 62
                                      478899**************9999988555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.06
                            AAA_30  61 vLaeelgieastiakllkrlk.........grarlepg.tllivDEagmv.dtkqlaallkaaek...agakvilvG 123
                                       +La++ g++ +  ak+++            +  +l ++ +lli DE   v   +++++l++++e+   +g ++i++ 
  gi|344210242|ref|YP_004786418.1| 152 DLADQYGFDIDVSAKIWELDVgqqqrveilK--ALYRDvDLLILDEPTAVlTPTEAERLFDSLERltdEGLSIIFIT 226
                                       4555555555555555533336677777532..344555*******8777455677777766554211577777773 PP

                            AAA_30 124 DerQlasVea 133
                                         + l+ V+a
  gi|344210242|ref|YP_004786418.1| 227 --HKLTEVDA 234
                                       ..33455555 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   5.7e-05      0.11      22      46 ..      35      58 ..      13      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.7e-05
                            AAA_23 22 tlItGpNGaGKTTildAiklaLyge 46
                                        + G+NGaGK+T++  i ++Ly +
  gi|344210242|ref|YP_004786418.1| 35 HGLLGENGAGKSTLMK-ILYGLYSQ 58
                                      5678**********98.55666665 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00018      0.36      84     140 ..     174     229 ..     168     278 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                                       HTT-HHHHHHHHTT-SEEEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-EEEEEESS- CS
                          Bac_DnaA  84 rdkkaeefkeklrkvDvLliDDiqflagkektqeelfhtfnalleegkqvvlssDrs 140
                                       +++++e +k  +r+vD+L++D+   + + +   e lf  ++ l++eg  +++ + + 
  gi|344210242|ref|YP_004786418.1| 174 QQQRVEILKALYRDVDLLILDEPTAVLTPT-EAERLFDSLERLTDEGLSIIFITHKL 229
                                       56788899**************88777766.5799****************988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3590.84
//
Query:       gi|344210243|ref|YP_004786419.1|  [L=383]
Description: basic membrane protein [Haloarcula hispanica ATCC 33960]
Scores for 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-44  150.8   0.0    4.9e-44  150.5   0.0    1.0  1  Bmp       ABC transporter substrate-binding protein PnrA-like


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 !  150.5   0.0   2.7e-48   4.9e-44       3     271 ..      66     333 ..      64     353 .. 0.93

  Alignments for each domain:
  == domain 1  score: 150.5 bits;  conditional E-value: 2.7e-48
                                       EEEEECSS-TTTSCHHHHHHHHHHHHHHHC.TTEEEEEEEEC.GGGHHHHHHHHHHCTT-SEEEEESCCHHHHHHHH CS
                               Bmp   3 kvavlvegtidDksfnessyeGirrlkkeq.nieliskesslltdedyiadlknlkeegsdlivatgfalqdalqev 78 
                                       ++a ++++ + D +++  ++eG++++ +e+  +++ + e+++   +d ++++++ ++   d+i+++ f++qd + +v
  gi|344210243|ref|YP_004786419.1|  66 TAAWVYNSEVGDLGWSWAHNEGREAVTEEYdWLKTEYTEAVA--PADSERVFEQYAQGDADIIFGCTFEYQDPMAAV 140
                                       6788999***********************************..7******************************** PP

                                       HHH-TTS-EEEESS--TT-STTEEEEEE-HHHHHHHHHHHHHHHHHCTTTTEECSS-SCCCHHCHHHHHHHHHHH-T CS
                               Bmp  79 ssdfpkvkFliiDavvekeyknvlsvaFrseegaFLaGvaaAlmsktnkigfvgGveipvvksfingFeaGikyvnp 155
                                       ++++p+++F +  ++ + e  n+  + +r ++ ++LaG aa+ +++t   g+v++ +ip+v + in++++G++ vn 
  gi|344210243|ref|YP_004786419.1| 141 AEQYPDTYFEHNTGYLTME--NMGRYMGRIYQPRYLAGQAAGTVTETDTLGYVAAFPIPEVIRGINAYALGAASVND 215
                                       *******************..******************************************************** PP

                                       T-EEEEEE-SSSS-HHHHHHHHHHHHHCT--EEEEE-GGGHHHHHHHHHHHCHCTEEEEEES--CGCSTTCCEEEEE CS
                               Bmp 156 dievvvkvagtfsDakkgkslAsslykegvdvifpaagkagkgvieaakelglsnyvIgvdkdqsylapenvitsii 232
                                        + ++v++++++ D+ +++++A+ l +e vdv+++  ++++++++ aa + g+   + g+d  + ++a en +ts i
  gi|344210243|ref|YP_004786419.1| 216 SATLKVRWTNSWFDPPTESEAANALLDEDVDVMAQ--HQDSPAALRAASDAGIW--ATGYDAPMGDIAGENYLTSPI 288
                                       ***********************************..***************98..********************* PP

                                       EEHHHHHHHHHHHHHCCT---TTEEEEE-CCCTSEEE-........S CS
                               Bmp 233 knvedlvvsiiekvakgevlaggevitlglkegvvgld........e 271
                                       + +e+ +   ie v  g+  +++ + + g++ g+  ld        e
  gi|344210243|ref|YP_004786419.1| 289 WHWEEFYGPTIESVRDGT--WESDAYWEGIDSGICSLDdwgpdvpqE 333
                                       ******************..***************999533322222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2450.17
//
Query:       gi|344210244|ref|YP_004786420.1|  [L=375]
Description: basic membrane protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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-43  147.5   0.0    5.1e-43  147.2   0.0    1.0  1  Bmp       ABC transporter substrate-binding protein PnrA-like


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 !  147.2   0.0   2.9e-47   5.1e-43       3     295 ..      58     341 ..      56     346 .. 0.92

  Alignments for each domain:
  == domain 1  score: 147.2 bits;  conditional E-value: 2.9e-47
                                       EEEEECSS-TTTSCHHHHHHHHHHHHHHHC.TTEEEEEEEEC.GGGHHHHHHHHHHCTT-SEEEEESCCHHHHHHHH CS
                               Bmp   3 kvavlvegtidDksfnessyeGirrlkkeq.nieliskesslltdedyiadlknlkeegsdlivatgfalqdalqev 78 
                                       ++a ++ + + D +++  ++eG++++ +++  +e+ + e+++   ed ++++++ ++   d++++t f +qd + ++
  gi|344210244|ref|YP_004786420.1|  58 TAAWVYISEVGDLGWSHAHDEGRKAVDEKYdWLETEYTEAVA--PEDSERVFEQYAQGDADIVFGTTFGYQDPMFNI 132
                                       5677888999********************************..7******************************** PP

                                       HHH-TTS-EEEESS--TT-STTEEEEEE-HHHHHHHHHHHHHHHHHCTTTTEECSS-SCCCHHCHHHHHHHHHHH-T CS
                               Bmp  79 ssdfpkvkFliiDavvekeyknvlsvaFrseegaFLaGvaaAlmsktnkigfvgGveipvvksfingFeaGikyvnp 155
                                       ++++p+++F +  ++ + e  n+  + +r ++ ++LaG aa+ +++ n ig+v++ +ip+v + in+ ++G++ vnp
  gi|344210244|ref|YP_004786420.1| 133 AEQYPDTYFEHATGYRTRE--NMGRYMGRIYQPRYLAGQAAGMVTENNTIGYVAAFPIPEVIRSINAMALGARSVNP 207
                                       *******************..******************************************************** PP

                                       T-EEEEEE-SSSS-HHHHHHHHHHHHHCT--EEEEE-GGGHHHHHHHHHHHCHCTEEEEEES--CGCSTTCCEEEEE CS
                               Bmp 156 dievvvkvagtfsDakkgkslAsslykegvdvifpaagkagkgvieaakelglsnyvIgvdkdqsylapenvitsii 232
                                       d+  ++++++ + D++++k++A+sl++eg+dvi +   +++++ + aa e  +   + g++  + +++ +n ++s +
  gi|344210244|ref|YP_004786420.1| 208 DATFKIRWVNAWFDPQTSKQAANSLIDEGCDVISQ--EQDSPAPVRAANEADVW--ASGYNAPMGEFGGDNYLVSPV 280
                                       ***********************************..89999999999887765..********************* PP

                                       EEHHHHHHHHHHHHHCCT---TTEEEEE-CCCTSEEE-S--TCCHHHHCHHHHHHHHHHHCCC CS
                               Bmp 233 knvedlvvsiiekvakgevlaggevitlglkegvvgldeesdvledekvkeqlkkenkkiike 295
                                       +n+e+++   i+ v  g+  +++ + + g+++    lde    + +e  +   + e++++++e
  gi|344210244|ref|YP_004786420.1| 281 WNWEEVYDPTISAVRDGT--WEADAFWGGMETNLPALDEWGPEVPQEVKDTVAETEEQIVNGE 341
                                       *****************9..9********9999999995555555555555555556666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2541.39
//
Query:       gi|344210245|ref|YP_004786421.1|  [L=597]
Description: urease subunit [Haloarcula hispanica ATCC 33960]
Scores for complete 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   93.4   3.2    4.1e-25   89.2   3.2    2.3  1  Amidohydro_3  Amidohydrolase family
    6.6e-12   45.4   0.0    1.2e-05   24.9   0.0    2.5  2  Amidohydro_1  Amidohydrolase family


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 !   89.2   3.2   4.6e-29   4.1e-25       1     472 [.      74     562 ..      74     563 .. 0.80

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 4.6e-29
                      Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagtt...................... 55 
                                       +v+D++G +++PGF+D+H+H     ++lrl+  p+ar +  +g++t+v +q g++                      
  gi|344210245|ref|YP_004786421.1|  74 RVVDLDGSYLAPGFIDMHAH-----SELRLFENPGAREKLTQGITTEVLGQDGVSvapvppnltdewaervksldgt 145
                                       69******************.....****************************************988888888888 PP

                      Amidohydro_3  56 ..pkgrwivgeGw.........deaqfaeerfpyalaeldevledapvllaaldtHaavrnsaaldlagiteatpdp 121
                                         +   w+ ++G+          ++  +++ +++ +  l   +ed+p+  +++   a  +  + ld++  +++t+ +
  gi|344210245|ref|YP_004786421.1| 146 lgETWPWHTVSGYlealesaepAVNCAYYAPHGNIRSMLAG-FEDRPLGGEHV-VAAGPVTGHRLDRPKSDHDTAPG 220
                                       88888888888888888888865555556666655555554.48888888887.44444447777777777777777 PP

                      Amidohydro_3 122 ...aggeilrdangegatgllregafhlvldla.....plareaeaaavaaalaalasyGitsveagggnvsslddl 190
                                          a++  l  a ++ga g+++          +     ++ar++e+ a+a  la+  s+ i +v  + + +   + +
  gi|344210245|ref|YP_004786421.1| 221 eldAIRQELEVALEQGAFGMSK--------G-MiyppsSYARDDELVALADTLAKRDSFMISHV--WNETDRVVESI 286
                                       3444444444444444444444........3.34787466************************..9999999**** PP

                      Amidohydro_3 191 eplfeltaeeklplrviikelldaaerlglplspgseeltigavklfadgvlgsrtalltepyftgwpdfedealae 267
                                       ++++++ ++++++ +v++        ++g + + g+ e  ++ ++ +ad   g r+   + py  g ++++    a 
  gi|344210245|ref|YP_004786421.1| 287 DRYLDICRRGGCHAHVSH-------LKVGGQQNWGDSEAVLDLFDDAAD--RGQRVTFDQYPYTAGSTMLT----AL 350
                                       *****************7.......567777777888888888888888..35555555666666666666....78 PP

                      Amidohydro_3 268 lvaaadergldvaihaigdaavddvldafeaaaekngnqdrr..rlehaegv.......tesqiervaalqvaagvq 335
                                       l  +a++ + ++  h++   av+d ++a  +++ ++ n   +  + ++  ++        +++ie++a   +  +v 
  gi|344210245|ref|YP_004786421.1| 351 LPPWARQGDSEAIRHRLNSVAVRDRIAADISQPGDWENLAYAagSWDNILVTrtgsgrhQGDTIEDIATEMGSEPVD 427
                                       88999999999999999999999777777777888888877756333333336666888999999999999999999 PP

                      Amidohydro_3 336 pvfnfedelldsrlgperargs...tpvkellnagvkvalgsDapvgpf..dpwprigaavmrktrrggevlrpdee 407
                                        + +    l+ ++l+  +a+ +   + + + l+++ + ++ +D   g+f  +p+pr ++a+ r      +++r++  
  gi|344210245|ref|YP_004786421.1| 428 AMCEL---LVSEELDVTMADFVmaeADIERFLADD-RGTFCTD---GIFggKPHPRAIGAFSRILE---RYVRERDV 494
                                       88877...888889999999998887787777776.66999**...555448**********9997...99****** PP

                      Amidohydro_3 408 lsleealalyTrgpAkalgledrkGtLevGadADlvvld....adpldvdppelaearvrltvvdGrvv 472
                                       ls e ++     +pA +lgl+dr G +++G+ ADlv +d     + ++ ++p  ++++ ++++v+G+v 
  gi|344210245|ref|YP_004786421.1| 495 LSPELMAYKAAGHPADILGLRDR-GYVREGYVADLVAFDldsvSANATYEDPFQFSDGMEYVLVGGEVA 562
                                       **********************9.***************8888555555556666666********996 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.8e-07    0.0017       2     160 ..      83     284 ..      82     307 .. 0.84
   2 !   24.9   0.0   1.3e-09   1.2e-05     240     341 ..     459     559 ..     447     562 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.8e-07
                                       EEE-EEEEEEECETTECSSS....GHHHHH...................................STTHHHHHHHHH CS
                      Amidohydro_1   2 vlPGlIDaHvHleqsllrga....tledwl...................................vppetaaeales 39 
                                       + PG+ID+H H e +l+ ++    +l                                       + +et+ + + s
  gi|344210245|ref|YP_004786421.1|  83 LAPGFIDMHAHSELRLFENPgareKL---TqgittevlgqdgvsvapvppnltdewaervksldgTLGETWPWHTVS 156
                                       78**********99988888855533...2444788889999999999999999999********9*********** PP

                                       HHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEEEESSEGGS.......GCCCSHHHHHHHHHHHHHHHH CS
                      Amidohydro_1  40 giktalksGtttvadmgattstgiealleaaeelplglrilggkvsldr.......gsaetskasreklkagaaeti 109
                                       g  +al+s    v+ ++++ + +i+ +l  +e+ plg + +++ ++++        ++++t + +  +++++ + ++
  gi|344210245|ref|YP_004786421.1| 157 GYLEALESAEPAVNCAYYAPHGNIRSMLAGFEDRPLGGEHVVAAGPVTGhrldrpkSDHDTAPGELDAIRQELEVAL 233
                                       ********99888888887666***********88888777776666657******999999999999999986667 PP

                                       HHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE.TSSCHHHH CS
                      Amidohydro_1 110 kgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHa.letkgeve 160
                                        + a g+ k  ++p++ +a  d+el ++++  +krd  +  H+  et+  ve
  gi|344210245|ref|YP_004786421.1| 234 EQGAFGMSKGMIYPPSSYAR-DDELVALADTLAKRDSFMISHVwNETDRVVE 284
                                       76777777799999999987.78888999999999********888777664 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1.3e-09
                                       SCEEEEEECTTSSCCG.GHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EE CS
                      Amidohydro_1 240 vkvglgtDgaasgnsl.nlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlv 315
                                        + +++tDg   g+     +  +++   l r   y +e++ ls++   ++a  ++A++lgl ++ G + +G+ ADlv
  gi|344210245|ref|YP_004786421.1| 459 DRGTFCTDGIFGGKPHpRAI--GAFSRILER---YVRERDVLSPELMAYKAAGHPADILGL-RDRGYVREGYVADLV 529
                                       67788999885555441222..223332222...338999*********************.59************* PP

                                       EECCCT......CGGGTTTCTSEEEEEEEETT CS
                      Amidohydro_1 316 vvdldi......laafvglkkdgnvkkvivkG 341
                                       ++dld+      +++ +  ++      v v+G
  gi|344210245|ref|YP_004786421.1| 530 AFDLDSvsanatYEDPFQFSDG--MEYVLVGG 559
                                       ****665666664444444443..45555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.31s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 3633.51
//
Query:       gi|344210246|ref|YP_004786422.1|  [L=410]
Description: allantoate amidohydrolase/N-carbamoyl-L-amino acid amidohydrolase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-33  115.5   0.9      6e-33  114.3   0.6    1.7  2  Peptidase_M20  Peptidase family M20/M25/M40
      1e-07   31.8   0.0    2.1e-07   30.9   0.0    1.4  1  M20_dimer      Peptidase dimerisation domain
    5.1e-06   26.3   0.0    9.1e-06   25.5   0.0    1.5  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 ?   -1.7   0.0      0.34     2e+03     125     160 ..      30      70 ..      23      75 .. 0.71
   2 !  114.3   0.6     1e-36     6e-33       1     206 [.      79     405 ..      79     406 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.34
                                       ESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEES.....SSB CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.....xxx RF
                     Peptidase_M20 125 gapvtln.dsplvkalaeaaeelfgekvelivsg.....pgg 160
                                       ++p  ++ +++ +++l e  +e+ g++v+  ++g     ++g
  gi|344210246|ref|YP_004786422.1|  30 NRPSLSDeNKAARDTLVEWFREA-GLEVRIDTMGnifgrRAG 70 
                                       56777778888899999999997.988877766664444444 PP

  == domain 2  score: 114.3 bits;  conditional E-value: 1e-36
                                       EEEEES-BSSTTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                     Peptidase_M20   1 llgsHlDvVpeeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.. 75 
                                       l+gsH+D++     +g           G+++G        gvl++le+++a++d+g++++++++++++ +EEg r  
  gi|344210246|ref|YP_004786422.1|  79 LIGSHIDSQY----NG-----------GRYDGV------VGVLGGLEVIEAFNDAGVTTERPLEVVAWSNEEGVRfq 134
                                       689*******....77...........888888......*********************************98899 PP

                                       ...THHHHHHH......HHHT..........................TTCESEEEEEEEESSSBTCHSTETEEEE.. CS
                                       ...xxxxxxxx......xxxx..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                     Peptidase_M20  76 ...gGakalle......glee..........................rekvdavfelhieepgileagklaigvv.. 115
                                           G++ +++                                    +++++++fe+h+e+++ le++ + +  v  
  gi|344210246|ref|YP_004786422.1| 135 pdmLGSGVYCDifdldyA--YeredkesrrfgdelerigykgetpceADDIHCYFEMHVEQGPFLEQQDIPVAAVeg 209
                                       999999999996666541..045678888999999999999999999*******************8887777779* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|344210246|ref|YP_004786422.1| 210 vfgfswlnvtfegqanhagptpmdmrhdafvatadvtravrritategtdlvgtvgsvdvwpnainviperveftld 286
                                       ***************************************************************************** PP

                                       .............................EEEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEEEESSSBHTH CS
                                       .............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 116 .............................kvevelleggapvtlndsplvkalaeaaeelfgekvelivsgpggtda 163
                                                                    ++e+e++++  + +++ +++++++ eaae + g ++++ vsg +g+da
  gi|344210246|ref|YP_004786422.1| 287 frsyddavvdaavnqireevahaaereglEYEIEEIMRVDADPFD-QDCIDTVVEAAETV-GCEYMRLVSG-AGHDA 360
                                       ***************************999999999999988888.*************9.9999999***.***** PP

                                       HHHTTT.EEEEEEESS.GGCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                       xxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 164 rffagi.ptvmifgpg.sglaHspnEyvdledlekgikvlarlle 206
                                       +++++i pt mif+p+ +g++H + E+++ +d+++g++vl ++++
  gi|344210246|ref|YP_004786422.1| 361 NYLNKItPTSMIFVPSvDGISHRESEFTEWDDIVTGTEVLLNAVQ 405
                                       ******9*******9977**********************99886 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   3.4e-11   2.1e-07       3     106 ..     210     311 ..     209     314 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 3.4e-11
                                       B-EEEEEEEEEE-B-EEGG.-TTTTB-.HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-C...CCCEESS CS
                         M20_dimer   3 hkGlaggkitvkgkagHsg.apgagaN.AieklarllaeledeegdiaeerslprttlnvtgiegGs...aknvipd 74 
                                        +G+ + ++t++g+a H+g  p +++  A+ + a++  + +  +  ++       t l  t+++      a+nvip+
  gi|344210246|ref|YP_004786422.1| 210 VFGFSWLNVTFEGQANHAGpTPMDMRHdAFVATADVTRAVRRITATEG-------TDLVGTVGSVDVwpnAINVIPE 279
                                       689*******************99998899988888888888854444.......666666666655779******* PP

                                       EEEEEEEEEHHHHHHHHHHHHHHHHHHTSCCS CS
                         M20_dimer  75 eaeakidiRllpgedpeevleeieeilekeap 106
                                       ++e+++d+R ++   ++++ ++i+e ++++a+
  gi|344210246|ref|YP_004786422.1| 280 RVEFTLDFRSYDDAVVDAAVNQIREEVAHAAE 311
                                       *************************9998876 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.5e-09   9.1e-06       1      82 [.      63     144 ..      63     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.5e-09
                                       EEEEEESTTCE.SEEEEEEEE--B-TTTTCCT---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSG... CS
                     Peptidase_M28   1 Nviatlegkat.devlllgAHyDsvgvgrgpifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEa... 73 
                                       N+ ++  g+++ +  +l+g+H+Ds +        G  D  +gv   Le+++++++ g + +r + +++++ EE    
  gi|344210246|ref|YP_004786422.1|  63 NIFGRRAGTDSdAAPVLIGSHIDSQYN---G---GRYDGVVGVLGGLEVIEAFNDAGVTTERPLEVVAWSNEEGvrf 133
                                       778888888885669***********7...5...779********************999*************9888 PP

                                       ..SSHHHHHHH CS
                     Peptidase_M28  74 ..gllGSkafa 82 
                                          +lGS  ++
  gi|344210246|ref|YP_004786422.1| 134 qpDMLGSGVYC 144
                                       88888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2732.32
//
Query:       gi|344210247|ref|YP_004786423.1|  [L=184]
Description: carbon monoxide dehydrogenase small subunit [Haloarcula hispanica ATCC 33960]
Scores for complete 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  101.8   0.0    3.3e-29  100.7   0.0    1.5  1  Fer2_2    [2Fe-2S] binding domain
      4e-05   23.5   1.3      4e-05   23.5   1.3    3.1  3  Fer2      2Fe-2S iron-sulfur cluster binding domain
     0.0013   18.7   0.2     0.0025   17.8   0.2    1.5  1  Fer2_3    2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Fer2_2  [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.0   5.4e-33   3.3e-29       1      75 [.      72     144 ..      72     145 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 5.4e-33
                            Fer2_2   1 TveglgeeleelhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdAv 75 
                                       Tv+ lg++ ++lhpvq+afv++ a+qCG+C pG++++a+all++n p+pte e+real+ n+CRCtgY++ v+Av
  gi|344210247|ref|YP_004786423.1|  72 TVAALGTQ-DDLHPVQQAFVDNFAVQCGFCIPGMIIQAVALLDSN-PDPTEREVREALDDNICRCTGYQKPVEAV 144
                                       8999*988.78**********************************.99999**********************98 PP

>> 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 !   23.5   1.3   6.6e-09     4e-05       2      55 ..       6      58 ..       5      75 .. 0.81
   2 ?   -0.8   0.2      0.25   1.5e+03      40      65 ..      97     125 ..      94     135 .. 0.50
   3 ?   -5.7   6.5         3   1.8e+04      33      40 ..     175     182 ..     137     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.6e-09
                                      ETTTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCE.CTT CS
                              Fer2  2 tidgkevevevadgettlldaaeenggidipysCggggCgtClvevlegev.qsd 55
                                      ti+g++++ve+   e  l  ++++ g i+++ +C gg+Cg+ +v v+ gev  ++
  gi|344210247|ref|YP_004786423.1|  6 TINGERTRVEAGSAED-LATVLRQHGYIGVKCGCDGGACGASKVFVD-GEVrMAC 58
                                      89**************.*******99***************999766.7776333 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.25
                                       SSTTEEEEEESCE...CTTSSSSTHHHHH CS
                              Fer2  40 CgtClvevlegev...qsdetelegeeld 65 
                                       Cg C   +    v    s++  +e+e ++
  gi|344210247|ref|YP_004786423.1|  97 CGFCIPGMIIQAVallDSNPDPTEREVRE 125
                                       88887555555555432224444444444 PP

  == domain 3  score: -5.7 bits;  conditional E-value: 3
                                       TSSSSSSS CS
                              Fer2  33 ysCggggC 40 
                                       ++C gggC
  gi|344210247|ref|YP_004786423.1| 175 TGCCGGGC 182
                                       57777777 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 !   17.8   0.2   4.2e-07    0.0025      46     100 ..      32      82 ..      18      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.2e-07
                            Fer2_3  46 lafrasCregiCGscavainGkptlaCtatikdlakqkseieleplpkfpvirDL 100
                                       +  ++ C  g CG+  v ++G++++aC     d + +    e++ ++++  + DL
  gi|344210247|ref|YP_004786423.1|  32 IGVKCGCDGGACGASKVFVDGEVRMACGMAAADADGS----EIQTVAALGTQDDL 82 
                                       556899**********************999998765....45555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1221.37
//
Query:       gi|344210248|ref|YP_004786424.1|  [L=816]
Description: hypoxanthine oxidase XdhD [Haloarcula hispanica ATCC 33960]
Scores for complete 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-145  484.3   4.2   5.8e-145  483.8   4.2    1.2  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    1.5e-22   80.0   1.5    2.8e-22   79.1   1.5    1.5  1  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a


Domain annotation for each model (and alignments):
>> Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  483.8   4.2  6.5e-149  5.8e-145       3     550 .]     209     752 ..     206     752 .. 0.94

  Alignments for each domain:
  == domain 1  score: 483.8 bits;  conditional E-value: 6.5e-149
                                       TT-STTEEEEEEE..E-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHH CS
                     Ald_Xan_dh_C2   3 eeapdnvlakiek..GdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvae 77 
                                       + + +n +a+ie   Gdv+aa++   hv e e++t rq+h+  E +++la+  +ed++ ++ +stq+p ++rr++a+
  gi|344210248|ref|YP_004786424.1| 209 D-YDRNRMAHIEGelGDVDAALDGETHVHETEWETIRQSHANVEKHTSLAYT-NEDDRHVLITSTQVPNHTRRQLAH 283
                                       4.5556666555334*************************************.89********************** PP

                                       HHT--GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-E CS
                     Ald_Xan_dh_C2  78 vlglpenkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGki 154
                                       ++++p  ++rv++prvGGGFGgK q++ +e++  +++++t rpV +  +Ree++ a ++rhp+k+k+k+++++dG i
  gi|344210248|ref|YP_004786424.1| 284 LFDIPIRDIRVTKPRVGGGFGGK-QAMVVEPIPLALSLATDRPVLYEASREEEFYAMRSRHPMKVKAKTAVTDDGDI 359
                                       ***********************.***************************************************** PP

                                       EEEEEEEEEEESSTHHHCHCCHCCTTGGGTTTB.--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 155 taldvdlladaGayadlspavleralshldgpY.kipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAe 230
                                        a+d+  l+++Gay +++ +v+ ++ s+   +Y k+pnv++e+++v tNtp+++a+RG+G+pq+++alE ++de+A+
  gi|344210248|ref|YP_004786424.1| 360 EAIDIYALSNTGAYGSHGMTVAGNVGSKPLPLYsKVPNVHFEADIVHTNTPQTGAMRGYGAPQGTLALEGHLDEVAR 436
                                       *********************************99****************************************** PP

                                       HHT--HHHHHHHHBCECGCC.S.EEET.......EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEE CS
                     Ald_Xan_dh_C2 231 elgldplelRrrNlikpgeltp.ygqp.......vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglap 299
                                        lgldp+e+Rrr  ++ g+l    g+           s++l+e+++++k++++y+ +++  a+    + +rGig+a+
  gi|344210248|ref|YP_004786424.1| 437 DLGLDPVEFRRRHHMEVGDLDEiAGMMggegaerRIRSCGLDECIERGKDAIGYDDLEQPAAD----HLHRGIGMAL 509
                                       ******************9965345524445566679*****************999655444....347******* PP

                                       EEEEBS--S.EETTEEEEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S CS
                     Ald_Xan_dh_C2 300 vvegiglgftakflnqegalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgt 376
                                         +g+g++      + ++a++ +n+dGs+++++gg+++G+G++t++ qiaae+Lg++  d+ v+++dtd +p++ g+
  gi|344210248|ref|YP_004786424.1| 510 SAQGTGVAG----DELGAAQIMMNEDGSFHLQVGGVDIGTGADTAFLQIAAEVLGCDEADIVVKSADTDVTPFDYGA 582
                                       *****7775....33478*********************************************************** PP

                                       -TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET..EEEECHHHHHHHHHH...TTSSEEEE CS
                     Ald_Xan_dh_C2 377 aaSrstdlngnAvkkAaeklrerllkiaaellevspedleledgkvvvk..eksvslaelaaaayl...ervslsat 448
                                       +aS++t+++g+AvkkAae+ +er+l+  ++ll+ ++e+l+  dg+v+ +  + sv+l+++  +a++   er+++  +
  gi|344210248|ref|YP_004786424.1| 583 YASSTTYISGMAVKKAAEDAKERILDWGSKLLDEPTENLKTGDGTVYSEtsGDSVTLEDIGYEAVYgddEREHILGK 659
                                       *************************************************999999*******887779999999999 PP

                                       EEE...EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT--- CS
                     Ald_Xan_dh_C2 449 gfyktldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEel 525
                                       g++      t+++pp    +++a++a V+vD  tge +v ++v+++D+G +iNp ++egQieG+  + + +a++E +
  gi|344210248|ref|YP_004786424.1| 660 GTH-----CTEESPP----PFAAQFADVTVDETTGEFEVHELVVAVDCGVAINPGMAEGQIEGANHMSYEMAVSEGI 727
                                       997.....4666777....9********************************************************* PP

                                       EEETTTEESS-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 526 vydedGqlltasladYkiPtaadiP 550
                                       ++d++G+   a++++Y +P+a+++P
  gi|344210248|ref|YP_004786424.1| 728 TLDDEGRAEVADFDEYGLPSATETP 752
                                       **********************998 PP

>> Ald_Xan_dh_C  Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   1.5   3.1e-26   2.8e-22       1     108 [.      63     177 ..      63     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 3.1e-26
                                       TT-SCCGGGCC..-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHH..HHCCGTECCT..TSSS-EE.EE CS
                      Ald_Xan_dh_C   1 tGeavYvdDip..apgalylafvrStkahAkivsidvsaalalpGVvavitak..dlpkenkaig..siledee.da 70 
                                       tG+a+Y+ D++  +p+ +y+a+vrS ++h++++ id+saa+a++GV av+t +   +p+ +++++  s +e+++ d+
  gi|344210248|ref|YP_004786424.1|  63 TGQAKYTADYEerYPDLAYAAVVRSEIPHGRVTDIDTSAAEAMDGVEAVLTPEsdAVPDAKYTSAgqSYPEPSPwDM 139
                                       8********964355666*********************************65215788888777665555555889 PP

                                       SS-SSEESSTT-EEEEEEESSHHHHHHHHHT-EEEEEE CS
                      Ald_Xan_dh_C  71 llaedkvrsvgqavaavvAedeetArkAaklvkveYee 108
                                         ++++vr+ g+++aav+A+d+ tA +A+++++v Yee
  gi|344210248|ref|YP_004786424.1| 140 RVLNEHVRYIGDPIAAVAADDRTTASAAVEAIEVSYEE 177
                                       999**********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (816 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 5714.74
//
Query:       gi|344210249|ref|YP_004786425.1|  [L=122]
Description: hypothetical protein HAH_5308 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-06   26.9   0.0      6e-06   26.1   0.0    1.4  1  MarR_2          MarR family
     0.0056   16.6   0.0     0.0073   16.3   0.0    1.2  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0059   16.4   0.0      0.009   15.8   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.019   15.1   0.0       0.03   14.5   0.0    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.035   14.2   0.2      0.046   13.8   0.2    1.1  1  Shadoo          Shadow of prion protein, neuroprotective
       0.21   11.5   0.0        0.3   11.0   0.0    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
       0.25   11.2   0.0       0.43   10.5   0.0    1.4  1  TFIIE_alpha     TFIIE alpha subunit


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 !   26.1   0.0   2.3e-09     6e-06       9      54 ..      26      71 ..      22      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.3e-09
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                       +La+L+++p++ +t +e+a+++g++k++v  +l rL ++G v  r
  gi|344210249|ref|YP_004786425.1| 26 AILAFLRDNPEKAFTRSEIAAETGVKKGSVGPTLVRLRERGRVDHR 71
                                      58**************************************977655 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 !   16.3   0.0   2.8e-06    0.0073      21      63 ..      38      81 ..      24      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.8e-06
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEEEEES-HH CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rgrririldle 63
                                       +t+ e+A+  G+   +v  +l +L+++g ++ rg+  ri d e
  gi|344210249|ref|YP_004786425.1| 38 AFTRSEIAAETGVKKGSVGPTLVRLRERGRVDhRGNYWRISDHE 81
                                      58******************************766339999987 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 !   15.8   0.0   3.5e-06     0.009       5      48 ..      24      68 ..      22      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.5e-06
                                      HHHHHCT-CTTBSS-.BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  5 alaiLdalaeapqel.tlselArrtglpkStvhRlLqtLvelGyv 48
                                      a aiL +l+  p+   t se+A++tg+ k +v   L  L e+G v
  gi|344210249|ref|YP_004786425.1| 24 AGAILAFLRDNPEKAfTRSEIAAETGVKKGSVGPTLVRLRERGRV 68
                                      779***********88****************9999999999976 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 ?   14.5   0.0   1.2e-05      0.03      21      55 ..      37      71 ..      31      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                                      SSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                    Fe_dep_repress 21 kvvktkdlaerLnvspssVsemlkkLekdGyveye 55
                                      k  +++++a + +v++ sV  +l +L++ G v++ 
  gi|344210249|ref|YP_004786425.1| 37 KAFTRSEIAAETGVKKGSVGPTLVRLRERGRVDHR 71
                                      556899************************99996 PP

>> Shadoo  Shadow of prion protein, neuroprotective
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   1.8e-05     0.046      16      67 ..      45      97 ..      39     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                            Shadoo 16 sargglrggargasrvrvrpaprysaagsslrvaaagaaagaa.agaaaglaa 67
                                      +a  g++ g+ g + vr+r   r    g   r++   a+  +a a aaa +aa
  gi|344210249|ref|YP_004786425.1| 45 AAETGVKKGSVGPTLVRLRERGRVDHRGNYWRISDHEASVDTAtAHAAAAIAA 97
                                      57899***************************998777655441445555554 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00012       0.3      21      55 ..      37      71 ..      24      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      +  t +eia e+gv + +v  +L +L ++G V+ +
  gi|344210249|ref|YP_004786425.1| 37 KAFTRSEIAAETGVKKGSVGPTLVRLRERGRVDHR 71
                                      567899************************99865 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00017      0.43      14      60 ..      23      71 ..      17      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                                      HHHHHHHHHHCTTS..EBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEE CS
                       TFIIE_alpha 14 eavlvldvLlekge..vteedlakelkidlnelrklLnrLyearlvkyk 60
                                      +a  +l  L  + e  +t  ++a e+++++  +++ L rL+e + v+ +
  gi|344210249|ref|YP_004786425.1| 23 NAGAILAFLRDNPEkaFTRSEIAAETGVKKGSVGPTLVRLRERGRVDHR 71
                                      55666666665543228999**********************9988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 900.79
//
Query:       gi|344210250|ref|YP_004786426.1|  [L=119]
Description: hypothetical protein HAH_5309 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.081   13.3   0.0      0.092   13.1   0.0    1.1  1  PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antit


Domain annotation for each model (and alignments):
>> PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.2e-06     0.092       2      98 ..       8      97 ..       7     108 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.2e-06
                                      TTEEEEEEE-S.--TTS--SEEEEEE-S-HHHHCH.SEEEEEEEE.SSSTSSGCSTTEEEE-HHHCSSSSSSSSEEEEC CS
                        PemK_toxin  2 rGeIvlvdldp.srgseqgkrRpvvVvsndafnek.ntvivvplt.skdkdkkklpfhveleseildlngldkdswvkl 77
                                       G++++++  p +rg+    +Rp +V++ da++ + +  i++ lt s  +d+++      +  ++l+  + d++s+   
  gi|344210250|ref|YP_004786426.1|  8 SGDVFWAPD-PyNRGNN---PRPWLVLTADALPFSgEEYICAGLTlSDLQDNIA------IGDNWLAGGNPDRESYCSP 76
                                      599****99.8455888...**********888775799999999666665544......4433222222234566666 PP

                                      CCEEEEEGGGEEEEEEE--HH CS
                        PemK_toxin 78 dqirtvdkarlrkkigklsre 98
                                        ++tv ++ + ++ g++ +e
  gi|344210250|ref|YP_004786426.1| 77 WVLATVKHDAVSNPQGRVVPE 97
                                      666666666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 887.05
//
Query:       gi|344210251|ref|YP_004786427.1|  [L=189]
Description: isoquinoline 1-oxidoreductase alpha subunit [Haloarcula hispanica ATCC 33960]
Scores for 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  112.1   4.9      1e-32  112.0   0.1    2.2  2  Fer2_2    [2Fe-2S] binding domain
    1.2e-08   34.8   0.5    1.2e-08   34.8   0.5    2.5  3  Fer2      2Fe-2S iron-sulfur cluster binding domain
    4.8e-06   26.5   1.1    1.1e-05   25.3   0.2    2.1  2  Fer2_3    2Fe-2S iron-sulfur cluster binding domain
     0.0019   18.2   1.1     0.0084   16.1   1.1    2.1  1  Fer2_4    2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Fer2_2  [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.1     0.067     3e+02      26      31 ..      42      47 ..      34      49 .. 0.83
   2 !  112.0   0.1   2.2e-36     1e-32       1      75 [.      72     144 ..      72     145 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.067
                            Fer2_2 26 qCGyCt 31
                                       CG+Ct
  gi|344210251|ref|YP_004786427.1| 42 ACGFCT 47
                                      6****9 PP

  == domain 2  score: 112.0 bits;  conditional E-value: 2.2e-36
                            Fer2_2   1 TveglgeeleelhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdAv 75 
                                       T+eglge+ +elhpvq+afv++ a+qCG+C pG++m  +alle n ++pte+e+reals nlCRCtgY++iv+Av
  gi|344210251|ref|YP_004786427.1|  72 TIEGLGEQ-DELHPVQQAFVDNTALQCGFCIPGMIMRSTALLEAN-TDPTEQEVREALSDNLCRCTGYKKIVEAV 144
                                       9*****88.88********************************99.89999***********************8 PP

>> 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 !   34.8   0.5   2.7e-12   1.2e-08       2      55 ..       6      58 ..       5      73 .. 0.84
   2 ?   -1.7   0.3      0.67     3e+03      40      44 ..      97     101 ..      92     134 .. 0.55
   3 ?   -1.3   0.4      0.48   2.2e+03      20      31 ..     145     157 ..     139     184 .. 0.58

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 2.7e-12
                                      ETTTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCE.CTT CS
                              Fer2  2 tidgkevevevadgettlldaaeenggidipysCggggCgtClvevlegev.qsd 55
                                      +i++ e +v++a+ ++ lld++++ng ++ + +C  g+Cg C+v+v+ ge  +s+
  gi|344210251|ref|YP_004786427.1|  6 EINDVEWTVDAAKSDS-LLDVLRRNGYTGAKRGCDTGACGFCTVHVD-GEPvKSC 58
                                      68999***********.***************************988.4433444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.67
                                       SSTTE CS
                              Fer2  40 CgtCl 44 
                                       Cg C 
  gi|344210251|ref|YP_004786427.1|  97 CGFCI 101
                                       77776 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.48
                                       HHHHHH.TTTTTS CS
                              Fer2  20 ldaaee.nggidi 31 
                                       ldaae+ +gg+++
  gi|344210251|ref|YP_004786427.1| 145 LDAAERmDGGTAV 157
                                       5555553434333 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 !   25.3   0.2   2.5e-09   1.1e-05      21      91 ..      12      76 ..       7      95 .. 0.75
   2 ?   -2.0   0.0      0.79   3.5e+03      53      76 ..     148     171 ..     140     181 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.5e-09
                            Fer2_3 21 yeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatikdlakqkseielepl 91
                                      ++v+a+++d++ld+L +   +       ++ C  g CG c+v ++G+p   C + + ++++ +   ++e l
  gi|344210251|ref|YP_004786427.1| 12 WTVDAAKSDSLLDVLRRNGYT-----GAKRGCDTGACGFCTVHVDGEPVKSCVEPVMNVEDAS-VETIEGL 76
                                      677777777777777654333.....34789**************************999765.3445444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.79
                            Fer2_3  53 regiCGscavainGkptlaCtati 76 
                                        e++ G  ava +G +++  ++++
  gi|344210251|ref|YP_004786427.1| 148 AERMDGGTAVAADGGKAVEGNERV 171
                                       577888888888887766555555 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 !   16.1   1.1   1.9e-06    0.0084      19      71 ..      20      62 ..       1      73 [. 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.9e-06
                            Fer2_4 19 dtvasAllangvdvprsckygrprgelcaggeCrnClVevegepnvracstpv 71
                                      d+++++l +         ++g++rg  c  g+C  C V+v+gep v++c+ pv
  gi|344210251|ref|YP_004786427.1| 20 DSLLDVLRR-------NGYTGAKRG--CDTGACGFCTVHVDGEP-VKSCVEPV 62
                                      444444444.......446666666..888**************.*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1219.29
//
Query:       gi|344210252|ref|YP_004786428.1|  [L=808]
Description: hypoxanthine oxidase XdhD [Haloarcula hispanica ATCC 33960]
Scores for complete 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-149  499.3   0.1   1.6e-149  498.9   0.1    1.1  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    3.9e-24   85.1   0.1    8.6e-24   84.0   0.1    1.6  1  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a


Domain annotation for each model (and alignments):
>> Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  498.9   0.1  1.8e-153  1.6e-149      12     550 .]     202     741 ..     190     741 .. 0.93

  Alignments for each domain:
  == domain 1  score: 498.9 bits;  conditional E-value: 1.8e-153
                                       EEEEE-HHHHHHH-S......EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHHHT--G CS
                     Ald_Xan_dh_C2  12 kiekGdveaafaead.....hvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaevlglpe 83 
                                       + e Gdveaaf++a      hv++ e++t+ q+h+  E+++++a+  ded++ t  ++tq+p+++rr++a+++++p 
  gi|344210252|ref|YP_004786428.1| 202 EGELGDVEAAFERASndddrHVIKTEWETPYQSHCVPEPHTTIAYT-DEDDRHTFITATQVPFHTRRQIAHLFDVPI 277
                                       3446**********9888889*************************.89**************************** PP

                                       GGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-EEEEEEE CS
                     Ald_Xan_dh_C2  84 nkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGkitaldvd 160
                                        +vrv++pr+G GFG+K q++++e++a ++ +++grpVkl ++R+e+++a + rhp++++++++++++G i a+d+ 
  gi|344210252|ref|YP_004786428.1| 278 RDVRVTKPRIGAGFGSK-QEMAIEPIAFALHLAAGRPVKLEMSRQEEFTALRFRHPMQMQMRTAVTDEGDIEAMDLY 353
                                       *****************.*********************************************************** PP

                                       EEEEESSTHHHCHCCHCCTTGGGTTTB.--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHHT--H CS
                     Ald_Xan_dh_C2 161 lladaGayadlspavleralshldgpY.kipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeelgldp 236
                                       +l++ Gay +++ +v++++ ++   +Y ++pnvr+ g+vv tN p   a+RG+G+pq+ fa+E +mde+A++l+ dp
  gi|344210252|ref|YP_004786428.1| 354 TLSNSGAYGTHGMTVANNVGTKPLPLYpRVPNVRFAGDVVHTNLPMGAAMRGYGAPQGHFAVEAHMDEVARRLDFDP 430
                                       ***************************99************************************************ PP

                                       HHHHHHHBCECGCC.SEEET..........EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEE CS
                     Ald_Xan_dh_C2 237 lelRrrNlikpgeltpygqp..........vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvveg 303
                                       +e+R rN++++g+l     +             s++++e++d+++e+++y+ +++  ++ +    krG+g+a++ +g
  gi|344210252|ref|YP_004786428.1| 431 IEFRLRNAVQEGDLDRSV-AilkdgdrftrRIRSCGIRECVDRGREAIGYDDLEQPDEDHR----KRGVGMALIAQG 502
                                       ************995222.122233445555799*****************9977776666....79********** PP

                                       BS--S.EETTEEEEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT- CS
                     Ald_Xan_dh_C2 304 iglgftakflnqegalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSr 380
                                       +g++     ++ ++a+v++n+dGs+++++gg++ G+G++t + qiaae+Lg+++edv v+ +dtd +p++ g++aS+
  gi|344210252|ref|YP_004786428.1| 503 SGVAG----KELGAAQVQMNEDGSFHLQVGGVDTGTGADTMFSQIAAEVLGCTPEDVVVIAADTDLTPFDYGAYASS 575
                                       *7775....33468*************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET..EEEECHHHHHHHHHH...TTSSEEEEEEE. CS
                     Ald_Xan_dh_C2 381 stdlngnAvkkAaeklrerllkiaaellevspedleledgkvvvk..eksvslaelaaaayl...ervslsatgfyk 452
                                       +t+++g Avk+Aae+ +erll+  ++ll+ +p+ l+  dg v+ +  +++vsl+e+  +a++   er+++   g + 
  gi|344210252|ref|YP_004786428.1| 576 TTYISGRAVKNAAEDAKERLLEWGSKLLDEPPDVLDTGDGGVFSErtGNRVSLEEIGYEATYgddEREHILGDGNH- 651
                                       ********************************************9999999*******887778888899999997. PP

                                       ..EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEET CS
                     Ald_Xan_dh_C2 453 tldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvyde 529
                                           +t ++pp    +yga+++ V+vDtetge++++++v + D+G +iNpa+vegQieGG  + + +a++ +l++de
  gi|344210252|ref|YP_004786428.1| 652 ----STDESPP----PYGAQFVDVTVDTETGEYELNKLVFAADCGVAINPALVEGQIEGGEHMSLEYATSGDLTFDE 720
                                       ....5666777....9************************************************************* PP

                                       TTEESS-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 530 dGqlltasladYkiPtaadiP 550
                                       +G++   ++++Y +P+++d P
  gi|344210252|ref|YP_004786428.1| 721 EGNPEVLGFRQYGMPRTTDHP 741
                                       *******************98 PP

>> Ald_Xan_dh_C  Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.1   9.6e-28   8.6e-24       1     109 [.      46     161 ..      46     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 9.6e-28
                                       TT-SCCGGGCC..-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEE.HHH.HCCGTECCT..TSSS-EE.EE CS
                      Ald_Xan_dh_C   1 tGeavYvdDip..apgalylafvrStkahAkivsidvsaalalpGVvavit.akd.lpkenkaig..siledee.da 70 
                                       tGea+Y+ D+   +p+ +++++vrS +ah+++ s+d+saa+a++GV avit  +d +p++ +++   s +e+++ d 
  gi|344210252|ref|YP_004786428.1|  46 TGEARYTADYRdrFPDLAHGKVVRSDIAHGYVESVDTSAAEAMDGVDAVITpFDDvVPDKLYSSSgqSYPEPSPwDL 122
                                       8********963367777*********************************44553444444444555555555788 PP

                                       SS-SSEESSTT-EEEEEEESSHHHHHHHHHT-EEEEEE- CS
                      Ald_Xan_dh_C  71 llaedkvrsvgqavaavvAedeetArkAaklvkveYeel 109
                                         ++++vr+vg++vaav+A+d e+A++Aa++++veY+el
  gi|344210252|ref|YP_004786428.1| 123 KVLREHVRFVGDPVAAVAADDPEAADRAARKIEVEYREL 161
                                       999**********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (808 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:                        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: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 4935.67
//
Query:       gi|344210253|ref|YP_004786429.1|  [L=123]
Description: intracellular sulfur reduction protein, DsrE/DsF family protein [Haloarcula hispanica ATCC 33960]
Scores for 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-31  107.1   0.0    7.4e-31  107.0   0.0    1.0  1  DrsE      DsrE/DsrF-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 !  107.0   0.0   4.1e-35   7.4e-31       2     116 ..       3     122 ..       2     123 .] 0.97

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 4.1e-35
                                       EEEEEE-S-TTTBSHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS---TGGGTS---.....GGGGGGCGGGT-E CS
                              DrsE   2 kvfilvtggpygseaarealelalaaaalghevsvffygdGvllllkgqtanpadeknl.....aellkalkeygvk 73 
                                       ++ +l tggp++se++r+a+el +aa+++ghevs+f+y dG+l+++++qt ++++++ l     +e++++l++ g++
  gi|344210253|ref|YP_004786429.1|   3 YIGFLLTGGPFDSERWRTAYELGRAALDQGHEVSYFHYLDGALVPVADQTLPGCSDSGLydempTEKFQELIADGAD 79 
                                       689************************************************************************** PP

                                       EEEEHHHHHHTT--GGGE-T--EEEE-HHHHHHHHHH-SEEEE CS
                              DrsE  74 lyvCgqaakargldededlgvgvevsglgelaelqnegdrvit 116
                                       +++Cg +++arg+d++ d   gvev+ l++la+++ e+drv++
  gi|344210253|ref|YP_004786429.1|  80 VICCGLCVDARGIDAPADYPEGVEVGLLPDLADIIGEADRVVS 122
                                       **************9988844********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 890.30
//
Query:       gi|344210254|ref|YP_004786430.1|  [L=117]
Description: intracellular sulfur reduction protein, DsrE/DsF family protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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-08   34.5   0.0    2.2e-08   34.5   0.0    1.1  1  DrsE      DsrE/DsrF-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 !   34.5   0.0   1.2e-12   2.2e-08       7     115 ..       9     115 ..       3     117 .] 0.75

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.2e-12
                                       E-S-TTTBSHHHHHHHHHHHH.HTTT.-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEHHHH CS
                              DrsE   7 vtggpygseaarealelalaa.aalg.hevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvCgqaa 81 
                                        t +p g     e+l++a+ + a ++ h+v v+f++dGv+ ++    a + +  n++  ++ l+e+g ++++ ++a+
  gi|344210254|ref|YP_004786430.1|   9 LTRAPCGRVHIPEGLRAARGVaAGFDmHDVTVIFTQDGVYGARD---AVGREALNMSGHVADLAEQGGQMIADRAAM 82 
                                       555555555555666666644133447*****************...77777889********************** PP

                                       HHTT--GGGE-T--EEEE-HHHHHHHHHH-SEEE CS
                              DrsE  82 kargldededlgvgvevsglgelaelqnegdrvi 115
                                       ++rg+de e    +v+v +  ++   + ++d+ +
  gi|344210254|ref|YP_004786430.1|  83 AERGVDEGEIA-DDVTVWSDDRVTARIRDADHTL 115
                                       ******87544.4777776666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); 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 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 794.12
//
Query:       gi|344210255|ref|YP_004786431.1|  [L=80]
Description: hypothetical protein HAH_5314 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-05   24.3   0.6    0.00019   21.5   0.6    1.9  1  DsrH      DsrH like protein


Domain annotation for each model (and alignments):
>> DsrH  DsrH like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.6   1.1e-08   0.00019      18      85 ..      20      75 ..       9      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.1e-08
                                      TT-EEEE-GGGGGGGBTTBTTHHHHHTSSSEEEEEHHHHHHTT-TTSB-TTSEEE-HHHHHHHHHHSS CS
                              DsrH 18 egDavlLieDgVyaalkgsrllkalkeasvklyaLkeDleARGlteqlsegvkvidydgfVeltvkhk 85
                                      ++ +v+Li+DgVy+  +       +++    + a + D++ RG++  l + ++ i yd++V+ +v+++
  gi|344210255|ref|YP_004786431.1| 20 PEAHVVLIQDGVYLSPD-------IDA---PVSAVARDVDVRGVD--LTPDIDPIPYDDVVAAIVEQE 75
                                      5569*********9944.......444...59999**********..9***************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 536.52
//
Query:       gi|344210256|ref|YP_004786432.1|  [L=526]
Description: putative xanthine dehydrogenase accessory factor [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-36  124.3   1.8    3.7e-35  121.2   0.1    2.3  2  XdhC_C           XdhC Rossmann domain
    1.5e-17   63.5   1.4    1.5e-17   63.5   1.4    3.6  5  XdhC_CoxI        XdhC and CoxI family
      0.004   17.7   1.6      0.046   14.3   0.0    2.7  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
     0.0062   15.8   2.4      0.022   14.0   0.1    2.2  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
     0.0093   16.2   1.7        4.4    7.6   0.0    2.7  2  TrkA_N           TrkA-N domain
  ------ inclusion threshold ------
      0.025   14.5   1.5       0.66    9.8   0.3    2.5  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.045   13.8   1.6      0.074   13.1   0.2    1.9  2  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
      0.061   12.7   0.9          7    6.0   0.0    2.7  3  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.12   12.2   0.0       0.24   11.3   0.0    1.5  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens


Domain annotation for each model (and alignments):
>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.2   0.1   1.8e-38   3.7e-35       1     125 []     105     247 ..     105     247 .. 0.99
   2 ?    2.4   0.1       0.1     2e+02       1      32 [.     268     299 ..     268     384 .. 0.78

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 1.8e-38
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE..................-EEEE--S-HHHHHH CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade..................tavvvlthdhklDae 59 
                                       l+i G+gh++ +la+la++lg+ vtvvd+re++a++ +fp+a++                  tav+v+t++ ++D++
  gi|344210256|ref|YP_004786432.1| 105 LYIAGGGHISTELAPLAERLGYAVTVVDDREAYADPGQFPDATDvihgdygealgdlpmgteTAVAVATRSGTFDQD 181
                                       79**************************************9999********************************* PP

                                       HHHHHSSS--SEEEESS-HHHHHHHCTTS.--.......TTEESS-S--S---SHHHHHHHHHHHH CS
                            XdhC_C  60 aleaalrkkaayigllGSrkkaarrlerlraaglseeelarlhaPiGldigaktpeeIAvsilAei 125
                                       a++aal+++a+y+gl++S++ka+++l+ l+++g+++ +l+r+++P+Gld+g+  p+ +A+silAe+
  gi|344210256|ref|YP_004786432.1| 182 AVAAALDGEAGYVGLVASETKANHVLDSLAESGYARRDLSRVRTPVGLDLGGSGPAAVALSILAEV 247
                                       ******999********************999********************************96 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.1
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GG CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpree 32 
                                       +v+ G+g+ +  ++  ++++gf v+v + ++ 
  gi|344210256|ref|YP_004786432.1| 268 VVVRGGGDLGSGVVYRLQQAGFPVIVTEVEQP 299
                                       5889**********************988774 PP

>> XdhC_CoxI  XdhC and CoxI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   1.4   7.6e-21   1.5e-17       2      67 ..      11      76 ..      10      77 .. 0.87
   2 ?   -1.2   0.1       1.2   2.5e+03      11      26 ..     128     142 ..     125     192 .. 0.68
   3 ?   -3.0   0.1       4.3   8.6e+03      50      58 ..     330     338 ..     301     341 .. 0.61
   4 ?   -3.1   0.2       4.6   9.2e+03      34      58 ..     457     481 ..     453     484 .. 0.75
   5 ?   -2.7   0.1       3.6   7.3e+03      40      49 ..     514     523 ..     513     525 .. 0.87

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 7.6e-21
                                      HHCT..EEEEEEEEEECSSSSGTT-EEEEETTS-EEE-SSSSCHHHHHHHHHHHHHH.CT--EEEEE CS
                         XdhC_CoxI  2 laagrpvalaTVvdteGsaprplGakmlvrpdgrviGsvgggclEaavideAralla.agrtalvry 67
                                      + +g p+al T+v+++Gsapr +G km+v++d+  +G++ggg +E+ ++++Ar +l  a  +++++y
  gi|344210256|ref|YP_004786432.1| 11 AGQGVPAALLTIVRKDGSAPRDVGDKMVVTDDE-EYGTIGGGTVEHLAVQDARSVLSgADDPGVRTY 76
                                      5689****************************9.57********************83333446666 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.2
                                       EEEEEEECSSSSGTT- CS
                         XdhC_CoxI  11 aTVvdteGsaprplGa 26 
                                       +TVvd +  a++ +G 
  gi|344210256|ref|YP_004786432.1| 128 VTVVD-DREAYADPGQ 142
                                       78888.6677777774 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.3
                                       HHHHHHHHH CS
                         XdhC_CoxI  50 ideAralla 58 
                                       +deA++lla
  gi|344210256|ref|YP_004786432.1| 330 VDEALELLA 338
                                       566777665 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 4.6
                                       S-EEE-SSSSCHHHHHHHHHHHHHH CS
                         XdhC_CoxI  34 grviGsvgggclEaavideAralla 58 
                                       g v+G+v    +E ++   +r+l+ 
  gi|344210256|ref|YP_004786432.1| 457 GDVVGTVDDRPVETEIDGLVRGLVH 481
                                       6689999888888888877777765 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 3.6
                                       SSSSCHHHHH CS
                         XdhC_CoxI  40 vgggclEaav 49 
                                       +ggg lEa++
  gi|344210256|ref|YP_004786432.1| 514 LGGGVLEATL 523
                                       79*****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 !   14.3   0.0   2.3e-05     0.046       4      35 ..     107     138 ..     105     159 .. 0.85
   2 ?    1.3   0.6      0.26   5.1e+02       2      29 ..     268     295 ..     267     323 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-05
                                       EECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox   4 vvGgGyiglElAgalaelgkkVtvversdkll 35 
                                       + GgG i  ElA  + +lg  Vtvv+ ++   
  gi|344210256|ref|YP_004786432.1| 107 IAGGGHISTELAPLAERLGYAVTVVDDREAYA 138
                                       89************************998765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.26
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvve 29 
                                       vvv GgG++g  +   l++ g  V v e
  gi|344210256|ref|YP_004786432.1| 268 VVVRGGGDLGSGVVYRLQQAGFPVIVTE 295
                                       7999******999999999884444333 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 !   14.0   0.1   1.1e-05     0.022     143     178 ..     103     138 ..      75     176 .. 0.87
   2 ?    1.3   0.4      0.08   1.6e+02     142     207 ..     265     331 ..     233     365 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                                       SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardrll 178
                                       +++ + GgG i++ElA  + +lg+ vt+v++r+   
  gi|344210256|ref|YP_004786432.1| 103 AWLYIAGGGHISTELAPLAERLGYAVTVVDDREAYA 138
                                       67899*************************998765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.08
                                       TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 142 pkrivvvGgGyiGvElAaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvk 207
                                       ++ +vv GgG  G+ +   l ++g  v + e  +  + r      +a +e++++ eGv+ +  + v 
  gi|344210256|ref|YP_004786432.1| 265 DDLVVVRGGGDLGSGVVYRLQQAGFPVIVTEVEQPTVvRRAVAFGAALYEDEVTVEGVTGQAASDVD 331
                                       3445677888888888888888877765555443333366666667777777777777766555555 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0022       4.4       3      50 ..     107     155 ..     105     210 .. 0.77
   2 !    7.4   0.4    0.0025         5       1      50 [.     268     318 ..     268     365 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0022
                                       EES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT.SEEEES-TT CS
                            TrkA_N   3 iiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg.levvvgdat 50 
                                       i+G G + ++la   ++ g+  v+v+d++e+ ++  +    ++v++gd+ 
  gi|344210256|ref|YP_004786432.1| 107 IAGGGHISTELAPLAERlGYA-VTVVDDREAYADPGQFPDaTDVIHGDYG 155
                                       89***************9995.*******999988875554779999975 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0025
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSH.HHHHHHHHTTSEEEES-TT CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkde.erveelreeglevvvgdat 50 
                                       +++ G G++G+ ++ +L+++g +v+v + ++  +v+++ + g+  +  ++t
  gi|344210256|ref|YP_004786432.1| 268 VVVRGGGDLGSGVVYRLQQAGFPVIVTEVEQpTVVRRAVAFGAALYEDEVT 318
                                       6899***************66358887765525566666666555555555 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 ?    3.3   0.0     0.034        68       4      35 ..     107     138 ..     105     187 .. 0.89
   2 ?    9.8   0.3   0.00033      0.66       2      40 ..     268     306 ..     267     341 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.034
                                       EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHH CS
                           3HCDH_N   4 viGaGtmGagiaavfasagleVvlvdiseeal 35 
                                       + G G + +++a ++ + g+ V++vd +e+ +
  gi|344210256|ref|YP_004786432.1| 107 IAGGGHISTELAPLAERLGYAVTVVDDREAYA 138
                                       679***********************988765 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00033
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekale 40 
                                       v v G G +G+g+ + + +ag++V ++++++ ++ + + 
  gi|344210256|ref|YP_004786432.1| 268 VVVRGGGDLGSGVVYRLQQAGFPVIVTEVEQPTVVRRAV 306
                                       6788*************************8766554444 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 ?   -1.4   0.1       1.1   2.2e+03      30      52 ..      44      66 ..      33      71 .. 0.75
   2 ?   13.1   0.2   3.7e-05     0.074      25      56 ..     267     298 ..     254     324 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.1
                                      --SHHHHHHHHHHHHCT-EEEEE CS
                     AdoHcyase_NAD 30 GyGdvGkGcaaslkglGarvivt 52
                                       yG +G G+ + l  + ar +++
  gi|344210256|ref|YP_004786432.1| 44 EYGTIGGGTVEHLAVQDARSVLS 66
                                      59***********9999998776 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.7e-05
                                       EEEEE--SHHHHHHHHHHHHCT-EEEEE-S-H CS
                     AdoHcyase_NAD  25 vavvaGyGdvGkGcaaslkglGarvivtevdP 56 
                                        +vv G Gd+G G    l+++G  vivtev+ 
  gi|344210256|ref|YP_004786432.1| 267 LVVVRGGGDLGSGVVYRLQQAGFPVIVTEVEQ 298
                                       6899**************************74 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 ?    6.0   0.0    0.0035         7      39      69 ..     105     135 ..      80     149 .. 0.82
   2 ?   -2.5   0.0       1.4   2.7e+03     127     142 ..     173     188 ..     165     196 .. 0.81
   3 ?    4.4   0.0     0.011        22      39      70 ..     268     299 ..     246     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0035
                                       EEEES-SHHHHHHHHHHHHTT-EEEEESSSH CS
                      2-Hacid_dh_C  39 vGiiGlGrIGqavakrlkafgmkviaydrsk 69 
                                       + i G G+I +++a +++ +g  v+++d ++
  gi|344210256|ref|YP_004786432.1| 105 LYIAGGGHISTELAPLAERLGYAVTVVDDRE 135
                                       4599***********************9875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
                                       S-GGGB-HHHHHHHHH CS
                      2-Hacid_dh_C 127 aRGglvdeeaLleaLk 142
                                        R g+ d++a+++aL+
  gi|344210256|ref|YP_004786432.1| 173 TRSGTFDQDAVAAALD 188
                                       599999******9997 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.011
                                       EEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C  39 vGiiGlGrIGqavakrlkafgmkviaydrskk 70 
                                       v + G G++G+ v  rl++ g+ vi++++ + 
  gi|344210256|ref|YP_004786432.1| 268 VVVRGGGDLGSGVVYRLQQAGFPVIVTEVEQP 299
                                       67889*********************998765 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 ?   11.3   0.0   0.00012      0.24      35      60 ..     443     468 ..     427     484 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                       EEEESS-TT-EEETT-EEEEEECTTC CS
                   ATP-synt_ab_Xtn  35 efkpkvkvgdkvsggdilGtvqetel 60 
                                       +++p+v+ gd+v++gd++Gtv++  +
  gi|344210256|ref|YP_004786432.1| 443 NWTPTVAIGDSVTAGDVVGTVDDRPV 468
                                       689******************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); 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:                         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 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3604.73
//
Query:       gi|344210257|ref|YP_004786433.1|  [L=346]
Description: putative selenophosphate synthase [Haloarcula hispanica ATCC 33960]
Scores for 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   68.9   0.0      9e-19   68.1   0.0    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain
      2e-11   44.4   1.6      6e-11   42.8   1.6    1.8  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 !   68.1   0.0     1e-22     9e-19       2     153 ..     175     336 ..     174     338 .. 0.79

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 1e-22
                                       TTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT.......TSEHHHHHHHHHHHHHHHHHHHH.HTTECEEEE--TT CS
                            AIRS_C   2 pGdvliltgslGlggagtslkrkileeegldds.......avqlgdvlleptliyvkralaal.kglvkaahDvTgG 70 
                                       pGd+l+lt++lG++ a+  + r  +++  +          ++  +++++  ++   +r + ++ ++ ++aa+D+Tg+
  gi|344210257|ref|YP_004786433.1| 175 PGDRLYLTKPLGTQPAM-GATRVTDAQFVETVTdaadrplDSIASEAIA--WMTTPNRDATLAcREYATAATDITGF 248
                                       9*********9999888.6666555543333334586664444444444..566666666666779*********** PP

                                       HHHHHHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHC.........STTTEEEEEEEHGGHHHHHHHHHHTTCCC CS
                            AIRS_C  71 GLlgalaemapasgvgaeidldkvpifdelesplemlls.........ensGrllvavppeeadavlaileeeglpe 138
                                       GL+g    ma+ s+vg+e++    p+++ +  +l  l+          e+sG+l+v+vpp++ dav a+++++ +  
  gi|344210257|ref|YP_004786433.1| 249 GLAGQSRVMADRSNVGIELTHL--PVIAGT-PALSTLFGygltdgesaETSGGLFVSVPPAATDAVEAAFDDASV-F 321
                                       **********************..777776.55555555677899999**************************9.7 PP

                                       EEEEEEEEESSSEEE CS
                            AIRS_C 139 aavIGevtakeelsv 153
                                       ++ +G+vt++ ++++
  gi|344210257|ref|YP_004786433.1| 322 YRAVGRVTGGSGVTL 336
                                       *********987765 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 !   42.8   1.6   6.7e-15     6e-11       2      84 ..      57     152 ..      47     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 6.7e-15
                                       SSE........EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEE.EEEEEEEEC.....HHHHHHHHHHH CS
                              AIRS   2 Daa........vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPl.alllslalp.....wleevvrglae 64 
                                       Daa         +v+t ++++p++ +p++f G+ a+++++sD +a+GA     +l++l lp      ++ +++g+a+
  gi|344210257|ref|YP_004786433.1|  57 DAAarkltdelALVSTVDFFTPIVDDPYDF-GRVAACNAASDAFATGAVENvDCLVVLGLPreltdSAASILAGMAD 132
                                       777566555542555655************.*****************665589************99********* PP

                                       HHHHTT-EEEEEEEEEESSE CS
                              AIRS  65 aaeelgvplvgGdtsfsnep 84 
                                       a+++++  ++gG+t  s+ p
  gi|344210257|ref|YP_004786433.1| 133 ALDAMDGVIAGGHTIMSPWP 152
                                       **************988754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2404.25
//
Query:       gi|344210258|ref|YP_004786434.1|  [L=82]
Description: SirA family protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   57.1   0.0    1.5e-15   56.8   0.0    1.1  1  TusA      Sulfurtransferase TusA
  ------ inclusion threshold ------
      0.012   15.5   0.1      0.013   15.4   0.1    1.3  1  DUF2249   Uncharacterized conserved protein (DUF2249)


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 !   56.8   0.0   1.6e-19   1.5e-15       3      67 ..       4      70 ..       3      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 1.6e-19
                                      EEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-..GCC-EEEE CS
                              TusA  3 lDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelvevee..edgeyriv 67
                                      +D+rG++CP P l +++al  l++ge+l v+ d p+a+++++r++  +g +++  e   e +e+++ 
  gi|344210258|ref|YP_004786434.1|  4 VDVRGEICPRPALIVRQALSDLDPGETLVVRGDYPPAEKNLRRMCTTHGIDVTTAETagESDEFELE 70
                                      8**************************************************9988776655777665 PP

>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.1   1.4e-06     0.013       2      34 ..       4      36 ..       3      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-06
                           DUF2249  2 lDvRelppperhaaIfeafeaLapGetlelvnd 34
                                      +DvR+   p +   + +a+++L+pGetl++  d
  gi|344210258|ref|YP_004786434.1|  4 VDVRGEICPRPALIVRQALSDLDPGETLVVRGD 36
                                      7***************************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 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:                        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 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 570.68
//
Query:       gi|344210259|ref|YP_004786435.1|  [L=259]
Description: anaerobic dehydrogenase cluster protein [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1662.56
//
Query:       gi|344210260|ref|YP_004786436.1|  [L=205]
Description: UDP-N-acetylglucosamine pyrophosphorylase [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-37  128.1   1.0    4.8e-37  127.8   1.0    1.0  1  NTP_transf_3  MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.016   15.2   0.0    1.2  1  CTP_transf_3  Cytidylyltransferase


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 !  127.8   1.0   5.4e-41   4.8e-37       1     157 [.      11     172 ..      11     176 .. 0.96

  Alignments for each domain:
  == domain 1  score: 127.8 bits;  conditional E-value: 5.4e-41
                                       EEEEEESS-TTTT.TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHC..HHHHHHTTCTS-EEE-TTSS-SHHH CS
                      NTP_transf_3   1 aviLAGGrSsRmg.gdKallplggkpllervldalraagvdevvvvggde..evlaalarlgvrvvededpgkgpla 74 
                                       +v+LA+GrSsR+  g+K+l+ +gg+ ++++v++++ ++++++vv v g+e  +v++al+ l v++ +++d+ +g++a
  gi|344210260|ref|YP_004786436.1|  11 GVVLAAGRSSRYEpGNKLLATIGGRAVVRQVAETACESPLSDVVAVLGYEgvAVAEALEALSVSLRHNDDYAAGQSA 87 
                                       79**********966**********************************8668999********************* PP

                                       HHHHHHHHH...SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEEGGGHHHHHHHCTHTT CS
                      NTP_transf_3  75 slaaalraaa..dadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpllfrarllsalaallgdqg 149
                                       s++++++ a+  + da+l+l++DmP++++e++e l++a++   a vvvp++eg+rg+p+lf    ++ala+++gd+g
  gi|344210260|ref|YP_004786436.1|  88 SVRHGVDYAQesGWDAALFLLGDMPFVRAETIEVLIEAYRTGTATVVVPEHEGTRGNPVLFDGYHFDALASVSGDRG 164
                                       *******988778999************************************************************* PP

                                       HHHCHHHH CS
                      NTP_transf_3 150 arrllrrl 157
                                       +r++++  
  gi|344210260|ref|YP_004786436.1| 165 GRDIIETT 172
                                       ****9865 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.8e-06     0.016       4     119 ..      13     130 ..      11     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-06
                                       EEE-SSSSSST..TGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTT.SEEEE-.-TTCSSHHHH CS
                      CTP_transf_3   4 ipARsgSkRlp..gKnlldlggkpliayvleaalkskafekvivaTDseeiknvakefg.asvlvt.rsslesdter 76 
                                       ++A   S+R +  +K l+ +gg+  ++ v e a +s++ +   va    e + va+++   sv ++   +  +++++
  gi|344210260|ref|YP_004786436.1|  13 VLAAGRSSRYEpgNKLLATIGGRAVVRQVAETACESPLSDV--VAVLGYEGVAVAEALEaLSVSLRhNDDYAAGQSA 87 
                                       55666666665459************************665..6666677777777776555544413467788888 PP

                                       HHHHHHHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHHST CS
                      CTP_transf_3  77 flevvkaflmseneeiivnlqGdnPllqeevikkaietlkenq 119
                                       ++    +++ +   + ++ l Gd P++  e+i+ +ie+++   
  gi|344210260|ref|YP_004786436.1|  88 SVRHGVDYAQESGWDAALFLLGDMPFVRAETIEVLIEAYRTGT 130
                                       888888888887777***********************98764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1309.92
//
Query:       gi|344210261|ref|YP_004786437.1|  [L=126]
Description: endoribonuclease L-PSP [Haloarcula hispanica ATCC 33960]
Scores for 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-38  129.3   0.1    7.9e-38  129.2   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 !  129.2   0.1   4.4e-42   7.9e-38       2     120 ..       8     124 ..       7     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 129.2 bits;  conditional E-value: 4.4e-42
                                       TTSTTTSSS-BSEEEETTEEEEEEE-SB-TTTSCB..-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEESSGG CS
                     Ribonuc_L-PSP   2 eaapaaaapYsqavkagnlvyvsGqlpldpetgelv.egdveeqtrqalenlkavLaaagaslsdvVkvtvFladie 77 
                                        +ap+a+++Ysqa ++g lv+++Gq+p++p +g+l  ++ ++ q++qal+n++av+a+ g+++sdv+kvtv+l di+
  gi|344210261|ref|YP_004786437.1|   8 ADAPDAVGAYSQATTNGSLVFTAGQIPMTP-DGDLLdDEPIATQAEQALSNVEAVIASEGLEMSDVLKVTVYLDDID 83 
                                       689**************************9.777776999************************************* PP

                                       GHHHHHHHHHHHSSSSTS--EEEEEE-SBSGGG-SEEEEEEEE CS
                     Ribonuc_L-PSP  78 dfaevnevyaeafdelkeaParsaveVaaLpkgakvEIeaiav 120
                                       df+ +n+ ya++fd++   ParsaveVa+Lpk++ vEIeaia+
  gi|344210261|ref|YP_004786437.1|  84 DFESMNDTYAGFFDDEP--PARSAVEVASLPKDVGVEIEAIAT 124
                                       ****************5..**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 872.42
//
Query:       gi|344210262|ref|YP_004786438.1|  [L=444]
Description: N-ethylammeline chlorohydrolase [Haloarcula hispanica ATCC 33960]
Scores for 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-67  226.6   0.2    6.2e-67  226.3   0.2    1.1  1  Amidohydro_1  Amidohydrolase family
    4.4e-11   42.9   3.2    4.5e-11   42.9   0.5    2.0  2  Amidohydro_3  Amidohydrolase family
     0.0024   17.3   0.0      0.004   16.5   0.0    1.3  1  A_deaminase   Adenosine/AMP deaminase


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.3   0.2     1e-70   6.2e-67       1     343 [.      50     404 ..      50     405 .. 0.95

  Alignments for each domain:
  == domain 1  score: 226.3 bits;  conditional E-value: 1e-70
                                       EEEE-EEEEEEECETTECSSS....GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgi 63 
                                       ++lPGl+  H+H  qsl+rg+     l+dwl          ++ e+ ++a++ g  ++++sGttt++d+  ++  ++
  gi|344210262|ref|YP_004786438.1|  50 VLLPGLVGGHIHSVQSLGRGIaddtELLDWLfdyilpmeasLTAEEMEVAAKLGYLEMIESGTTTCIDHLSVA--HA 124
                                       589********************************************************************99..9* PP

                                       HHHHHHHHTSSSEEEEEEESSEGGS.......GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHH CS
                      Amidohydro_1  64 ealleaaeelplglrilggkvsldr.......gsaetskasreklkagaaetikgkadgvvkvalapheapafsdee 133
                                       ++ +eaa e+  g+r ++gkv +d+       ++++  +++ e+l+++     +g  ++++  a++p++a+++s++ 
  gi|344210262|ref|YP_004786438.1| 125 DRAFEAAGEI--GIRGVLGKVLMDQrspdgllEDTQAALEESERLIQQY----HGAYNDRIRYAVTPRFAVSCSEAC 195
                                       *********8..*************999999988888899999999998....8888999***************** PP

                                       HHHHHHHHHHH.TTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHH CS
                      Amidohydro_1 134 lkealkeakkr.dlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellker 209
                                       l+ + ++++k+ ++ +++Ha+e++ e+e ++++ g   ++    ++++++gl +e  ++lah+v+ + +e e+l+e 
  gi|344210262|ref|YP_004786438.1| 196 LRGVRELVDKYdGVRIHTHASENQSEIETVKEDTG---MR--NIHWLDEVGLTGE-DVVLAHCVWTDESEREVLAET 266
                                       ***********************************...44..7779999******.********************* PP

                                       HHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHH CS
                      Amidohydro_1 210 lkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkeal 286
                                         ++ v+hcp+sn++l+sg++++++  d+G++v++g Dg  ++n+l+ ++e+r+a +lq+ + + d+++  +++e++
  gi|344210262|ref|YP_004786438.1| 267 --GTHVTHCPSSNMKLASGIAPIWDYRDRGINVAIGNDGPPCNNTLDAFTEMRQASLLQK-VDQLDPTV-TPAAEIF 339
                                       ..******************************************************9999.44448888.9999*** PP

                                       HHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCT.........CGGGTTTCTSEEEEEEEETTEE CS
                      Amidohydro_1 287 rmaTingAkalglddkvGsievGkdADlvvvdldi.........laafvglkkdgnvkkvivkGkl 343
                                       +maT ngAka g+d ++G+i +G +AD+v +d+d+         l+++v+ ++   v+ ++v+G++
  gi|344210262|ref|YP_004786438.1| 340 EMATRNGAKAAGFD-ELGAIREGWRADIVGLDTDLtratplhdvLSHLVFAAHGDDVRFTMVDGNV 404
                                       *************6.******************44445568888********************97 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1     0.071   4.3e+02       9      21 ..      50      62 ..      49      74 .. 0.81
   2 !   42.9   0.5   7.5e-15   4.5e-11     305     472 ..     242     405 ..     193     406 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.071
                      Amidohydro_3  9 lvlPGFvDsHtHl 21
                                      ++lPG+v  H+H 
  gi|344210262|ref|YP_004786438.1| 50 VLLPGLVGGHIHS 62
                                      689*********4 PP

  == domain 2  score: 42.9 bits;  conditional E-value: 7.5e-15
                      Amidohydro_3 305 nqdrr.rlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsD.apv. 378
                                       +++    l+h+ +++es++e +a+ +     +p +n            + a+g++p+   ++ g++va g+D +p+ 
  gi|344210262|ref|YP_004786438.1| 242 LTGEDvVLAHCVWTDESEREVLAETGTHVTHCPSSNM-----------KLASGIAPIWDYRDRGINVAIGNDgPPCn 307
                                       4444358889999999999999999999999999988...........88999*******************97763 PP

                      Amidohydro_3 379 gpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdpp 455
                                       +++d + +++ a  ++++ +     +    +  e++ + Tr++Aka g ++  G +++G +AD+v ld+d+ +++p 
  gi|344210262|ref|YP_004786438.1| 308 NTLDAFTEMRQASLLQKVDQL----DPTVTPAAEIFEMATRNGAKAAGFDEL-GAIREGWRADIVGLDTDLTRATPL 379
                                       689**************8665....888999********************8.**********************96 PP

                      Amidohydro_3 456 elaear...........vrltvvdGrvv 472
                                         ++++           vr t+vdG+v+
  gi|344210262|ref|YP_004786438.1| 380 --HDVLshlvfaahgddVRFTMVDGNVL 405
                                       ..4555559****************985 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.6e-07     0.004     233     300 ..     262     326 ..     249     357 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.6e-07
                                       HHHHCT-EEEE-HHHHCCCSST-TTTT-CHHHHHHTT-EEEE--BSCCCCT-S.HHHHHHHHHHHHT-- CS
                       A_deaminase 233 llalaqiplevcPlSNvalgafleyaenPlkeflerglnvslntDDPlqfgtt.LieeYaiaaqvfkls 300
                                        la+  ++++ cP+SN++l    +    P+ ++ +rg+nv+++ D P   +t    +e+ +a+   k +
  gi|344210262|ref|YP_004786438.1| 262 VLAETGTHVTHCPSSNMKL----ASGIAPIWDYRDRGINVAIGNDGPPCNNTLdAFTEMRQASLLQKVD 326
                                       6788999************....77789*******************9887766445555444333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 3076.70
//
Query:       gi|344210263|ref|YP_004786439.1|  [L=65]
Description: 30S ribosomal protein S17e [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   13.4   0.0      0.057   13.3   0.0    1.1  1  Ribosomal_S17e  Ribosomal S17


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 ?   13.3   0.0   3.2e-06     0.057      16      64 ..      15      62 ..       8      65 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-06
                                      HHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHHHHTTSS CS
                    Ribosomal_S17e 16 iiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlmkriqkg 64
                                      ++ +y + +t++++tn ++++  a + s + +++ + y+t+  kr ++g
  gi|344210263|ref|YP_004786439.1| 15 LLSEYPELFTEQYETNTRLVQRLASVDSFRTQTRLTRYITRQ-KRTRNG 62
                                      677899999*****************************9984.666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 396.40
//
Query:       gi|344210264|ref|YP_004786440.1|  [L=282]
Description: NH(3)-dependent NAD(+) synthetase [Haloarcula hispanica ATCC 33960]
Scores for complete 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  158.8   0.0    1.5e-46  158.5   0.0    1.0  1  NAD_synthase  NAD synthase
  ------ inclusion threshold ------
      0.026   13.9   0.1      0.074   12.5   0.1    1.7  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
      0.056   13.2   0.0       0.14   11.9   0.0    1.6  1  HTH_38        Helix-turn-helix domain
       0.13   12.1   0.1       0.34   10.8   0.1    1.7  1  HTH_23        Homeodomain-like domain
       0.22   11.9   1.4        8.7    6.8   0.1    2.8  2  HTH_31        Helix-turn-helix domain


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 !  158.5   0.0   4.2e-50   1.5e-46       8     242 .]      36     275 ..      31     275 .. 0.98

  Alignments for each domain:
  == domain 1  score: 158.5 bits;  conditional E-value: 4.2e-50
                                       HHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHH CS
                      NAD_synthase   8 flkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpi 84 
                                       fl++++++a+a+g+v+ l G + S+++aalav+ +g + v++l++P + s+e  ++ a ++a  l+i+ + ++++p+
  gi|344210264|ref|YP_004786440.1|  36 FLENKITEAEANGLVVPLDGSIESTVAAALAVDGIGADYVTGLVMPVQLSDEGPARTAETVASLLDIDCHRLNLQPV 112
                                       9**************************************************************************** PP

                                       HHHHHHHHHHHH....-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS-HH CS
                      NAD_synthase  85 vrafeqelkeak....edlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaellKt 157
                                       ++af+  + e+     + +a +N   R Rma++y++an  n+lv+gT  ++++++G + k+G  ++dl   ++l++t
  gi|344210264|ref|YP_004786440.1| 113 LTAFQRVVGETGgptdDLVAMQNAGERFRMACKYYVANTRNELVVGTVSRTDRLLGSVAKHGENGVDLSLFGDLYRT 189
                                       ******888877777788999******************************************************** PP

                                       HHHHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHT.HSSSS...HHHHHTTT--HHHHHHHHHHHH CS
                      NAD_synthase 158 evkeLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLk.lvekkkspeeiikekelpaevvekieklvk 233
                                       e+ +La++l+vP  +l++ P     +g tD +eLgi    lD +L+  ++++ s   ++++ +++++vve+++++  
  gi|344210264|ref|YP_004786440.1| 190 EIEALAAALAVPSDLLDQSPHPMEHTGATDAAELGIDQRDLDSVLHfAIDRGCSVSAVADKVGVSESVVERTVQWCA 266
                                       **********************************************99***************************** PP

                                       HTGGGGSSS CS
                      NAD_synthase 234 ksehKrklp 242
                                       +++hKr++p
  gi|344210264|ref|YP_004786440.1| 267 STRHKRHTP 275
                                       ******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 ?   12.5   0.1   2.1e-05     0.074      26      47 ..     241     261 ..     237     263 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
                      HTH_Tnp_ISL3  26 esrsvkavArqlgvSwtTVwri 47 
                                        + sv+avA+ +gvS++ V+r 
  gi|344210264|ref|YP_004786440.1| 241 GC-SVSAVADKVGVSESVVERT 261
                                       68.****************995 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.9e-05      0.14      18      41 ..     239     262 ..     235     263 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.9e-05
                            HTH_38  18 aeGlslreIArrLgrspsTIsREl 41 
                                       ++G+s++++A ++g+s s + R +
  gi|344210264|ref|YP_004786440.1| 239 DRGCSVSAVADKVGVSESVVERTV 262
                                       79******************9966 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   9.5e-05      0.34      17      41 ..     241     265 ..     232     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.5e-05
                            HTH_23  17 GlsvreIAreLgvsrrTvyrwlkry 41 
                                       G sv+++A++ gvs++ v r +++ 
  gi|344210264|ref|YP_004786440.1| 241 GCSVSAVADKVGVSESVVERTVQWC 265
                                       7799*****************9997 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2     0.042   1.5e+02      45      62 ..     189     206 ..     184     207 .. 0.87
   2 ?    6.8   0.1    0.0024       8.7      13      34 ..     240     261 ..     232     274 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.042
                            HTH_31  45 avlealaralgldpaera 62 
                                         +eala al ++ ++++
  gi|344210264|ref|YP_004786440.1| 189 TEIEALAAALAVPSDLLD 206
                                       579**********99886 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0024
                            HTH_31  13 aGLsqeevAerlgvsestlsrl 34 
                                       +G s  +vA+ +gvses + r 
  gi|344210264|ref|YP_004786440.1| 240 RGCSVSAVADKVGVSESVVERT 261
                                       68899************88875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1763.64
//
Query:       gi|344210265|ref|YP_004786441.1|  [L=274]
Description: hypothetical protein HAH_5324 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   13.7   0.7      0.082   12.9   0.7    1.4  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
       0.44   10.3   2.0       0.51   10.1   0.4    1.8  2  zinc_ribbon_2  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 ?   12.9   0.7   9.2e-06     0.082      21      44 ..      87     116 ..      80     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.2e-06
                     Zn_Tnp_IS1595  21 CPhCgsr.kayrikt.....rglfqCkeCr 44 
                                       CP+Cg++  ++++++      +  +C++C 
  gi|344210265|ref|YP_004786441.1|  87 CPNCGNElVHFTVERplgcsVFEMECQRCL 116
                                       *******99999999***999999*****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 ?   10.1   0.4   5.7e-05      0.51       2       9 ..      87      94 ..      86      95 .. 0.89
   2 ?   -1.9   0.1      0.36   3.2e+03      16      22 ..     112     118 ..     107     119 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5.7e-05
                     zinc_ribbon_2  2 CpnCGael 9 
                                      CpnCG+el
  gi|344210265|ref|YP_004786441.1| 87 CPNCGNEL 94
                                      99999997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.36
                     zinc_ribbon_2  16 CpyCGtp 22 
                                       C +C t+
  gi|344210265|ref|YP_004786441.1| 112 CQRCLTH 118
                                       7777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1722.28
//
Query:       gi|344210266|ref|YP_004786442.1|  [L=596]
Description: chromosome segregation ATPase-like protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   28.9  33.9       0.44   11.0   0.1    8.0  8  FlaC_arch        Flagella accessory protein C (FlaC)
    2.5e-06   27.7  42.5     0.0002   21.6   7.5    5.1  4  FliJ             Flagellar FliJ protein
    1.1e-05   25.5  60.0      0.043   13.9  20.2    6.0  5  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
    2.5e-05   24.4  54.4      0.031   14.5   4.2    5.7  6  ABC_tran_CTD     ABC transporter C-terminal domain
    6.4e-05   22.5  14.6    6.4e-05   22.5  14.6    3.1  3  DUF2353          Uncharacterized coiled-coil protein (DUF2353
    6.7e-05   21.8  34.4       0.28    9.8  34.1    3.6  2  AAA_13           AAA domain
     0.0001   21.5  38.0    0.00071   18.8  11.9    3.0  3  Atg14            Vacuolar sorting 38 and autophagy-related su
    0.00011   21.8   1.2      0.094   12.1   0.0    2.2  2  SMC_N            RecF/RecN/SMC N terminal domain
    0.00016   21.7  57.2      0.025   14.6  11.0    4.8  5  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    0.00016   22.2  39.3         49    4.3  39.3    3.7  1  AAA_23           AAA domain
    0.00018   20.5  56.0      0.024   13.5  18.6    3.7  3  Spc7             Spc7 kinetochore protein
    0.00019   21.5  29.5       0.35   10.9   6.3    5.0  4  DUF1664          Protein of unknown function (DUF1664)
     0.0005   19.5  45.2      0.064   12.6   3.3    4.3  4  GAS              Growth-arrest specific micro-tubule binding
    0.00079   19.5  40.9      0.034   14.2   0.2    6.4  6  TolA_bind_tri    TolA binding protein trimerisation
      0.001   18.9   8.5      0.001   18.9   8.5    4.0  4  DUF724           Protein of unknown function (DUF724)
      0.001   19.5  29.0      0.066   13.7   1.2    5.8  5  NPV_P10          Nucleopolyhedrovirus P10 protein
     0.0015   17.9  10.9     0.0015   17.9  10.9    4.0  4  CorA             CorA-like Mg2+ transporter protein
     0.0022   18.0  36.7      0.046   13.7   9.4    4.2  5  Laminin_II       Laminin Domain II
     0.0028   17.5   0.5     0.0028   17.5   0.5    1.9  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
     0.0062   15.9   8.3     0.0062   15.9   8.3    4.1  4  HemX             HemX, putative uroporphyrinogen-III C-methyl
     0.0073   16.5  40.6      0.016   15.4   2.6    5.2  4  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
     0.0077   16.2  11.9     0.0077   16.2  11.9    2.5  2  Alpha-2-MRAP_C   Alpha-2-macroglobulin RAP, C-terminal domain
     0.0088   16.3  37.9      0.085   13.1   5.8    4.3  4  DUF5082          Domain of unknown function (DUF5082)
  ------ inclusion threshold ------
       0.01   16.3  48.5       0.22   11.9  19.9    3.2  3  Fez1             Fez1
      0.011   16.0  55.8       0.05   13.8   7.1    5.4  3  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
      0.011   15.7  26.2      0.016   15.3   3.1    4.3  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.014   15.0  51.3       0.23   11.0  21.1    3.2  2  PspA_IM30        PspA/IM30 family
      0.016   15.0  40.3       0.31   10.8   3.6    4.4  4  Phage_GP20       Phage minor structural protein GP20
      0.018   14.9  28.5        1.5    8.7   0.1    5.4  5  Sec34            Sec34-like family
      0.022   14.2   2.1       0.39   10.1   0.1    3.2  3  Med14            Mediator complex subunit MED14
      0.034   13.7  35.9       0.11   12.0  12.6    2.6  2  Exonuc_VII_L     Exonuclease VII, large subunit
      0.035   13.6   0.3      0.035   13.6   0.3    2.0  2  ApbE             ApbE family
       0.05   11.8  40.6       0.02   13.1  18.0    2.3  2  FPP              Filament-like plant protein, long coiled-coi
       0.07   13.3  57.0        1.7    8.8  11.3    4.2  2  Tropomyosin_1    Tropomyosin like
       0.13   11.8  64.3       0.23   11.0  25.7    4.2  2  MscS_porin       Mechanosensitive ion channel porin domain
       0.16   10.3  46.8      0.014   13.8  18.3    2.3  2  MAD              Mitotic checkpoint protein
       0.17   12.5  67.0      1e+02    3.4  31.5    5.3  2  APG6_N           Apg6 coiled-coil region
       0.21   11.7  35.5        1.2    9.2   5.0    5.1  5  COG2             COG (conserved oligomeric Golgi) complex com
       0.29    8.6  53.6       0.18    9.3  47.1    2.6  3  DUF3584          Protein of unknown function (DUF3584)
       0.42    9.3  50.1      0.059   12.1  23.0    2.8  3  WEMBL            Weak chloroplast movement under blue light
       0.67    9.5  53.0       0.11   12.1  33.8    3.3  3  Filament         Intermediate filament protein
       0.77    9.5  37.0      0.023   14.4  12.8    3.5  4  DUF745           Protein of unknown function (DUF745)
        0.8    9.9  60.3      0.021   15.0  16.8    4.0  4  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
       0.85    8.5  35.4       0.11   11.4   8.9    3.9  4  IFT57            Intra-flagellar transport protein 57
       0.98    9.6  64.5       0.75   10.0  28.8    4.2  2  ATG16            Autophagy protein 16 (ATG16)
       0.99    9.1  14.4         31    4.3   0.0    4.8  4  Vac_Fusion       Chordopoxvirus multifunctional envelope prot
          1    9.0  39.8          3    7.6  12.7    4.5  4  DUF4201          Domain of unknown function (DUF4201)
        1.3    8.8  21.6       0.22   11.3   1.3    3.8  5  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
        1.4    9.0  71.2      0.093   12.8   8.4    5.7  5  DHR10            Designed helical repeat protein 10 domain
        1.4    9.1  33.9       0.22   11.7   4.2    4.4  4  Fib_alpha        Fibrinogen alpha/beta chain family
          2    7.2  52.4      0.039   12.8  18.9    2.6  3  CALCOCO1         Calcium binding and coiled-coil domain (CALC
        2.1    8.5  28.2       0.68   10.1   2.9    4.2  3  Cob_adeno_trans  Cobalamin adenosyltransferase
        2.4    8.3  27.9        4.1    7.6   1.2    5.2  6  DUF2730          Protein of unknown function (DUF2730)
        2.7    8.1  42.3        1.2    9.2  11.8    4.3  5  Mod_r            Modifier of rudimentary (Mod(r)) protein
        3.1    8.4  53.6        2.8    8.6  10.5    4.9  5  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
        3.3    7.7  51.3        1.9    8.5   4.2    7.7  7  Prefoldin_2      Prefoldin subunit
        3.5    7.7  42.6       0.26   11.4  13.6    3.4  3  End3             Actin cytoskeleton-regulatory complex protei
        3.5    5.6  56.4        2.2    6.3  29.5    2.8  2  HOOK             HOOK protein
        3.9    6.0  31.6        1.9    7.0  11.2    3.8  4  FapA             Flagellar Assembly Protein A
          4    7.8  22.5       0.17   12.2   2.2    5.1  5  DUF948           Bacterial protein of unknown function (DUF94
        5.2    4.9  25.6       0.18    9.8   7.0    2.8  3  Prominin         Prominin
        6.1    6.8  43.0        5.3    7.0  11.0    4.4  3  YscO-like        YscO-like protein
        6.7    6.0  50.9       0.29   10.4  18.7    3.4  1  DUF4407          Domain of unknown function (DUF4407)
        6.9    7.2  35.3        7.4    7.1   2.7    4.8  4  Snapin_Pallidin  Snapin/Pallidin
        7.4    5.8  23.4       0.61    9.4   6.1    2.2  2  FAM76            FAM76 protein
        7.7    6.0  27.2        3.1    7.3   1.6    5.1  5  Fzo_mitofusin    fzo-like conserved region
        8.2    6.4  12.8         65    3.5   0.3    4.3  3  ApoO             Apolipoprotein O
        8.3    6.8  33.9        6.3    7.2   2.2    5.5  5  BLOC1_2          Biogenesis of lysosome-related organelles co
        9.4    6.5  52.5       0.12   12.6   4.7    7.1  5  Spc24            Spc24 subunit of Ndc80


Domain annotation for each model (and alignments):
>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   1.9    0.0093       2.4       9      49 ..     130     170 ..     128     173 .. 0.86
   2 ?    3.8   0.3       0.3        78       4      27 ..     163     186 ..     160     190 .. 0.63
   3 ?    7.7   0.8     0.018       4.7      14      39 ..     200     225 ..     193     232 .. 0.86
   4 ?    0.3   0.1       3.5   9.2e+02      11      44 ..     239     273 ..     229     279 .. 0.65
   5 ?    7.3   0.1     0.024       6.2       7      35 ..     316     344 ..     312     352 .. 0.82
   6 !   11.0   0.1    0.0017      0.44       2      38 ..     363     399 ..     359     403 .. 0.93
   7 ?    3.0   0.2      0.54   1.4e+02       8      36 ..     404     432 ..     402     436 .. 0.86
   8 ?    7.8   0.1     0.016       4.2       8      36 ..     435     463 ..     429     477 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0093
                         FlaC_arch   9 lsklsteletvkkeneelsksveelkenVkdllsLYEvVsn 49 
                                       ++++++++et+++e e++++++++  e  k+l s+ E V++
  gi|344210266|ref|YP_004786442.1| 130 FQNIDSQIETLQREREQIETELTQAREAKKRLPSVQEKVTR 170
                                       689*******************9998888888888777775 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.3
                         FlaC_arch   4 elEnklsklsteletvkkeneels 27 
                                       ++++k+ +l+ e+e ++++ e + 
  gi|344210266|ref|YP_004786442.1| 163 SVQEKVTRLENEIEDLRAKRETID 186
                                       566677777777777777666664 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.018
                         FlaC_arch  14 teletvkkeneelsksveelkenVkd 39 
                                        +l+ +++e+++ ++ ve+l++++++
  gi|344210266|ref|YP_004786442.1| 200 RQLSQARTEQNQAKNRVERLEQSIER 225
                                       58999*****************9964 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 3.5
                         FlaC_arch  11 klst.eletvkkeneelsksveelkenVkdllsLY 44 
                                        l++ e + v ++++e ++s+ +++++ + l s+Y
  gi|344210266|ref|YP_004786442.1| 239 ALEIpEYNDVADKLSEARESLSQVERDAEVLQSVY 273
                                       55555666677777777777777776665555555 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.024
                         FlaC_arch   7 nklsklsteletvkkeneelsksveelke 35 
                                        +l+ l  el+ ++++ e  +++veel+ 
  gi|344210266|ref|YP_004786442.1| 316 DQLDALGNELTALRAQKETYRDTVEELET 344
                                       67888899999999999999999999985 PP

  == domain 6  score: 11.0 bits;  conditional E-value: 0.0017
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVk 38 
                                       i elE  l + + +l+ +++ +e+ +++ve+l + V 
  gi|344210266|ref|YP_004786442.1| 363 IAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVD 399
                                       679******************************9996 PP

  == domain 7  score: 3.0 bits;  conditional E-value: 0.54
                         FlaC_arch   8 klsklsteletvkkeneelsksveelken 36 
                                       +ls++++e++  ++e+e+  +++ +l+ +
  gi|344210266|ref|YP_004786442.1| 404 ELSDVESEIKYREAELEDTADELAQLETR 432
                                       79999999999999999999999999865 PP

  == domain 8  score: 7.8 bits;  conditional E-value: 0.016
                         FlaC_arch   8 klsklsteletvkkeneelsksveelken 36 
                                       +++ l+t letv++++ el++  +++k++
  gi|344210266|ref|YP_004786442.1| 435 RVDTLETDLETVRDDLAELRNRKDRIKRE 463
                                       56778888999999999998888888875 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   5.5      0.14        37      48     110 ..     131     179 ..      97     189 .. 0.61
   2 !   21.6   7.5   7.6e-07    0.0002       2      71 ..     197     266 ..     196     276 .. 0.91
   3 !    9.6   9.7    0.0039         1      18      92 ..     322     394 ..     308     409 .. 0.56
   4 ?    8.1   3.8     0.012       3.1       1      86 [.     378     454 ..     378     471 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.14
                              FliJ  48 rnyqafisaldeaiaqqkqelaqaekqvekareewqearqerkklekLkerekkeeqkeenrr 110
                                       +n+ ++i++l+++ +q++ el+qa++               +k l  ++e+  + e++ e+ r
  gi|344210266|ref|YP_004786442.1| 131 QNIDSQIETLQREREQIETELTQARE--------------AKKRLPSVQEKVTRLENEIEDLR 179
                                       45555555555555555555555544..............44444444444444444333333 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 7.6e-07
                              FliJ   2 eaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqa 71 
                                         +r+L +a++e++qa++++e+leq +++ +++ls+++ +l+a e+  y+   ++l ea +++ q+  +a
  gi|344210266|ref|YP_004786442.1| 197 SVRRQLSQARTEQNQAKNRVERLEQSIERTEQRLSERQDALDALEIPEYNDVADKLSEARESLSQVERDA 266
                                       5789*********************************99********************99988876555 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0039
                              FliJ  18 eekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqerkkl 92 
                                        ++l++l+ + + y+   ++     + +e+ + ++ ++ l+e ia+++ +la+ ++ +++ar+++ +a+  +++l
  gi|344210266|ref|YP_004786442.1| 322 GNELTALRAQKETYRDTVEELE--TQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQL 394
                                       3344444444444444444433..444666666666666666666666666666666666666666666665554 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.012
                              FliJ   1 deaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvek 77 
                                       d+a+++L++aq  ++q   ++++   ++++ +++++++      ael  +   +++l+++ a+    ++ +e ++e+
  gi|344210266|ref|YP_004786442.1| 378 DAARNRLEQAQSDVEQLSDHVDAAVAELSDVESEIKYRE-----AELEDTADELAQLETRAAR----VDTLETDLET 445
                                       789999999999999999999999999999999998888.....5555555555555555443....2333333333 PP

                              FliJ  78 areewqear 86 
                                        r+++ e r
  gi|344210266|ref|YP_004786442.1| 446 VRDDLAELR 454
                                       333333333 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 !   12.8   5.8   0.00035     0.092      30      86 ..     132     188 ..     130     194 .. 0.90
   2 !    8.3   7.1     0.009       2.3      62     100 ..     198     236 ..     193     241 .. 0.44
   3 ?    6.2   7.7     0.039        10      19     119 ..     247     346 ..     244     351 .. 0.76
   4 !   13.9  20.2   0.00017     0.043       2     109 ..     317     427 ..     316     435 .. 0.84
   5 ?    3.6   0.8      0.25        65      48      89 ..     425     466 ..     423     473 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00035
                        TPR_MLP1_2  30 dlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakae 86 
                                       ++ +q e +++  ++ e+el++  e+ k l ++ e++ +l++ei++l+a++e+  +e
  gi|344210266|ref|YP_004786442.1| 132 NIDSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRETIDSE 188
                                       6789999999999999*********************************99998776 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.009
                        TPR_MLP1_2  62 lreelnelkaeiaelkaeaesakaeleeseesweeqkee 100
                                       +r +l+++++e +++k+++e++++++e+ e+ ++e++++
  gi|344210266|ref|YP_004786442.1| 198 VRRQLSQARTEQNQAKNRVERLEQSIERTEQRLSERQDA 236
                                       344444444444444444444444444444444444433 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.039
                        TPR_MLP1_2  19 eaeaklqklqedlekqaeiakeaqqkYe.relvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesw 94 
                                       + ++kl++++e l + ++ a+  q  Y+ +e+v+ ++ ++ l+++  +++   +++a ++   e+++a+l+ +  ++
  gi|344210266|ref|YP_004786442.1| 247 DVADKLSEARESLSQVERDAEVLQSVYSaTEMVLSEDRLDLLTEVERDIDG--DTVACWTCGSETTRADLADQLDAL 321
                                       6788999********************647*****************9964..556666666666666666666666 PP

                        TPR_MLP1_2  95 eeqkeelekelselekriedlneqN 119
                                        ++ ++l+ +++  +  +e+l++q 
  gi|344210266|ref|YP_004786442.1| 322 GNELTALRAQKETYRDTVEELETQR 346
                                       6666666666666666666666663 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 0.00017
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqkl...qedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiae 75 
                                       +l++l +e+++l+++ke +++++++l   +e++ + +++ ++ +++ ++     a+  ++l a+r++l+++++++++
  gi|344210266|ref|YP_004786442.1| 317 QLDALGNELTALRAQKETYRDTVEELetqREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQ 393
                                       78899999999999999999887776222566667777777777777777777788899****************** PP

                        TPR_MLP1_2  76 lkaeaesakaeleeseesweeqkeelekelsele 109
                                       l + +++a ael+  e++++ ++ ele+  +el 
  gi|344210266|ref|YP_004786442.1| 394 LSDHVDAAVAELSDVESEIKYREAELEDTADELA 427
                                       ***************************9777764 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.25
                        TPR_MLP1_2  48 elvkhaedvkelqalreelnelkaeiaelkaeaesakaelee 89 
                                       el + ++ +  + +l ++l+++++++ael+++ ++ k e  e
  gi|344210266|ref|YP_004786442.1| 425 ELAQLETRAARVDTLETDLETVRDDLAELRNRKDRIKRETRE 466
                                       555666666677777777777777777777777777776655 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 !   14.5   4.2   0.00012     0.031      10      60 ..     130     178 ..     126     194 .. 0.92
   2 !   12.8   5.2   0.00041      0.11       5      58 ..     211     267 ..     206     273 .. 0.80
   3 ?    2.2   2.2      0.86   2.2e+02      41      68 ..     316     343 ..     307     351 .. 0.59
   4 !    8.6   7.9    0.0082       2.1       9      61 ..     348     395 ..     344     404 .. 0.78
   5 ?    8.3   4.9      0.01       2.7       9      60 ..     404     453 ..     398     456 .. 0.90
   6 ?    7.3   5.3     0.022       5.7       7      62 ..     416     469 ..     410     470 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00012
                      ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeel 60 
                                       +++++++Ie L+ e +++e+el ++   +  ++l  ++++ ++le+e+e l
  gi|344210266|ref|YP_004786442.1| 130 FQNIDSQIETLQREREQIETELTQAR--EAKKRLPSVQEKVTRLENEIEDL 178
                                       7899*********************8..77799***************987 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00041
                      ABC_tran_CTD   5 keqreleeleaeIeaLEeeiaeleaeladpel..ysdp.eklaelsaeleeleaeLe 58 
                                       + +++ e+le+ Ie+ E++++e +++l + e+  y+d  +kl+e+ + l ++e + e
  gi|344210266|ref|YP_004786442.1| 211 QAKNRVERLEQSIERTEQRLSERQDALDALEIpeYNDVaDKLSEARESLSQVERDAE 267
                                       678999*******************77665552256667888888888888887765 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.86
                      ABC_tran_CTD  41 eklaelsaeleeleaeLeelyerWeeLe 68 
                                       ++l +l +el++l+a+ e+  +  eeLe
  gi|344210266|ref|YP_004786442.1| 316 DQLDALGNELTALRAQKETYRDTVEELE 343
                                       4555666666666666666655555555 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0082
                      ABC_tran_CTD   9 eleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeely 61 
                                       e+ +  ++ + LEe+iaelea lad       + l ++ ++le+++++ e+l 
  gi|344210266|ref|YP_004786442.1| 348 EISQARRRKADLEEDIAELEATLADRK-----QSLDAARNRLEQAQSDVEQLS 395
                                       566666666889************998.....778888888888888888764 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.01
                      ABC_tran_CTD   9 eleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeel 60 
                                       el  +e+eI   E+e+++  +ela+ e  ++ +++  l + le+++++L+el
  gi|344210266|ref|YP_004786442.1| 404 ELSDVESEIKYREAELEDTADELAQLE--TRAARVDTLETDLETVRDDLAEL 453
                                       899999999999999999999999999..99999999999999999999997 PP

  == domain 6  score: 7.3 bits;  conditional E-value: 0.022
                      ABC_tran_CTD   7 qreleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelye 62 
                                       + ele   +e+++LE++ a +++   d e   d+  lael +++++++ e  e+++
  gi|344210266|ref|YP_004786442.1| 416 EAELEDTADELAQLETRAARVDTLETDLETVRDD--LAELRNRKDRIKRETREAFD 469
                                       57999999999****9999999999999966666..*************9999986 PP

>> DUF2353  Uncharacterized coiled-coil protein (DUF2353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   4.8      0.97   2.5e+02      43      90 ..     134     181 ..      93     198 .. 0.52
   2 !    8.8   7.1    0.0037      0.95      15      91 ..     199     273 ..     193     283 .. 0.88
   3 !   22.5  14.6   2.5e-07   6.4e-05      26     169 ..     319     463 ..     308     497 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.97
                           DUF2353  43 kkqleeekakaadlkeekekekklsqlleesreenkalkleveeLrqk 90 
                                        +q e+ +  ++++++e ++ ++  + l  ++e+  +l++e+e+Lr k
  gi|344210266|ref|YP_004786442.1| 134 DSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAK 181
                                       333333333333333333333333333333333333333333333333 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0037
                           DUF2353  15 skeLekcrqerdqyklmaeqLqerlsalkkqleeekakaadlkeekekekklsqlleesreenkalkleveeLrqkl 91 
                                       ++ L ++r+e++q k+++e+L++ +++++++l+e+++  + l+    + +++++ l+e+re  ++ ++++e L++ +
  gi|344210266|ref|YP_004786442.1| 199 RRQLSQARTEQNQAKNRVERLEQSIERTEQRLSERQDALDALE--IPEYNDVADKLSEARESLSQVERDAEVLQSVY 273
                                       6899**********************99999988888777655..6788899******************9998755 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 2.5e-07
                           DUF2353  26 dqyklmaeqLqerlsalkkqleeekakaadlkeekekekklsqlleesreenkalkleveeLrqklkeaqgDiklLR 102
                                       d + + +  L+ + ++++ + ee +++++++++ ++++++l + ++e        k+ +++ r++l+ aq D++ L 
  gi|344210266|ref|YP_004786442.1| 319 DALGNELTALRAQKETYRDTVEELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLS 395
                                       555666777899999999999999999999999999999*************************************9 PP

                           DUF2353 103 ..eqlarqrlglkdedlletrhssaeereelvkqlEklkekiqqlerdlkavldekeelvterdaykeK 169
                                          ++a  +l+ ++e+ ++ r+ ++e+  + ++qlE+  ++   le+dl++v d+  el   +d  k+ 
  gi|344210266|ref|YP_004786442.1| 396 dhVDAAVAELS-DVESEIKYREAELEDTADELAQLETRAARVDTLETDLETVRDDLAELRNRKDRIKRE 463
                                       65555555566.556669999999***************************************998875 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   2.8      0.18        47     405     451 ..     131     180 ..     105     188 .. 0.48
   2 !    9.8  34.1    0.0011      0.28      94     511 ..     143     519 ..     134     534 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.18
                            AAA_13 405 eeleseldeykkkykklekaieklekelk...eeeaelkkleeeikeLek 451
                                       ++++s++++++++ +++e++++++ +++k     ++++  le+ei++L++
  gi|344210266|ref|YP_004786442.1| 131 QNIDSQIETLQREREQIETELTQAREAKKrlpSVQEKVTRLENEIEDLRA 180
                                       34444444444444444433333332222000233333334444444433 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0011
                            AAA_13  94 kqekieklkkeikkleekleaaeaqlqkaekekkklekeledeawkkivkkknsalsealkglkyeekfkerllkel 170
                                       ++e+ie++ ++ ++++++l + +++++ +e+e ++l ++ e+  ++   +   + ++++l++ + e++++++ +++l
  gi|344210266|ref|YP_004786442.1| 143 EREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRETIDSEAGSDDSPESVRRQLSQARTEQNQAKNRVERL 219
                                       46899999999999999999999999999999999999888777777778888999999999999************ PP

                            AAA_13 171 kkknrkaaellsdeelkakletvesenlpe.laplslssidldalekaeilkkkvvgkdseieeLienldladWVkq 246
                                       ++ +  + +  +++e++++l+++e  + ++  ++ls   + l+++e+++ + ++v +      e++ + d  d + +
  gi|344210266|ref|YP_004786442.1| 220 EQSI--ERTEQRLSERQDALDALEIPEYNDvADKLSEARESLSQVERDAEVLQSVYSA----TEMVLSEDRLDLLTE 290
                                       **86..44445778888999999766666625677999999999***99999999774....677777777777777 PP

                            AAA_13 247 GlelheassdtCpFCgqplpa.erkaaLeahFddefeekqerLekliekveskkselleklkavsdeasensafeed 322
                                         + +++++  C  Cg+++++ +++ +L+a  ++       +L   +e++  + +el ++              +e+
  gi|344210266|ref|YP_004786442.1| 291 VERDIDGDTVACWTCGSETTRaDLADQLDALGNE-----LTALRAQKETYRDTVEELETQ--------------REE 348
                                       77777777799******98751344444444333.....445666666666665443333..............344 PP

                            AAA_13 323 keelkaeaealeeqLkglqraleaKrkepfksve.lesvkakiesikklvaeineliakhNekvanleeekeeakkk 398
                                       ++++++++  lee + +l+  l ++++ + +  + le++++++e++++ v+++ +  ++    ++  e+e e+ +++
  gi|344210266|ref|YP_004786442.1| 349 ISQARRRKADLEEDIAELEATLADRKQSLDAARNrLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADE 425
                                       55555555555555555555555555443332222555666666666666666666655555555555555555555 PP

                            AAA_13 399 lelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkafGlgel 475
                                       l +            ++      ++ +  le++l+   ++l++l+++   +++++r+   +a  + ++L++fG +++
  gi|344210266|ref|YP_004786442.1| 426 LAQ------------LE----TRAARVDTLETDLETVRDDLAELRNRKDRIKRETREAFDTA--MKDILSRFG-TGF 483
                                       555............22....33344556777777777777777777777777777777765..678888886.455 PP

                            AAA_13 476 eLkfeeekkgYrivrkggsqaaetLSeGEktaIafl 511
                                       e +   ++    + r g++   + LSeGE  +I f+
  gi|344210266|ref|YP_004786442.1| 484 ETARLTADFDIVVARDGQEASLDALSEGELELIGFV 519
                                       555554444444455444444488888888888775 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 !    9.3  14.1     0.002      0.53      33     154 ..     139     266 ..     107     294 .. 0.57
   2 !   18.8  11.9   2.7e-06   0.00071      32     130 ..     312     431 ..     300     434 .. 0.79
   3 ?    3.8   1.6     0.096        25      37      99 ..     404     466 ..     392     470 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.002
                             Atg14  33 klksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrer.............lqelkdklsqlkke 96 
                                        l+ e+e++++++++a e k+       ++ + ++k+ +l ++i+dlr++              + ++ +lsq + e
  gi|344210266|ref|YP_004786442.1| 139 TLQREREQIETELTQAREAKK-------RLPSVQEKVTRLENEIEDLRAKretidseagsddsPESVRRQLSQARTE 208
                                       344444444444444444444.......3333333333333333333333333333344455577777777777777 PP

                             Atg14  97 ieekkkklaklsdklkkRrsdleslqneleerrkkqiaklqdaikrieqklsslsskt 154
                                        +++k+++++l +++ +  ++l+  q+ l + +  + + + d++ + ++ ls+++++ 
  gi|344210266|ref|YP_004786442.1| 209 QNQAKNRVERLEQSIERTEQRLSERQDALDALEIPEYNDVADKLSEARESLSQVERDA 266
                                       7777777777777776555555555655555555555555555555555555444444 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.7e-06
                             Atg14  32 aklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklakls 108
                                       a+l  + ++l+++++++ ++ke   ++ ++++++++ +++ + ++adl+e ++el+++l  +k+++++++++l++ +
  gi|344210266|ref|YP_004786442.1| 312 ADLADQLDALGNELTALRAQKETYRDTVEELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQ 388
                                       56667778888888888888887777888888888899999999999999999999999999999999999999988 PP

                             Atg14 109 dklk.....................kRrsdleslqneleerrk 130
                                       +++                      +R ++le + +el++ ++
  gi|344210266|ref|YP_004786442.1| 389 SDVEqlsdhvdaavaelsdveseikYREAELEDTADELAQLET 431
                                       8888777777777777777777777888888888888887765 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.096
                             Atg14  37 ekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeiee 99 
                                       e   ++++i+  +++ e++ ++ +++++++a++++l ++ +  r+ l+el+ + ++ k+e++e
  gi|344210266|ref|YP_004786442.1| 404 ELSDVESEIKYREAELEDTADELAQLETRAARVDTLETDLETVRDDLAELRNRKDRIKRETRE 466
                                       445556666666666666677788888888888888888888888888888888888887766 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 !   12.1   0.0   0.00036     0.094      21      52 ..      19      50 ..       5      74 .. 0.87
   2 !    8.3   0.5    0.0056       1.4      92     188 ..     216     562 ..     128     571 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00036
                                      ETTSSEEEEEESTTSSHHHHHHHHHHHCTT.T CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 21 pfsksftaivGpNGSGKsnlldAilFvLGers 52
                                       ++++++++ G+N  GKs+++++++  LG+++
  gi|344210266|ref|YP_004786442.1| 19 TVEPGVNVVRGSNWQGKSSFIESVKTALGTST 50
                                      57899************************543 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0056
                                       SSSSCEEEEEEEETTSEEEEEETTEEE-H.HHHHHHHHCTT-STT................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx................................ RF
                             SMC_N  92 iekeevsisrrvkrkgeseykingkevtk.kevsellesagiske................................ 135
                                       +e+ e si+r+ +r  e + +++  e+ + ++v++ l++a+ s +                                
  gi|344210266|ref|YP_004786442.1| 216 VERLEQSIERTEQRLSERQDALDALEIPEyNDVADKLSEARESLSqverdaevlqsvysatemvlsedrldllteve 292
                                       44444444444444444444444444433344444444443333366777777777777777777777777777777 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|344210266|ref|YP_004786442.1| 293 rdidgdtvacwtcgsettradladqldalgneltalraqketyrdtveeletqreeisqarrrkadleediaeleat 369
                                       77777777777777777777777777777777777777777777777777777777777777777777778888888 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|344210266|ref|YP_004786442.1| 370 ladrkqsldaarnrleqaqsdveqlsdhvdaavaelsdveseikyreaeledtadelaqletraarvdtletdletv 446
                                       888888888888888888888888888888888899999999999999999999999999999999*********** PP

                                       ............................................................CS-HHHHHHHHHHHHHH CS
                                       ............................................................xxxxxxxxxxxxxxxxx RF
                             SMC_N 136 ............................................................lLSgGektLvalaLlfA 152
                                                                                                   +LS Ge  L+     +A
  gi|344210266|ref|YP_004786442.1| 447 rddlaelrnrkdrikretreafdtamkdilsrfgtgfetarltadfdivvardgqeasldALSEGELELIGFVAALA 523
                                       *********************************************************************98888888 PP

                                       ....HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCT CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 153 ....iqkvkpaplyllDeidaaLDeknvkkvaellkeksk 188
                                               +  pl l+D +   LD+ n + + e+l++ ++
  gi|344210266|ref|YP_004786442.1| 524 grqsFDVGDAVPLLLVDGLG-GLDDDNLHTLTEYLQQGTE 562
                                       65556666899*******96.7*************98774 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 ?    7.1   7.1      0.02       5.2      57     106 ..     133     178 ..     128     187 .. 0.47
   2 ?    3.6  13.8      0.24        63      14     100 ..     156     241 ..     155     241 .. 0.91
   3 ?    5.6   9.3     0.058        15      36     112 ..     198     275 ..     193     286 .. 0.86
   4 !   11.8  10.7   0.00072      0.19      16      99 ..     308     394 ..     306     394 .. 0.82
   5 !   14.6  11.0   9.5e-05     0.025       7      91 ..     379     466 ..     372     473 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.02
                    CENP-F_leu_zip  57 lkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnssl 106
                                       + ++ie+l++e++++e++L++ r+ k+ L       qe+v  Le+  ++l
  gi|344210266|ref|YP_004786442.1| 133 IDSQIETLQREREQIETELTQAREAKKRL----PSVQEKVTRLENEIEDL 178
                                       44555555555555555555555555544....33333333333333333 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.24
                    CENP-F_leu_zip  14 eserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelq 90 
                                       e++++  s+++kv +Le e+e++ +++e +  ea +     e+++ ++ + ++e ++ +  ++ l +  e  e+ l 
  gi|344210266|ref|YP_004786442.1| 156 EAKKRLPSVQEKVTRLENEIEDLRAKRETIDSEAGS-DDSPESVRRQLSQARTEQNQAKNRVERLEQSIERTEQRLS 231
                                       677778899********************9999975.577899********************************** PP

                    CENP-F_leu_zip  91 kkqervseLe 100
                                       + q+  + Le
  gi|344210266|ref|YP_004786442.1| 232 ERQDALDALE 241
                                       ***9998887 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.058
                    CENP-F_leu_zip  36 seenqekvileaEtskaevetlkeeieelaeelreleldLvalr.sekeeLekelqkkqervseLeslnsslenlle 111
                                       + ++++++ +e  ++k+ ve l++ ie+ +++l+e +  L+al   e ++++ +l + +e  s+ e+  + l+++ +
  gi|344210266|ref|YP_004786442.1| 198 VRRQLSQARTEQNQAKNRVERLEQSIERTEQRLSERQDALDALEiPEYNDVADKLSEARESLSQVERDAEVLQSVYS 274
                                       56778999999********************************9779999999999999999999988777776655 PP

                    CENP-F_leu_zip 112 e 112
                                        
  gi|344210266|ref|YP_004786442.1| 275 A 275
                                       5 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00072
                    CENP-F_leu_zip  16 erkadsLkdkvenLerelemseenqe...kvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekel 89 
                                       e   + L d+ ++L  el  + +++e   +++ e Et+++e+++ +  +  l+e   ele+ L++ ++  +   + l
  gi|344210266|ref|YP_004786442.1| 308 ETTRADLADQLDALGNELTALRAQKEtyrDTVEELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRL 384
                                       66677899999999999988887777333468899999999999999999999999999999999999999999999 PP

                    CENP-F_leu_zip  90 qkkqervseL 99 
                                       ++ q+ v++L
  gi|344210266|ref|YP_004786442.1| 385 EQAQSDVEQL 394
                                       9999999887 PP

  == domain 5  score: 14.6 bits;  conditional E-value: 9.5e-05
                    CENP-F_leu_zip   7 hvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlke...eieelaeelreleldLvalrs 80 
                                        ++++L +++++ ++L d+v++  +el ++e++    + e E+   e+ +l++    +++l++ l+  + dL++lr+
  gi|344210266|ref|YP_004786442.1| 379 AARNRLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADELAQLETraaRVDTLETDLETVRDDLAELRN 455
                                       46789**************************99988888888877777666652227899***************** PP

                    CENP-F_leu_zip  81 ekeeLekelqk 91 
                                        k+ +++e ++
  gi|344210266|ref|YP_004786442.1| 456 RKDRIKRETRE 466
                                       ******99876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  39.3      0.19        49       4     194 ..       7     261 ..       4     475 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.19
                            AAA_23   4 ienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfe 80 
                                       ie +  + d +   ++g++++ G N  GK+++++ +k aL+  t+ ++     g+ ++ v++e+     +++++t++
  gi|344210266|ref|YP_004786442.1|   7 IERIAGILDGSATVEPGVNVVRGSNWQGKSSFIESVKTALGTSTELTE-----GADSGAVHLETP---TGVYDVTLT 75 
                                       5555555555556689*************************9664433.....444555555443...334555555 PP

                            AAA_23  81 nkdgry.......................................................trsiererelskkkgk 102
                                       +++g+                                                         ++++rere ++++  
  gi|344210266|ref|YP_004786442.1|  76 RENGTVvrhgepylsdeydviraelfacldernevrravrtgenledvllrpldfqnidsqIETLQREREQIETELT 152
                                       55555455666666666666666654444444444444444444555555555555555555666666666666666 PP

                            AAA_23 103 ttkkaklelleideleqfisellgskkiilnlilflgqer...........feefelkdkkerleelekeleelede 168
                                       + ++ak++l +++e+  +++++++   +  + i+  + ++           +++ e+++ k+r+e le+++e  e++
  gi|344210266|ref|YP_004786442.1| 153 QAREAKKRLPSVQEKVTRLENEIEDLRAKRETIDSEAGSDdspesvrrqlsQARTEQNQAKNRVERLEQSIERTEQR 229
                                       66666666666666666666666655554444443333332333333332211112222223333333333333333 PP

                            AAA_23 169 kkllekleqekekek......eleeleeelee 194
                                        ++ ++ ++++e  +      +l+e +e l +
  gi|344210266|ref|YP_004786442.1| 230 LSERQDALDALEIPEyndvadKLSEARESLSQ 261
                                       33333333333333344444444444444444 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6  23.0    0.0014      0.36     144     256 ..     133     265 ..     130     293 .. 0.61
   2 !   13.5  18.6   9.3e-05     0.024     142     252 ..     312     428 ..     306     430 .. 0.57
   3 !    7.9   9.6    0.0047       1.2     144     224 ..     384     466 ..     382     478 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                              Spc7 144 leenlegleedkelLekqeeel...dellpeleeekaeleeeleklqeaaeeles................idkeeL 201
                                       +++++e+l++++e++e +  ++   ++ lp+++e+ ++le+e+e+l++++e ++s                  ++e 
  gi|344210266|ref|YP_004786442.1| 133 IDSQIETLQREREQIETELTQAreaKKRLPSVQEKVTRLENEIEDLRAKRETIDSeagsddspesvrrqlsQARTEQ 209
                                       678899**********988777222555678899999***********99999996554455544444442224444 PP

                              Spc7 202 eelreelaelkaeieekkkelaelqeqleelee.kieelkeqkseleeeiaeaerv 256
                                       +++++++++l++ ie+ +++l+e+q+ l++le  + ++++++ se++e +++ er 
  gi|344210266|ref|YP_004786442.1| 210 NQAKNRVERLEQSIERTEQRLSERQDALDALEIpEYNDVADKLSEARESLSQVERD 265
                                       44555555555555555555555555555544324444555555555555555544 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 9.3e-05
                              Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaelee...eleklqeaaeeles..id.keeLeelreelaelk 212
                                         l ++l++l ++ + L +q+e   + ++ele++++e+++   + ++l+e  +ele+   d k++L ++r++l++++
  gi|344210266|ref|YP_004786442.1| 312 ADLADQLDALGNELTALRAQKETYRDTVEELETQREEISQarrRKADLEEDIAELEAtlADrKQSLDAARNRLEQAQ 388
                                       44556666666666666666666666666666666655441113344555555555555344666666666666666 PP

                              Spc7 213 aeieekkkelaelqeqleeleekieelkeqkseleeeiae 252
                                       +++e++++ ++   ++l ++e++i+  +++ +++ +e+a+
  gi|344210266|ref|YP_004786442.1| 389 SDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADELAQ 428
                                       6666666666666666666666666666666666666655 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0047
                              Spc7 144 leenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid..keeLeelreelaelkaeieek 218
                                       le+  +++e+ ++++++  +el+++  e++ ++aele+++++l + ++  + +d  +++Le++r++lael +  ++ 
  gi|344210266|ref|YP_004786442.1| 384 LEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADELAQLETRAARVDtlETDLETVRDDLAELRNRKDRI 460
                                       45555556666666667778888888888888999998888888888777887777788999999998888888888 PP

                              Spc7 219 kkelae 224
                                       k+e+ e
  gi|344210266|ref|YP_004786442.1| 461 KRETRE 466
                                       887765 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   1.1     0.005       1.3      69     123 ..     131     181 ..     127     188 .. 0.68
   2 !    9.9   2.2    0.0028      0.74      36     114 ..     199     277 ..     193     282 .. 0.74
   3 !   10.9   6.3    0.0013      0.35      37     118 ..     333     413 ..     309     418 .. 0.85
   4 ?    7.0   1.2     0.022       5.7      39     106 ..     394     460 ..     393     476 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.005
                           DUF1664  69 drvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieek 123
                                       +++d++++  ++  ++i+ e+t++re     ++ + sv+e v+ le+++e++ +k
  gi|344210266|ref|YP_004786442.1| 131 QNIDSQIETLQREREQIETELTQARE----AKKRLPSVQEKVTRLENEIEDLRAK 181
                                       67777777777777777777777665....4556667777777777777766544 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0028
                           DUF1664  36 krslsdav...esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkea 109
                                       +r ls+a    ++  +++e++ +s+++t ++Ls+r d +d+     +   ++++++++e+re ls++++d e ++++
  gi|344210266|ref|YP_004786442.1| 199 RRQLSQARteqNQAKNRVERLEQSIERTEQRLSERQDALDAL---EIPEYNDVADKLSEARESLSQVERDAEVLQSV 272
                                       677777762224566788899999999999999999998863...23335678899999999999999999999887 PP

                           DUF1664 110 vegle 114
                                        +  e
  gi|344210266|ref|YP_004786442.1| 273 YSATE 277
                                       66655 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.0013
                           DUF1664  37 rslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                          +d ve++ +q e++s++ ++ k +L+++i++++++l + k+   + ++ ++++++d++++++ v++  +  +++
  gi|344210266|ref|YP_004786442.1| 333 ETYRDTVEELETQREEISQA-RRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVDAAVAELSDV 408
                                       55567777777777777765.677999*************************************9999988888888 PP

                           DUF1664 114 eskle 118
                                       es+++
  gi|344210266|ref|YP_004786442.1| 409 ESEIK 413
                                       88776 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.022
                           DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesv 106
                                       lsd v+    +l +v ++++    +L++  d++  +l+  ++    ++ ++++vr+dl+e+++  + +
  gi|344210266|ref|YP_004786442.1| 394 LSDHVDAAVAELSDVESEIKYREAELEDTADELA-QLETRAARVDTLETDLETVRDDLAELRNRKDRI 460
                                       4555555555566666666666666666555553.455555555556666666666666655555555 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 !   12.6   3.3   0.00025     0.064      58     110 ..     132     184 ..     128     190 .. 0.86
   2 ?    4.9   5.8     0.056        15      30     108 ..     197     273 ..     193     296 .. 0.65
   3 !   12.0  12.5   0.00037     0.097      57     142 ..     312     397 ..     307     424 .. 0.78
   4 !   10.3  10.4    0.0012      0.32      27     139 ..     362     474 ..     361     478 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00025
                               GAS  58 rlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehev 110
                                       ++  +++++++e+e+ + +l + ++ k++l ++++++++le+e++dl+ + e 
  gi|344210266|ref|YP_004786442.1| 132 NIDSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRET 184
                                       56678999999999999999999999999999999999999999999988775 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.056
                               GAS  30 slKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkw 106
                                       s + ++ + ++++++++++++ ++q  +r ++ L + +  ++ L+  + +y+    +l ++++ l+++e+  + l+ 
  gi|344210266|ref|YP_004786442.1| 197 SVRRQLSQARTEQNQAKNRVERLEQSIERTEQRLSERQDALDALE--IPEYNDVADKLSEARESLSQVERDAEVLQS 271
                                       566777777777777777777777777777777777777777774..455555555555555555555555554444 PP

                               GAS 107 eh 108
                                        +
  gi|344210266|ref|YP_004786442.1| 272 VY 273
                                       43 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00037
                               GAS  57 krlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaai 133
                                        +l ++L ++ +e+  Lr+q ++y+   ++l+ ++++++++ +   dl+++   le  ++  +++ d+ +++ e+a 
  gi|344210266|ref|YP_004786442.1| 312 ADLADQLDALGNELTALRAQKETYRDTVEELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQ 388
                                       56788888999999999999999999999999999999999999999999999999999999999999999999999 PP

                               GAS 134 qevqqktgl 142
                                        +v q ++ 
  gi|344210266|ref|YP_004786442.1| 389 SDVEQLSDH 397
                                       999887765 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.0012
                               GAS  27 lIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkd 103
                                        I +l   +++ k+  ++++++l++++++ ++l++ + +a +e+   + ++k  e + ++ +   a+l++    + +
  gi|344210266|ref|YP_004786442.1| 362 DIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADELAQLETRAARVDT 438
                                       6999999********************************************************9************* PP

                               GAS 104 lkwehevleqrfekvekerdelykkfeaaiqevqqk 139
                                       l+ + e +++ ++++ + +d+++++ ++a+++++++
  gi|344210266|ref|YP_004786442.1| 439 LETDLETVRDDLAELRNRKDRIKRETREAFDTAMKD 474
                                       **********************99999998887765 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 ?   -0.3   0.9       4.4   1.1e+03      33      47 ..     136     150 ..     129     161 .. 0.47
   2 ?    3.8   1.0      0.23        60       9      43 ..     151     184 ..     145     189 .. 0.78
   3 ?    5.7   3.5     0.061        16       3      31 ..     213     241 ..     211     266 .. 0.87
   4 !   14.2   0.2   0.00013     0.034      19      58 ..     310     349 ..     286     356 .. 0.85
   5 !   12.6   5.4   0.00041      0.11       2      53 ..     359     410 ..     358     432 .. 0.90
   6 ?    3.5   1.4       0.3        77      25      57 ..     434     466 ..     407     471 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 4.4
                     TolA_bind_tri  33 elreLRGqiEelqyq 47 
                                       ++ +L+ + E+ + +
  gi|344210266|ref|YP_004786442.1| 136 QIETLQREREQIETE 150
                                       333333333333333 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.23
                     TolA_bind_tri   9 LErilearsqlllelqqqlealqqelreLRGqiEe 43 
                                       L ++ ea ++ l  +q+++ +l++e+ +LR + E 
  gi|344210266|ref|YP_004786442.1| 151 LTQAREA-KKRLPSVQEKVTRLENEIEDLRAKRET 184
                                       5555555.3778889***************98776 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.061
                     TolA_bind_tri   3 edrvarLErilearsqlllelqqqlealq 31 
                                       ++rv+rLE+ +e  +q l e q  l+al+
  gi|344210266|ref|YP_004786442.1| 213 KNRVERLEQSIERTEQRLSERQDALDALE 241
                                       78************************996 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 0.00013
                     TolA_bind_tri  19 lllelqqqlealqqelreLRGqiEelqyqleqleerQrdl 58 
                                       +  +l  ql+al +el  LR q E  +  +e+le++  ++
  gi|344210266|ref|YP_004786442.1| 310 TRADLADQLDALGNELTALRAQKETYRDTVEELETQREEI 349
                                       66799****************************9987665 PP

  == domain 5  score: 12.6 bits;  conditional E-value: 0.00041
                     TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqlee 53 
                                       le+ +a+LE  l+ r+q+l    ++le+ q+++ +L  +++    +l+++e 
  gi|344210266|ref|YP_004786442.1| 359 LEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVDAAVAELSDVES 410
                                       89***************************************99999999886 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.3
                     TolA_bind_tri  25 qqlealqqelreLRGqiEelqyqleqleerQrd 57 
                                        ++++l+++l + R ++ el+++ +++++  r+
  gi|344210266|ref|YP_004786442.1| 434 ARVDTLETDLETVRDDLAELRNRKDRIKRETRE 466
                                       345555555555555555555555555555555 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   5.2     0.078        20     108     160 ..     137     189 ..     118     201 .. 0.72
   2 ?    2.0   5.4      0.61   1.6e+02     109     172 ..     200     271 ..     191     282 .. 0.49
   3 !   18.9   8.5     4e-06     0.001      89     182 ..     320     413 ..     317     418 .. 0.94
   4 ?    3.8   0.3      0.18        45      66     113 ..     415     466 ..     411     478 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.078
                            DUF724 108 leerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkei 160
                                        e++++  ++ie+e ++ r++++ +  +++k+ +le++ + l++k+e+ d+e 
  gi|344210266|ref|YP_004786442.1| 137 IETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRETIDSEA 189
                                       34445556667777777777777888888888888888888888888888775 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.61
                            DUF724 109 eerkklekkieeeesekrkleeeidelekkilelerqlallk........ekkeaadkeiarlkseaeklee 172
                                       ++++++  +  +++++ ++le++i+ +e++ +e +  l++l          k ++a +++++++ +ae l+ 
  gi|344210266|ref|YP_004786442.1| 200 RQLSQARTEQNQAKNRVERLEQSIERTEQRLSERQDALDALEipeyndvaDKLSEARESLSQVERDAEVLQS 271
                                       333333334444444444444444444444444444444444665555544444555555555555555544 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 4e-06
                            DUF724  89 alqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlks 165
                                       al + l+ L + k+ ++ + ee++   ++i++++ +k+ lee+i+ele + ++ ++ l++++++ e+a++++ +l+ 
  gi|344210266|ref|YP_004786442.1| 320 ALGNELTALRAQKETYRDTVEELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSD 396
                                       5667899999******************************************************************* PP

                            DUF724 166 eaekleeeledveqeFe 182
                                       +++++  el+dve+e +
  gi|344210266|ref|YP_004786442.1| 397 HVDAAVAELSDVESEIK 413
                                       *************9976 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.18
                            DUF724  66 srseleslkeslaeLekhGFdVkalqsrl....nkLlslkdeqtklleerkk 113
                                        ++ele++ ++la+Le+    V +l++ l    ++L +l+++++++++e+++
  gi|344210266|ref|YP_004786442.1| 415 REAELEDTADELAQLETRAARVDTLETDLetvrDDLAELRNRKDRIKRETRE 466
                                       5678999999999999999999999999955555666777777776665543 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   1.2   0.00025     0.066      12      61 ..     129     178 ..     122     186 .. 0.94
   2 ?    4.2   1.1      0.23        59      11      66 ..     221     274 ..     202     283 .. 0.82
   3 ?    3.6   1.7      0.36        94      16      52 ..     314     350 ..     309     388 .. 0.73
   4 ?    7.5   2.0     0.021       5.5      19      59 ..     373     413 ..     359     426 .. 0.75
   5 !    9.4   4.8    0.0056       1.5       4      60 ..     382     435 ..     379     477 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00025
                           NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenI 61 
                                       d +++d++++ lq + ++++++l +  e +++L + +++++ le+++e+ 
  gi|344210266|ref|YP_004786442.1| 129 DFQNIDSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDL 178
                                       6799*****************************************99986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.23
                           NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                       + i+ ++++++  q+++d ++   p+ +++ +kL +  ++L ++e   e  q++ +
  gi|344210266|ref|YP_004786442.1| 221 QSIERTEQRLSERQDALDALEI--PEYNDVADKLSEARESLSQVERDAEVLQSVYS 274
                                       6788888999999999998864..77778999999999999999988777777755 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.36
                           NPV_P10  16 vddkVdalqqqvddvqenlpdvtelnekLdaqsaqLa 52 
                                       + d++dal ++++ ++++ ++  +  e+L+ q +++ 
  gi|344210266|ref|YP_004786442.1| 314 LADQLDALGNELTALRAQKETYRDTVEELETQREEIS 350
                                       5677788888888887777777777777777766554 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.021
                           NPV_P10  19 kVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkve 59 
                                       + ++l+++ +++++   dv++l++++da  a+L ++e++++
  gi|344210266|ref|YP_004786442.1| 373 RKQSLDAARNRLEQAQSDVEQLSDHVDAAVAELSDVESEIK 413
                                       44567777788888888888899999999999888887765 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.0056
                           NPV_P10   4 niLlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                       n L +  +d+++++d Vda  +++ dv+++++     +++L++ +++La+let    
  gi|344210266|ref|YP_004786442.1| 382 NRLEQAQSDVEQLSDHVDAAVAELSDVESEIKY---REAELEDTADELAQLETRAAR 435
                                       55778899*********9999999999998877...457788888888888874332 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.7       1.1   2.8e+02     121     145 ..     131     155 ..     105     163 .. 0.74
   2 !   17.9  10.9   5.8e-06    0.0015     116     225 ..     164     276 ..     161     291 .. 0.93
   3 ?    3.5   7.9      0.14        37     131     208 ..     315     398 ..     280     406 .. 0.45
   4 ?    4.1   7.8     0.093        24     120     201 ..     391     475 ..     386     495 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.1
                              CorA 121 drlfellekleeeldeledeledst 145
                                       ++++ ++e+l +e++++e+el + +
  gi|344210266|ref|YP_004786442.1| 131 QNIDSQIETLQREREQIETELTQAR 155
                                       5678899999999999999993333 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 5.8e-06
                              CorA 116 ldeivdrlfellekleeeldeledel.edstkkeilrelaqlrrrlvklrralapnrevlkrlla..kaddklldde 189
                                       ++e v rl++++e+l ++++ +++e  +d++ ++ +r+l+q r++  + +  + ++++ ++r  +  +++++ ld+ 
  gi|344210266|ref|YP_004786442.1| 164 VQEKVTRLENEIEDLRAKRETIDSEAgSDDSPESVRRQLSQARTEQNQAKNRVERLEQSIERTEQrlSERQDALDAL 240
                                       688999***************************************99**9999999999986666888999999999 PP

                              CorA 190 dkeylrdlldelerllemlealrerleslqdtyssl 225
                                       + + ++d+ d+l+ + e l+++ + +e+lq+ ys++
  gi|344210266|ref|YP_004786442.1| 241 EIPEYNDVADKLSEARESLSQVERDAEVLQSVYSAT 276
                                       9999*****************************975 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.14
                              CorA 131 eeeldeledel.....edstkkeilrelaqlrrrlvklrralapnrevlkrlla.kaddkllddedkeylrdlldel 201
                                        ++ld l +el     +++t ++ ++el + r+++ + rr  a+++e + +l a  ad k+  d+++++l++ ++++
  gi|344210266|ref|YP_004786442.1| 315 ADQLDALGNELtalraQKETYRDTVEELETQREEISQARRRKADLEEDIAELEAtLADRKQSLDAARNRLEQAQSDV 391
                                       33333333333333333333333333333333333333333333333333222222222222222223334444444 PP

                              CorA 202 erlleml 208
                                       e+l++++
  gi|344210266|ref|YP_004786442.1| 392 EQLSDHV 398
                                       4443333 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.093
                              CorA 120 vdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrlla.kaddkllddedkey 193
                                       v++l + +++  +el ++e+e+  ++ + ++ ++elaql++r++++ +  +++++v ++l + +++++++++e +e 
  gi|344210266|ref|YP_004786442.1| 391 VEQLSDHVDAAVAELSDVESEIkyREAELEDTADELAQLETRAARVDTLETDLETVRDDLAElRNRKDRIKRETREA 467
                                       667777788888888888888888888889******************99999999999999999999999999998 PP

                              CorA 194 lrdlldel 201
                                       +++ + ++
  gi|344210266|ref|YP_004786442.1| 468 FDTAMKDI 475
                                       98888776 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   6.1     0.001      0.26      26     107 ..     130     210 ..     108     213 .. 0.75
   2 !   13.7   9.4   0.00018     0.046       4      97 ..     153     257 ..     151     261 .. 0.63
   3 ?    6.7   5.3     0.025       6.6       5      72 ..     202     270 ..     198     293 .. 0.86
   4 ?    4.3   2.0      0.14        37      17      81 ..     316     376 ..     307     381 .. 0.68
   5 !   10.7   8.7    0.0015      0.39       7     110 ..     358     461 ..     352     463 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.001
                                       XXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHHHHH CS
                        Laminin_II  26 lentkeklseinrsveetnekvk...dankairdArrsvkkLeklapqLldklkelkqleeassslsdniseikelI 99 
                                        +n+ +++++++r+ e+++ ++    +a+k + +++++v  Le+++++L +k ++++          d+ + ++ + 
  gi|344210266|ref|YP_004786442.1| 130 FQNIDSQIETLQREREQIETELTqarEAKKRLPSVQEKVTRLENEIEDLRAKRETIDSEAGS----DDSPESVRRQL 202
                                       4566666666666666666555433378889999****************998888877666....68888999999 PP

                                       HHHHHHHH CS
                        Laminin_II 100 aqARkaAn 107
                                       +qAR   n
  gi|344210266|ref|YP_004786442.1| 203 SQARTEQN 210
                                       99997666 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00018
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                        a+ea++ + +v+e+++ l++++e +++k ++i++++   ++  ++  +++ +Ar++  + ++ +++L++ +++ +q
  gi|344210266|ref|YP_004786442.1| 153 QAREAKKRLPSVQEKVTRLENEIEDLRAKRETIDSEA-GSDDSPESVRRQLSQARTEQNQAKNRVERLEQSIERTEQ 228
                                       589*******************************994.444444455555555555555555555555555555555 PP

                                       HHHH...............HHHHHHHHHH CS
                        Laminin_II  81 leeasss............lsdniseike 97 
                                       + ++++             + d++se +e
  gi|344210266|ref|YP_004786442.1| 229 RLSERQDaldaleipeyndVADKLSEARE 257
                                       54444433222222444466666666655 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.025
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX--TTTTTG CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetn.ekvkdankairdArrsvkkLeklapqLl 72 
                                       +++a    ++ ++ ++ l+q +e+t++ lse ++ ++  +  + +d    + +Ar+s +++e+ a++L 
  gi|344210266|ref|YP_004786442.1| 202 LSQARTEQNQAKNRVERLEQSIERTEQRLSERQDALDALEiPEYNDVADKLSEARESLSQVERDAEVLQ 270
                                       6677777788889999******************99987635788999*****************9986 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.14
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       +ql +l ++l  ++++ ++ +++     e+++   + i +Arr   +Le+ + +L++ l   kq 
  gi|344210266|ref|YP_004786442.1| 316 DQLDALGNELTALRAQKETYRDT----VEELETQREEISQARRRKADLEEDIAELEATLADRKQS 376
                                       45555555555555555555555....55667888899999999999999999998888776665 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.0015
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHH CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqlee 83 
                                       + +e ++e ++ la+ +q l+  ++ l++++++ve+  ++v++a   + d+++++k  e ++++  d l +l+++  
  gi|344210266|ref|YP_004786442.1| 358 DLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADELAQLETRAA 434
                                       5677888999999999***********************************************************99 PP

                                       H...HHHHHHHHHHHHHHHHHHHHT-- CS
                        Laminin_II  84 assslsdniseikelIaqARkaAnkik 110
                                          +l  +++ ++   a  R+   +ik
  gi|344210266|ref|YP_004786442.1| 435 RVDTLETDLETVRDDLAELRNRKDRIK 461
                                       9999*******9998888887777666 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 ?   -1.7   0.4       7.4   1.9e+03      84     134 ..     158     208 ..     120     271 .. 0.52
   2 !   17.5   0.5   1.1e-05    0.0028     101     264 ..     347     540 ..     320     540 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 7.4
                            AAA_21  84 eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvse 134
                                       + +l+sv ++  + +   ++ + ++   ++ea   ++ +sv+++ +  + e
  gi|344210266|ref|YP_004786442.1| 158 KKRLPSVQEKVTRLENEIEDLRAKRETIDSEAGSDDSPESVRRQLSQARTE 208
                                       444444444444444444444444444444444444444444444444333 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.1e-05
                            AAA_21 101 dkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfg 177
                                        + s  ++ + + e++ +   ++   +k+++ +  n+l++ +  ++  s++++++    +    ++      a++  
  gi|344210266|ref|YP_004786442.1| 347 EEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVDAAVAELSDV--ESEIKYREAELED 421
                                       45555555555555555555555555555555555555555555555555555555554422..3333333444444 PP

                            AAA_21 178 fakekrllqrlvrslklveielsdlgegeeliasvderlrer...........................gvvfleng 227
                                        a+e+ +l+ +  ++++ e  l++ ++   +   +++r++++                           ++ +++  
  gi|344210266|ref|YP_004786442.1| 422 TADELAQLETRAARVDTLETDLETVRDDLAELRNRKDRIKREtreafdtamkdilsrfgtgfetarltaDFDIVVAR 498
                                       4444444444444445555444444444444444455555559999999999************************* PP

                            AAA_21 228 dgqelparelSdGtkrllalltallralkkg.....sllliD 264
                                       dgqe +++ lS+G ++l+++++al+ + + +     +lll+D
  gi|344210266|ref|YP_004786442.1| 499 DGQEASLDALSEGELELIGFVAALAGRQSFDvgdavPLLLVD 540
                                       ************************999887777777777776 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 ?    4.8   5.9     0.055        14      38      95 ..     131     188 ..     121     205 .. 0.59
   2 ?    2.9   8.1      0.21        54      58     135 ..     199     278 ..     187     292 .. 0.59
   3 !   15.9   8.3   2.4e-05    0.0062      17      99 ..     320     401 ..     317     409 .. 0.90
   4 ?    3.0   6.3      0.19        50      44     100 ..     381     437 ..     373     477 .. 0.46

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.055
                              HemX  38 aelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqq 95 
                                       +++++q+++l+ + +q+e+e +q  e ++rl   +ek+ +le+e+e+l ++ e++ ++
  gi|344210266|ref|YP_004786442.1| 131 QNIDSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRETIDSE 188
                                       5566666666666666666666666666666666666666666666665555554444 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.21
                              HemX  58 keqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsgaerkd..WlLaeAdfLlklAgrkLvldqDvetA 132
                                       ++q ++  ++ +q+++++e+le+++e ++++l+e q++l +++  e +d   +L+eA   l+  +r   + q v +A
  gi|344210266|ref|YP_004786442.1| 199 RRQLSQARTEQNQAKNRVERLEQSIERTEQRLSERQDALDALEIPEYNDvaDKLSEARESLSQVERDAEVLQSVYSA 275
                                       45556666666666777777777777777777777777666655533331134555555555555555555555555 PP

                              HemX 133 lal 135
                                       +++
  gi|344210266|ref|YP_004786442.1| 276 TEM 278
                                       544 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 2.4e-05
                              HemX  17 avgaglyylgqqqvqeltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelq 93 
                                       a+g  l+ l++q+ ++++ +v+el++q ++++q+  + + ++e+ +ele++l++ +++l+a++++leq q+++e+l+
  gi|344210266|ref|YP_004786442.1| 320 ALGNELTALRAQK-ETYRDTVEELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLS 395
                                       6777888899988.5999999***************99999***********************************9 PP

                              HemX  94 qqlskv 99 
                                       +++ + 
  gi|344210266|ref|YP_004786442.1| 396 DHVDAA 401
                                       999875 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.19
                              HemX  44 laaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvs 100
                                        + leq+++ ve++  + +   ++l + +++++ +e+ele+++ +l++l+++ ++v+
  gi|344210266|ref|YP_004786442.1| 381 RNRLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADELAQLETRAARVD 437
                                       333333333333333333333333333333333333333333333333333333332 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 !   15.4   2.6   6.2e-05     0.016      26      96 ..     118     188 ..      93     191 .. 0.85
   2 ?    2.2   5.1      0.79   2.1e+02      46      99 ..     203     239 ..     192     272 .. 0.48
   3 !   10.9   6.2    0.0016      0.41      34     100 ..     314     380 ..     309     385 .. 0.90
   4 ?    3.1   5.7      0.42   1.1e+02      49     100 ..     381     429 ..     373     467 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  26 advdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleae 96 
                                       ++++++l      +++ +++e lq+er ++  e  +a ++k+   ++ ++v  l +e+++l a+ +++++e
  gi|344210266|ref|YP_004786442.1| 118 ENLEDVLLRPLDFQNIDSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRETIDSE 188
                                       5556666666666788899***********************************************99987 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.79
                                       HHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  46 eelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelek 99 
                                        +++                  + ++ +++v+ l + ++++e++l+e +++l++
  gi|344210266|ref|YP_004786442.1| 203 SQAR-----------------TEQNQAKNRVERLEQSIERTEQRLSERQDALDA 239
                                       2222.................233344444444444444444444444444433 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  34 ldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekl 100
                                       l ++  +l +el +l+a++ +   +++++  + e++++ + + ++l e++++lea+l++ ++ l+++
  gi|344210266|ref|YP_004786442.1| 314 LADQLDALGNELTALRAQKETYRDTVEELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAA 380
                                       66778889999**********************************************9999998875 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  49 qaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekl 100
                                       +++  +++  ++++++     ++ +ae +++  e+k  eael++  +el +l
  gi|344210266|ref|YP_004786442.1| 381 RNRLEQAQSDVEQLSD---HVDAAVAELSDVESEIKYREAELEDTADELAQL 429
                                       2233333333333332...234444444444444444444444444444332 PP

>> Alpha-2-MRAP_C  Alpha-2-macroglobulin RAP, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   5.5      0.55   1.4e+02     132     208 ..     157     233 ..     149     237 .. 0.65
   2 !   16.2  11.9     3e-05    0.0077      23     187 ..     317     472 ..     308     479 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.55
                    Alpha-2-MRAP_C 132 sedeLeslkeELkhyesrleklrhlqaelelseeklkdeekkkekkekhkkleekikklgrkveklhedlesrilqk 208
                                        ++ L s++e  +  e+ +e lr  ++  + ++   ++ e+ +++ +++++ ++++k+  +++e+  e  e+r++++
  gi|344210266|ref|YP_004786442.1| 157 AKKRLPSVQEKVTRLENEIEDLRAKRETIDSEAGSDDSPESVRRQLSQARTEQNQAKNRVERLEQSIERTEQRLSER 233
                                       56778899999999999999999998888888888875555555555555555555555555555555555555544 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3e-05
                    Alpha-2-MRAP_C  23 eLekLkeEfkhhqeKideYnsLleelekeeekheNaiseeeldkvneieeeeekkkeylekenelkekhrelkdgfd 99 
                                       +L++L +E++  +   + Y + +eele+++e    +is+ +    ++++     +++  e e++l +++++l    +
  gi|344210266|ref|YP_004786442.1| 317 QLDALGNELTALRAQKETYRDTVEELETQRE----EISQARR---RKADL----EEDIAELEATLADRKQSLDAARN 382
                                       6677777777777777777777777666666....4552222...22222....2346678999999********** PP

                    Alpha-2-MRAP_C 100 rLerlaakgpkskeFeepkVqeLWklAkeanfsedeLeslkeELkhyesrleklrhlqaelelseeklk..deekkk 174
                                       rLe+  ++ ++ ++ +++ V+eL ++  e ++ e eLe   +EL   e+r  + ++l+++le  +++l   ++ k++
  gi|344210266|ref|YP_004786442.1| 383 RLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADELAQLETRAARVDTLETDLETVRDDLAelRNRKDR 459
                                       *************************************************************9999988855445555 PP

                    Alpha-2-MRAP_C 175 ekkekhkkleeki 187
                                        k+e+ +  ++ +
  gi|344210266|ref|YP_004786442.1| 460 IKRETREAFDTAM 472
                                       5555555555555 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4  13.3    0.0011      0.29       7     114 ..     132     240 ..     130     243 .. 0.91
   2 ?   -1.3   0.0       9.7   2.5e+03      10      35 ..     250     275 ..     243     282 .. 0.62
   3 !   13.1   5.8   0.00033     0.085       7      53 ..     344     394 ..     338     401 .. 0.89
   4 ?    4.1   0.6       0.2        53       6      76 ..     406     476 ..     401     481 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0011
                           DUF5082   7 klqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGk.eennydgirsnlessyqty 82 
                                       +  +qi+ l+ e++++e  ++  +eak++l +++e++   ++++e+  ++ e+   +  +++  + ++   s+ +t 
  gi|344210266|ref|YP_004786442.1| 132 NIDSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRETIDSEaGSDDSPESVRRQLSQARTE 208
                                       6789***********************************************98888866666666777899999*** PP

                           DUF5082  83 vdkldelidaieeEIerLenqiseaqgvldtl 114
                                       + + ++ + ++e+ Ier e+ +se q  ld l
  gi|344210266|ref|YP_004786442.1| 209 QNQAKNRVERLEQSIERTEQRLSERQDALDAL 240
                                       ***************************99987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 9.7
                           DUF5082  10 aqiaelrseiaaleekIerLkeaktk 35 
                                        + +e+r+ ++++e + e L++++++
  gi|344210266|ref|YP_004786442.1| 250 DKLSEARESLSQVERDAEVLQSVYSA 275
                                       45566666666666666666666655 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.00033
                           DUF5082   7 klqaqiaelrseiaaleekIerLk....eaktklsdekeslkqkkkklekp 53 
                                       + +++i+++r + a+lee+I++L+      k++l+++ ++l+q+++++e+ 
  gi|344210266|ref|YP_004786442.1| 344 TQREEISQARRRKADLEEDIAELEatlaDRKQSLDAARNRLEQAQSDVEQL 394
                                       56789*******************777777*****************9986 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.2
                           DUF5082   6 sklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnle 76 
                                       s+++++i   ++e++++ + ++ L++   ++++ +  l++ + +l++  n ++  k ++++ +d++  ++ 
  gi|344210266|ref|YP_004786442.1| 406 SDVESEIKYREAELEDTADELAQLETRAARVDTLETDLETVRDDLAELRNRKDRIKRETREAFDTAMKDIL 476
                                       67788888888888899999999998888899999999999999999999998888888888888877765 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3  17.0    0.0027      0.69      54     153 ..     130     232 ..     114     239 .. 0.66
   2 ?    3.0  14.4      0.46   1.2e+02      35     156 ..     204     337 ..     197     348 .. 0.65
   3 ?   11.9  19.9   0.00086      0.22      31     154 ..     323     460 ..     309     471 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0027
                              Fez1  54 ikeleesleektlelevcenelqrk...kseaellrekvekleeelkelreelselsleeeeaa.......lesdea 120
                                        +++++++e+ ++e e++e el ++   k++   ++ekv++le+e+++lr + ++  +e+ +         +     
  gi|344210266|ref|YP_004786442.1| 130 FQNIDSQIETLQREREQIETELTQAreaKKRLPSVQEKVTRLENEIEDLRAKRETIDSEAGSDDspesvrrQL---- 202
                                       577888999999999999999988855566677889*************997777654443333334444222.... PP

                              Fez1 121 kaqrqeaeeleelkreverlraeLkeerqkkee 153
                                           q+++e ++ k++verl+++++  +q+  e
  gi|344210266|ref|YP_004786442.1| 203 ---SQARTEQNQAKNRVERLEQSIERTEQRLSE 232
                                       ...233344445555555555555544444332 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.46
                              Fez1  35 alkaqlrelrakleekeeeikeleesleektlelevce.nelqrkkseaellrekvekleeelkelreelselslee 110
                                       + +++  ++++++e+ e++i+++e++l+e+++ l+ +e  e +   ++ +  re ++++e++ + l++ +s++++  
  gi|344210266|ref|YP_004786442.1| 204 QARTEQNQAKNRVERLEQSIERTEQRLSERQDALDALEiPEYNDVADKLSEARESLSQVERDAEVLQSVYSATEMVL 280
                                       45667777777777777777777777777777777777346666677777777777777777777777666655444 PP

                              Fez1 111 eeaalesdeakaqrqe.............aeeleelkreverlraeLkeerqkkeeqas 156
                                       +e +l+  +  ++  +             +++ ++l  +++ l +eL+  r +ke+ ++
  gi|344210266|ref|YP_004786442.1| 281 SEDRLDLLTEVER--DidgdtvacwtcgsETTRADLADQLDALGNELTALRAQKETYRD 337
                                       4444333332222..13466777777776677778888899999999888888887654 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00086
                              Fez1  31 seivalkaqlrelrakleekeeeikeleesleek...tlelevcenelqrkkseaellrekvekleeelkelreels 104
                                       +e+ al+aq    r ++ee e++ +e++++++ k   ++++ ++e+ l+ +k++ +  r+++e++++++++l +++ 
  gi|344210266|ref|YP_004786442.1| 323 NELTALRAQKETYRDTVEELETQREEISQARRRKadlEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVD 399
                                       56666666654444444444444444444443331113344455555555556666666666666666666655544 PP

                              Fez1 105 elsleeeeaa...........lesdeakaqrqeaeeleelkreverlraeLkeerqkkeeq 154
                                       ++ +e ++ +            ++de  + +++a ++++l+ ++e +r  L+e r++k++ 
  gi|344210266|ref|YP_004786442.1| 400 AAVAELSDVEseikyreaeleDTADELAQLETRAARVDTLETDLETVRDDLAELRNRKDRI 460
                                       4333333322222222222112233322233336788889999999999998888888765 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 ?   13.8   7.1   0.00019      0.05      28      83 ..     130     185 ..     116     190 .. 0.93
   2 ?    9.6   9.7    0.0041       1.1      27     112 ..     317     402 ..     312     405 .. 0.86
   3 ?   13.0   6.5   0.00034     0.089      11      82 ..     388     459 ..     379     467 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00019
                       TMF_TATA_bd  28 laslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetl 83 
                                        +++ +++e+l++er++++ e+ +  +   +l + +++++ le+e+e+l+ + et+
  gi|344210266|ref|YP_004786442.1| 130 FQNIDSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRETI 185
                                       678999**********************************************9985 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0041
                       TMF_TATA_bd  27 ElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEeveELraDvaD 103
                                       +l +l +el+ l a++++ r+ + +l ++ ee +++ ++ ++le+ ++el+  +    + l     + e+ + Dv+ 
  gi|344210266|ref|YP_004786442.1| 317 QLDALGNELTALRAQKETYRDTVEELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQ 393
                                       56778889999999999999999999999999999999999999999999999999999999999999999999998 PP

                       TMF_TATA_bd 104 lKemykeqv 112
                                       l + +   v
  gi|344210266|ref|YP_004786442.1| 394 LSDHVDAAV 402
                                       877766666 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00034
                       TMF_TATA_bd  11 vqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryet 82 
                                       ++ ve+ls  +    +El+ +++e++  eae +++++e+++l ++  ++++l+++le+++  l+el++r + 
  gi|344210266|ref|YP_004786442.1| 388 QSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADELAQLETRAARVDTLETDLETVRDDLAELRNRKDR 459
                                       5669****************************************************************9886 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 ?    0.1   8.3         3   7.8e+02      30      78 ..     135     177 ..     119     281 .. 0.62
   2 ?   15.3   3.1   6.1e-05     0.016      13     100 ..     309     397 ..     300     399 .. 0.72
   3 ?   11.7   2.6   0.00079       0.2      25      99 ..     380     455 ..     377     462 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 3
                      Baculo_PEP_C  30 vqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalna 78 
                                       +qi   l++  ++iet+L++  e+ k+ l++++++++ l ++++     
  gi|344210266|ref|YP_004786442.1| 135 SQI-ETLQREREQIETELTQAREAKKR-LPSVQEKVTRLENEIE----D 177
                                       333.33444444444444443332222.3333332222222221....1 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 6.1e-05
                      Baculo_PEP_C  13 nqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksl...laeldtrldtlltnLtdalnalqdtlrne 86 
                                       +   dL ++L+a+ + ++ + aq +t  d++e+ L++  e+++++    a+l++++++l ++L d  ++l d+ rn+
  gi|344210266|ref|YP_004786442.1| 309 TTRADLADQLDALGNELTALRAQKETYRDTVEE-LETQREEISQArrrKADLEEDIAELEATLADRKQSL-DAARNR 383
                                       44689********99999999999998888776.777777777741114455555555555555555555.699*** PP

                      Baculo_PEP_C  87 LtnlnsiltnLlss 100
                                       L+  +s++ +L   
  gi|344210266|ref|YP_004786442.1| 384 LEQAQSDVEQLSDH 397
                                       ********999765 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00079
                      Baculo_PEP_C  25 irlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq..dtlrneLtnlnsiltnLls 99 
                                        r+ + q  +++++l d+++  + +ls+ ++s ++  +++l++++++L +   + +  dtl+++L+++  +l++L +
  gi|344210266|ref|YP_004786442.1| 380 ARNRLEQAQSDVEQLSDHVDAAVAELSD-VESEIKYREAELEDTADELAQLETRAArvDTLETDLETVRDDLAELRN 455
                                       4555555555555655555555555433.555555566677777777777777666779*************99975 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0  21.1   0.00087      0.23      92     188 ..     136     237 ..     133     286 .. 0.72
   2 ?    8.2  21.9    0.0063       1.6      91     206 ..     330     444 ..     308     459 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00087
                         PspA_IM30  92 eikslekqaealetqlaqqrsave...qlrkqlealetkieelkakkellkarekaakaqeavqkslgkls..tesa 163
                                       +i++l+ + e+ et+l+q+r+a +    +++++++le  ie+l+ak+e++ + + +    e v ++l +++   ++a
  gi|344210266|ref|YP_004786442.1| 136 QIETLQREREQIETELTQAREAKKrlpSVQEKVTRLENEIEDLRAKRETIDSEAGSDDSPESVRRQLSQARteQNQA 212
                                       567777777777777777777665111679*****************************************665567 PP

                         PspA_IM30 164 tdslerieeKieerearadaaaela 188
                                        +  er+e+ ie+ e+r + ++ + 
  gi|344210266|ref|YP_004786442.1| 213 KNRVERLEQSIERTEQRLSERQDAL 237
                                       7778888888888887766554443 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0063
                         PspA_IM30  91 aeikslekqaealetqla...qqrsaveqlrkqlealetkieelkakkellkarekaakaqeavqkslgkls..tes 162
                                       a+++++ +++e+letq +   q+r   ++l++ +++le+ +++ k+  ++  ar    +aq +v++ ++ ++  +++
  gi|344210266|ref|YP_004786442.1| 330 AQKETYRDTVEELETQREeisQARRRKADLEEDIAELEATLADRKQSLDA--ARNRLEQAQSDVEQLSDHVDaaVAE 404
                                       7999*********998762226788899**************98888875..7777778899999999999943333 PP

                         PspA_IM30 163 atdslerieeKieerearadaaaelaesaqdldakleaagiqke 206
                                        +d   +i+ + +e+e++ad  a+l+    ++ a ++ ++ + e
  gi|344210266|ref|YP_004786442.1| 405 LSDVESEIKYREAELEDTADELAQLE----TRAARVDTLETDLE 444
                                       34444566666666666666666666....44455555444444 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 ?   10.8   3.6    0.0012      0.31      17      72 ..     134     189 ..     109     194 .. 0.86
   2 ?    3.4   2.5      0.23        59      16      73 ..     212     267 ..     196     274 .. 0.74
   3 ?   10.4   6.6    0.0017      0.43      19      75 ..     324     380 ..     315     395 .. 0.90
   4 ?    6.6   5.8     0.023       6.1      17      89 ..     402     476 ..     385     506 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0012
                        Phage_GP20  17 kakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaey 72 
                                        +++++++ er++++++l+++ +  + L  +++ ++ L+++ie+l ak ++ ++e+
  gi|344210266|ref|YP_004786442.1| 134 DSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRETIDSEA 189
                                       68999*******************************************99988876 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.23
                        Phage_GP20  16 tkakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeye 73 
                                       +k++++++e+  +  +++l +r+  L+ L+    + +++  ++ e  + + + + ++e
  gi|344210266|ref|YP_004786442.1| 212 AKNRVERLEQSIERTEQRLSERQDALDALEIP--EYNDVADKLSEARESLSQVERDAE 267
                                       48888888999999999999999999999755..777777777777777777666654 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0017
                        Phage_GP20  19 kldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeak 75 
                                       +l+ + ++++t+ +++++ ++q e++ ++    ++L+++i+el+a++++ k+  +a 
  gi|344210266|ref|YP_004786442.1| 324 ELTALRAQKETYRDTVEELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAA 380
                                       6778999******************************************99988875 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.023
                        Phage_GP20  17 kakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkak..aeyeakiadlkldnaielaL 89 
                                        a+l++ve+e +  + +l+d   +L +L++ a  +++L++++e++  ++++    ++  +  +  ++d a++  L
  gi|344210266|ref|YP_004786442.1| 402 VAELSDVESEIKYREAELEDTADELAQLETRAARVDTLETDLETVRDDLAELRnrKDRIKRETREAFDTAMKDIL 476
                                       678899999999999999999999999999999999999999999999987431144445555556666666655 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   4.1     0.041        11       3      50 ..     138     185 ..     128     224 .. 0.63
   2 ?    4.8   0.4     0.093        24       3      46 ..     228     272 ..     226     296 .. 0.77
   3 ?    7.1   1.0     0.018       4.6      12      66 ..     311     365 ..     305     369 .. 0.92
   4 ?    3.2   0.2      0.29        75       3      37 ..     382     416 ..     380     426 .. 0.85
   5 ?    8.7   0.1    0.0058       1.5       2      52 ..     426     477 ..     425     482 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.041
                             Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceql 50 
                                       ++L++++e++++ l+q++ea++ L +++ek+++ +++ ++l+++ e++
  gi|344210266|ref|YP_004786442.1| 138 ETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRETI 185
                                       455555555555555555555555555555555555555555554444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.093
                             Sec34   3 dqLeskeeecdel.leqtdealeqLeeleekfksvsektsslhea 46 
                                       ++L+++++ +d+l + + +++ ++L+e +e+ ++v+ + + l++ 
  gi|344210266|ref|YP_004786442.1| 228 QRLSERQDALDALeIPEYNDVADKLSEARESLSQVERDAEVLQSV 272
                                       578899999999966899*******************99998863 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.018
                             Sec34  12 cdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeiee 66 
                                         +l +q+d++ ++L+ l+ + ++  +  ++l+++ e++ + ++r  +l e+i e
  gi|344210266|ref|YP_004786442.1| 311 RADLADQLDALGNELTALRAQKETYRDTVEELETQREEISQARRRKADLEEDIAE 365
                                       567999**********************************************986 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.29
                             Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvs 37 
                                       ++Le+ ++ +++l +++d+a  +L+++e++ k  +
  gi|344210266|ref|YP_004786442.1| 382 NRLEQAQSDVEQLSDHVDAAVAELSDVESEIKYRE 416
                                       7899**********************999877655 PP

  == domain 5  score: 8.7 bits;  conditional E-value: 0.0058
                             Sec34   2 ldqLeskeeecdelleqtdealeqLeeleekfksvsekts.slheaceqlle 52 
                                       l qLe++ +++d+l ++++++ ++L+el+++ ++++ +t+ ++++a++++l+
  gi|344210266|ref|YP_004786442.1| 426 LAQLETRAARVDTLETDLETVRDDLAELRNRKDRIKRETReAFDTAMKDILS 477
                                       579*********************************9996268888887775 PP

>> Med14  Mediator complex subunit MED14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       1.9   4.9e+02      75     126 ..     201     252 ..     189     286 .. 0.64
   2 ?   10.1   0.1    0.0015      0.39      64     108 ..     316     360 ..     310     364 .. 0.88
   3 ?    0.5   0.0       1.3   3.4e+02      64     109 ..     400     445 ..     390     452 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.9
                                       HHHHHHHCCCCCHCCCCCHHHHHHCCHHHHHHHHCHHCHCTTCHCHCCCCCC CS
                             Med14  75 flrqqneafedaadalkelkeslanaklpnpdlktAleVLstGrysrlpsli 126
                                       +l+q ++  ++a +++  l++s+++   +  + + Al+ L   +y+++ +  
  gi|344210266|ref|YP_004786442.1| 201 QLSQARTEQNQAKNRVERLEQSIERTEQRLSERQDALDALEIPEYNDVADKL 252
                                       5666666666666666666777777777766666676666666666555544 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0015
                                       HHCCHHHHHHHHHHHHHHCCCCCHCCCCCHHHHHHCCHHHHHHHH CS
                             Med14  64 ekvsklidllaflrqqneafedaadalkelkeslanaklpnpdlk 108
                                       ++++ l + l+ lr+q+e++ d++++l   +e++++a+ ++ dl+
  gi|344210266|ref|YP_004786442.1| 316 DQLDALGNELTALRAQKETYRDTVEELETQREEISQARRRKADLE 360
                                       666667777899*******************************97 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.3
                                       HHCCHHHHHHHHHHHHHHCCCCCHCCCCCHHHHHHCCHHHHHHHHC CS
                             Med14  64 ekvsklidllaflrqqneafedaadalkelkeslanaklpnpdlkt 109
                                       + v++l d+   ++ +++ +ed+ad+l +l++  a++ + + dl+t
  gi|344210266|ref|YP_004786442.1| 400 AAVAELSDVESEIKYREAELEDTADELAQLETRAARVDTLETDLET 445
                                       678899999999999999*********9999999999888888887 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  15.3     0.015       3.8     150     264 ..     141     268 ..      61     291 .. 0.52
   2 ?   12.0  12.6   0.00044      0.11     146     265 ..     339     476 ..     298     488 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.015
                      Exonuc_VII_L 150 eelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerler............alkkqlkkkrerl 214
                                       ++ ++++e+++        ++ +++++rl+s +e+++r ++++++l+++ e+            ++++ql+++r++ 
  gi|344210266|ref|YP_004786442.1| 141 QREREQIETEL--------TQAREAKKRLPSVQEKVTRLENEIEDLRAKRETidseagsddspeSVRRQLSQARTEQ 209
                                       22222222222........2222222333333333333333333322222222222222222223344444444444 PP

                      Exonuc_VII_L 215 eelkerl.k..ekleekkerlkklkerle............lleekkerleeleeklealsplkv 264
                                       +++k+r+ +  +++e++++rl+++++ l+            +l+e++e+l+++e+  e      v
  gi|344210266|ref|YP_004786442.1| 210 NQAKNRVeRleQSIERTEQRLSERQDALDaleipeyndvadKLSEARESLSQVERDAE------V 268
                                       4444444324455566666665555555555555333333333333333333333333......2 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00044
                      Exonuc_VII_L 146 eeqleelerrlekaikrll.............eekkqrleklasrlkspeellerkrqrldeleerleralkkqlkk 209
                                        e+le++++++++a +r+               ++kq l+++++rl+++++ +e+ ++++d + ++l+  +++++k 
  gi|344210266|ref|YP_004786442.1| 339 VEELETQREEISQARRRKAdleediaeleatlADRKQSLDAARNRLEQAQSDVEQLSDHVDAAVAELSD-VESEIKY 414
                                       233333333333333332211111111111114444444444444444444444444444444444444.4444555 PP

                      Exonuc_VII_L 210 krerleelkerl.kekleekkerlkklkerle.......lleekkerleeleeklealsplkvL 265
                                       ++++le ++++l +  le++++r+++l++ le       +l+++k+r+++ +++   +  + +L
  gi|344210266|ref|YP_004786442.1| 415 REAELEDTADELaQ--LETRAARVDTLETDLEtvrddlaELRNRKDRIKRETREAFDTAMKDIL 476
                                       55555555555522..333333333333333333333225666666666666655555555555 PP

>> ApbE  ApbE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.3       7.5     2e+03      16      37 ..     212     231 ..     198     293 .. 0.57
   2 ?   13.6   0.3   0.00014     0.035      14      95 ..     406     493 ..     383     515 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 7.5
                                       HHHHHHHHHHHC-SS-TTSHHH CS
                              ApbE  16 ieaelerlekllsryrpdSels 37 
                                       +++++erle+++ r+++   ls
  gi|344210266|ref|YP_004786442.1| 212 AKNRVERLEQSIERTEQ--RLS 231
                                       44445555554444443..222 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHHHC-SS-TTSHHHHHH.CT.SS-E........EE-HHHHHHHHHHHHHHHHTTTSS-TTTHHHHHH CS
                              ApbE  14 aaieaelerlekllsryrpdSelsrlN.ra.kkev........kvspelaellkaaleiseltdgafdptvgplvkl 80 
                                         +e+e++  e++l  +    el++l  ra +  v        +v ++lael ++  +i+++t  afd +++ +++ 
  gi|344210266|ref|YP_004786442.1| 406 SDVESEIKYREAELEDTA--DELAQLEtRAaR--VdtletdleTVRDDLAELRNRKDRIKRETREAFDTAMKDILSR 478
                                       333444444444444444..588888843332..333566777999******************************9 PP

                                       HCTTSGG.----HHH CS
                              ApbE  81 wgfgeekarvpsaee 95 
                                       +g g+e+ar+ ++ +
  gi|344210266|ref|YP_004786442.1| 479 FGTGFETARLTADFD 493
                                       998887666655544 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 ?    1.3  17.7      0.29        75     694     806 ..     134     241 ..     126     277 .. 0.73
   2 ?   13.1  18.0   7.7e-05      0.02     641     814 ..     276     448 ..     244     471 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.29
                               FPP 694 keeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletratel 770
                                         ++e l+ e+e++e+el +a     ++k +l    ++++ l+ e+e l+  ++ ++++      s es+  +++++
  gi|344210266|ref|YP_004786442.1| 134 DSQIETLQREREQIETELTQAR----EAKKRLPSVQEKVTRLENEIEDLRAKRETIDSEA-GSDDSPESVRRQLSQA 205
                                       4567777888888887776654....5677888888888999999999998888888865.4566788899999999 PP

                               FPP 771 eaelnelkqkieaLeveLeeekksheeleakckelq 806
                                       ++e n++k+++e+Le+ +e  ++   e + +   l+
  gi|344210266|ref|YP_004786442.1| 206 RTEQNQAKNRVERLEQSIERTEQRLSERQDALDALE 241
                                       999999999999999988888777776665555444 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.7e-05
                               FPP 641 dkvalsenkvaqkgessnecaeisklssekeipselplvsgsneskkeenkllkeeleelksekenle...velksa 714
                                        ++ lse++        +  +e+++  + +++ + ++ ++++  + +++   l +el+ l+++ke+      el+++
  gi|344210266|ref|YP_004786442.1| 276 TEMVLSEDR-------LDLLTEVERDIDGDTVACWTCGSETTRADLADQLDALGNELTALRAQKETYRdtvEELETQ 345
                                       333333333.......34455666666666664444444444444478899999*********99765221678888 PP

                               FPP 715 tenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletrateleaelnelkqkieaLeveLeee 791
                                        e++ ++  +  + E+ +ael++ L+  k+s   a + l++ +   e+l+ +   + ael+ ++++i+  e+eLe+ 
  gi|344210266|ref|YP_004786442.1| 346 REEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELEDT 422
                                       8899999999*****************************************************************98 PP

                               FPP 792 kksheele...akckelqeqlervek 814
                                        +   +le   a++  l+  le+v+ 
  gi|344210266|ref|YP_004786442.1| 423 ADELAQLEtraARVDTLETDLETVRD 448
                                       87766555111667889999998864 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  24.2     0.061        16       4     108 ..     139     242 ..     136     287 .. 0.62
   2 ?    8.8  11.3    0.0065       1.7      21     101 ..     375     455 ..     371     467 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.061
                     Tropomyosin_1   4 sLkleaeea...qekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnnea 77 
                                       +L+ e e+    +++a e+++++ + +++ ++ e+ei++L  k +++++e    ++  + ++++++++   +t++++
  gi|344210266|ref|YP_004786442.1| 139 TLQREREQIeteLTQAREAKKRLPSVQEKVTRLENEIEDLRAKRETIDSEAGSDDS-PESVRRQLSQA---RTEQNQ 211
                                       5555555550005566666666667899999*****************99865433.33344444433...344444 PP

                     Tropomyosin_1  78 ltrkiqlLEeeleesdkkLkettekLretdv 108
                                        + +++ LE+ +e+++++L e  + L   ++
  gi|344210266|ref|YP_004786442.1| 212 AKNRVERLEQSIERTEQRLSERQDALDALEI 242
                                       4568888888888888888888887776665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0065
                     Tropomyosin_1  21 ekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnnealtrkiqlLEeeleesdkkLk 97 
                                       +++ ++ ++ ++  +++++L+  ++++ +e+  +e+++k  ++++e+++ + ++ e+   +++ LE +le    +L+
  gi|344210266|ref|YP_004786442.1| 375 QSLDAARNRLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADELAQLETRAARVDTLETDLETVRDDLA 451
                                       55556677888899999*****************************************************9999999 PP

                     Tropomyosin_1  98 ette 101
                                       e  +
  gi|344210266|ref|YP_004786442.1| 452 ELRN 455
                                       8755 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 ?   -1.1  29.9       4.4   1.1e+03      30     182 ..     145     288 ..     131     296 .. 0.55
   2 ?   11.0  25.7   0.00087      0.23      28     169 ..     314     454 ..     309     456 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.4
                        MscS_porin  30 dkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlns 106
                                       ++i+    +a+e +k++ + ++++  l++e+e l++k e+ + e  +           +++  ql++++++++q+++
  gi|344210266|ref|YP_004786442.1| 145 EQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRETIDSEAGSD-------DSPESVRRQLSQARTEQNQAKN 214
                                       344444445555555555555555555555555522222222222222.......3344455555556666666666 PP

                        MscS_porin 107 qlvelqtrperaqqqltearqrlqeirnrLnstaaage..alsqaqrtalqaelaaleaqieeleqellsnnnrqeL 181
                                       ++  l++++er  q+l+e + +l++++     ++ ++   +ls+a+  + q+e+ a  +q  +  +e+  +  r +L
  gi|344210266|ref|YP_004786442.1| 215 RVERLEQSIERTEQRLSERQDALDALEI----PEYNDVadKLSEARESLSQVERDAEVLQSVYSATEMVLSEDRLDL 287
                                       6777777777777777777777777766....212222448999999999999888888887777776555555555 PP

                        MscS_porin 182 l 182
                                       l
  gi|344210266|ref|YP_004786442.1| 288 L 288
                                       4 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00087
                        MscS_porin  28 lLdkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaql 104
                                       l d+ d+  +++ +l+ + +++  +++el+ + e+    +++  ++ + +  ++eLe  l+++++ l +++++l q+
  gi|344210266|ref|YP_004786442.1| 314 LADQLDALGNELTALRAQKETYRDTVEELETQREEI---SQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQA 387
                                       678899999999999999999999999999999999...7778888888899************************* PP

                        MscS_porin 105 nsqlvelqtrperaqqqltearqrlqeirnrLnstaaage..alsqaqrtalqaelaaleaqieele 169
                                       +s++ +l++  + a ++l++   +++  +++L++ta++ +  + ++a+ + l++ l+  ++ ++el+
  gi|344210266|ref|YP_004786442.1| 388 QSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADELAqlETRAARVDTLETDLETVRDDLAELR 454
                                       ********************************99987777889999999999999998887777765 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6  20.4      0.27        69     392     475 ..     140     227 ..     129     277 .. 0.45
   2 ?   13.8  18.3   5.6e-05     0.014      69     198 ..     326     462 ..     304     465 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.27
                               MAD 392 vqahneeveaqleva...eeevggykqqastlerelqalrqqesladass.skeevdslkkkleeLelerqrLreqk 464
                                       +q   e++e++l++a   ++ + + +++++ le e++ lr + ++ d+   s++  +s++++l + + e+++ +++ 
  gi|344210266|ref|YP_004786442.1| 140 LQREREQIETELTQAreaKKRLPSVQEKVTRLENEIEDLRAKRETIDSEAgSDDSPESVRRQLSQARTEQNQAKNRV 216
                                       33333333333333300022344444444555555555554444444444444444455555555555555544444 PP

                               MAD 465 eelElelerre 475
                                       e lE ++er e
  gi|344210266|ref|YP_004786442.1| 217 ERLEQSIERTE 227
                                       44444444332 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.6e-05
                               MAD  69 ealreqiElarlkkknlealnkkekekesklaearevisalknelaelkrqiekqelelsekeseleelqerldllk 145
                                       +alr+q E  r +   le++ ++ ++   ++a+++e i +l+  la++k+++  +   l++ +s++e+l  + d   
  gi|344210266|ref|YP_004786442.1| 326 TALRAQKETYRDTVEELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVDAAV 402
                                       56777777777777777777777777788888888888888888999999999999999999999999999999999 PP

                               MAD 146 kklseleqli....qqlekkqkelaeae...qrikeLefeiqsqeddslivknskselar 198
                                       ++ls++e  i    ++le   +ela+ e   +r+ +Le  ++   dd ++++n k+++ r
  gi|344210266|ref|YP_004786442.1| 403 AELSDVESEIkyreAELEDTADELAQLEtraARVDTLETDLETVRDDLAELRNRKDRIKR 462
                                       999999988877887777777766654411168999999999999999999999998865 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6  26.8       2.9   7.5e+02      12     118 ..     131     258 ..     128     277 .. 0.66
   2 ?    3.4  31.5      0.39     1e+02      11     126 ..     318     433 ..     312     475 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 2.9
                            APG6_N  12 eeldkqleqaekerdaYeeflkklkkekkeeek...........................qdeeleeleeeleklek 61 
                                       +++d+q+e++++er++ e+ l + ++ kk   +                           +d++ e+ +++l++ + 
  gi|344210266|ref|YP_004786442.1| 131 QNIDSQIETLQREREQIETELTQAREAKKRLPSvqekvtrleneiedlrakretidseagSDDSPESVRRQLSQART 207
                                       67888888888888888888888888866644466666677777777777777777777767777777777777777 PP

                            APG6_N  62 eeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleee 118
                                       e++++ +  ++le+  e+ e+ l++ +  l+ale  e + + +      +l+e  e 
  gi|344210266|ref|YP_004786442.1| 208 EQNQAKNRVERLEQSIERTEQRLSERQDALDALEIPEYNDVAD------KLSEARES 258
                                       7777777777777777777777777777777777655544443......33333333 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.39
                            APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaal 87 
                                       l+ l ++l ++++++++Y++  ++l+++++e ++ +   ++lee++++le++ ++  + L+++ +  e+ ++++++l
  gi|344210266|ref|YP_004786442.1| 318 LDALGNELTALRAQKETYRDTVEELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQL 394
                                       6788899*********************9999985555555555555555555555555555555555555555555 PP

                            APG6_N  88 eeelealeeeeerfwreynelqlelleleeeldsleaqy 126
                                       +   +a  +e     +e +  + el++  +el++le++ 
  gi|344210266|ref|YP_004786442.1| 395 SDHVDAAVAELSDVESEIKYREAELEDTADELAQLETRA 433
                                       555555555555555555555555555555555555543 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 ?    8.6   2.0    0.0071       1.8      56     111 ..     129     187 ..     128     194 .. 0.83
   2 ?    6.3   5.2     0.037       9.5      66     131 ..     197     264 ..     189     266 .. 0.84
   3 ?    3.0   1.4      0.38        98      62     113 ..     316     363 ..     309     382 .. 0.45
   4 ?    9.2   5.0    0.0047       1.2      63     111 ..     383     431 ..     359     457 .. 0.57
   5 ?   -0.1   0.1       3.5   9.2e+02      72      90 ..     437     455 ..     419     478 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0071
                              COG2  56 dFvslSghLvglqeeleevesplaaar...kkvesvreklsereeeveskleeakelee 111
                                       dF ++ ++   lq+e e++e++l++ar   k++ sv+ek+ + e+e+e+  ++++ + +
  gi|344210266|ref|YP_004786442.1| 129 DFQNIDSQIETLQREREQIETELTQAReakKRLPSVQEKVTRLENEIEDLRAKRETIDS 187
                                       788999999999********99998752226899999****999999998888887765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.037
                              COG2  66 glqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr..ellklllkldevveklea 131
                                       +++++l++ +++ ++a+++ve ++++++++e++++++ ++  +le  +   + + l +  e ++++e+
  gi|344210266|ref|YP_004786442.1| 197 SVRRQLSQARTEQNQAKNRVERLEQSIERTEQRLSERQDALDALEIPEynDVADKLSEARESLSQVER 264
                                       57889999999999999999999999999999999988887777655444899999999999999986 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.38
                              COG2  62 ghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr 113
                                       ++L  l +el  ++ + ++ r+ ve+++     ++ee+++  + +++lee  
  gi|344210266|ref|YP_004786442.1| 316 DQLDALGNELTALRAQKETYRDTVEELET----QREEISQARRRKADLEEDI 363
                                       44444444444444444444444444333....3333333333333333333 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0047
                              COG2  63 hLvglqeeleevesplaaarkkvesvreklsereeeveskleeakelee 111
                                       +L   q+++e+++  + aa+ ++++v+++++ re+e+e+  +e ++le 
  gi|344210266|ref|YP_004786442.1| 383 RLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADELAQLET 431
                                       3444444444444444444444444444444444444444444444444 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 3.5
                              COG2  72 eevesplaaarkkvesvre 90 
                                       +++e++l+++r+++ ++r+
  gi|344210266|ref|YP_004786442.1| 437 DTLETDLETVRDDLAELRN 455
                                       3333333333333333333 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  47.1   0.00071      0.18     239     530 ..     129     423 ..     126     431 .. 0.65
   2 ?    7.2  24.0    0.0029      0.76     263     421 ..     317     468 ..     306     486 .. 0.43
   3 ?   -1.0   0.0      0.91   2.4e+02    1133    1171 ..     515     558 ..     514     571 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00071
                           DUF3584 239 aiekvrpeieklqeefeqleslelrLsllkgelkadeerlaekqeevq...eakaelkqqlrtle..delkeaidel 310
                                       +++++  +ie lq+e eq+e+ + +++  k+ l + +e++++  +e++   ++ + + +++ +++  + +  + +++
  gi|344210266|ref|YP_004786442.1| 129 DFQNIDSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEdlrAKRETIDSEAGSDDspESVRRQLSQA 205
                                       6999999**************99999999988777666665555555400044444555544444113455555666 PP

                           DUF3584 311 nqelsaakaklaakeselealeeqkkkyeda....dieklkadldqlpsirseleeleeeldaltekhqdvqekydr 383
                                       + e ++ak+ +++ e+ +e+ e++  + +da    +i++++  +d+l + r++l+++e++ + l +   + +  + +
  gi|344210266|ref|YP_004786442.1| 206 RTEQNQAKNRVERLEQSIERTEQRLSERQDAldalEIPEYNDVADKLSEARESLSQVERDAEVLQSVYSATEMVLSE 282
                                       66666667777777777777666655555543333677777777777777777777777777777777777777777 PP

                           DUF3584 384 rkqkikeeleeeleklkerleaireekdrlkaaieealealesqlrkqleaqkeelneeekelesrlselklrldsa 460
                                       ++  +  e e+++ +    ++    + ++ +a+  ++l+al ++l   l aqke  ++  +ele + +e  + ++  
  gi|344210266|ref|YP_004786442.1| 283 DRLDLLTEVERDIDGDT--VACWTCGSETTRADLADQLDALGNELT-ALRAQKETYRDTVEELETQREEISQARRR- 355
                                       77777777777776654..446666777778999999999999998.56666677777777776666665443332. PP

                           DUF3584 461 tateEeleqieeadealekaqeelekaeaevealqaeeeqlrkkrdeadealqkaerrleqlrqaleele 530
                                         + ++ e+i+e ++ l   +++l +a+++ e++q++ eql  + d a   l++ e  ++ + ++le+  
  gi|344210266|ref|YP_004786442.1| 356 --KADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTA 423
                                       ..34566667777777777777777777777777777777777777777777777766666666655543 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0029
                           DUF3584 263 rLsllkgelkadeerlaekqeevq..eakaelkqqlrtledelkeaidelnqelsaakaklaakeselealee...q 334
                                       +L  l  el a   + ++ +  v+  e+++e  +q+r  +++l+e i+el+  l + k+ l+a++++le++++   q
  gi|344210266|ref|YP_004786442.1| 317 QLDALGNELTALRAQKETYRDTVEelETQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSdveQ 393
                                       44444444444444333333333211334444455555555566666666666666666666666666665541112 PP

                           DUF3584 335 kkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkikeeleeeleklkerleaireekd 411
                                         ++ da + +l+   +++   ++ele++  el+ l++++  v+             le++le+ +++l+++r+ kd
  gi|344210266|ref|YP_004786442.1| 394 LSDHVDAAVAELSDVESEIKYREAELEDTADELAQLETRAARVD------------TLETDLETVRDDLAELRNRKD 458
                                       23344444444444444444444445555555554444444443............233333333333333333333 PP

                           DUF3584 412 rlkaaieeal 421
                                       r k + +ea+
  gi|344210266|ref|YP_004786442.1| 459 RIKRETREAF 468
                                       3322222222 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.91
                           DUF3584 1133 llgflrllRgdapvqi.....twpvDELGtLdaeNveklldald 1171
                                        l+gf++ l g++  ++      + vD LG Ld +N+  l + l+
  gi|344210266|ref|YP_004786442.1|  515 LIGFVAALAGRQSFDVgdavpLLLVDGLGGLDDDNLHTLTEYLQ 558 
                                        7888888888777777443335779************9988776 PP

>> WEMBL  Weak chloroplast movement under blue light
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  12.5      0.03       7.9     212     316 ..     121     223 ..      89     229 .. 0.81
   2 ?    4.1  42.0     0.058        15     139     436 ..     129     420 ..     128     428 .. 0.81
   3 ?   12.1  23.0   0.00023     0.059      30     172 ..     329     475 ..     326     495 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.03
                             WEMBL 212 gaalareqdklnwekeLkqaeeelqrLneellsakdlkskletasallldLkaeLaayvesklkeeaeeeeeekkse 288
                                       + +l r  d  n +++++  ++e ++++ el+ a++ k++l + +++ ++L++e+ +   ++ +   +e++ +  s 
  gi|344210266|ref|YP_004786442.1| 121 EDVLLRPLDFQNIDSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKR-ETIDSEAG-SDDSP 195
                                       556777889999999***************************************99876644.22333333.47788 PP

                             WEMBL 289 tsikealasarkELeevkaniekakdev 316
                                       +s++++l +ar+E ++ k  +e+ ++ +
  gi|344210266|ref|YP_004786442.1| 196 ESVRRQLSQARTEQNQAKNRVERLEQSI 223
                                       8999999999999999999999987765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.058
                             WEMBL 139 eLksvkeeLeslqkeyaslvserdaaikkaeeavsaskevekaveeltielialkesLesahaahleaeEkrlgaal 215
                                       +++ + +++e+lq+e++++ +e  +a + a++ + + +e   ++e+   +l a +e+++s   + +  e  r +++ 
  gi|344210266|ref|YP_004786442.1| 129 DFQNIDSQIETLQREREQIETELTQARE-AKKRLPSVQEKVTRLENEIEDLRAKRETIDSEAGSDDSPESVRRQLSQ 204
                                       67889999********999999877754.6666666666666777777789999******99999999999999997 PP

                             WEMBL 216 areqdklnwekeLkqaeeelqrLneellsakdlkskletasallldLkaeLaayvesklkeeaeeeeeekksetsik 292
                                       ar  ++ + ++ +++ e+ ++r +++l+ ++d    le  +    d  + L+   es  +  ++++e  ++  + ++
  gi|344210266|ref|YP_004786442.1| 205 ART-EQNQAKNRVERLEQSIERTEQRLSERQDALDALEIPE--YNDVADKLSEARESLSQ-VERDAEVLQSVYSATE 277
                                       775.567788999*******************999998765..56778888887776554.4445566688999999 PP

                             WEMBL 293 ealasarkE.LeevkaniekakdevklLkvaaasLrseLekek....aeLaslrqregmasiavssLeaelsrtkse 364
                                       ++l + r + L ev  +i+   d v + +  +++ r++L  +     +eL++lr +++    + +   +el+  ++e
  gi|344210266|ref|YP_004786442.1| 278 MVLSEDRLDlLTEVERDIDG--DTVACWTCGSETTRADLADQLdalgNELTALRAQKE----TYRDTVEELETQREE 348
                                       999999987359******95..778999888888888887776111155666666554....555666899999*** PP

                             WEMBL 365 lelvqakekearekmvelpkeLqeAaqeaeeAkslAqaareelrkakeeaeqakaavstvesrLeavlkEie 436
                                       ++ ++ ++++ +e ++el ++L + +q ++ A++  ++a+ ++++  + ++ a a++s ves ++  + E+e
  gi|344210266|ref|YP_004786442.1| 349 ISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELE 420
                                       **************************************************************9986555544 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00023
                             WEMBL  30 riqtverrklveeeLdkvqeeipeykkqaeaaeaaksqvleeLestkrlieeLklnLekaqteeaqAkqdselaklr 106
                                       r+q+   r++ve eL+  +eei++ +++    e++ ++    L + k+ ++  + +Le+aq + +q  +  + a   
  gi|344210266|ref|YP_004786442.1| 329 RAQKETYRDTVE-ELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVDAAVAE 404
                                       666666788887.*****************************************************99999999999 PP

                             WEMBL 107 veemeqgiasee.....svaakaqlevakerhaaavaeLksvkeeLeslqkeyaslvserdaaikkaeeav 172
                                       + ++e +i+ +e      +   aqle   +r  +  ++L++v+++L +l+++++ + +e+ +a   a + +
  gi|344210266|ref|YP_004786442.1| 405 LSDVESEIKYREaeledTADELAQLETRAARVDTLETDLETVRDDLAELRNRKDRIKRETREAFDTAMKDI 475
                                       99999888654411111555679*************************************99998887665 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   6.4     0.097        25     226     278 ..     131     182 ..     106     189 .. 0.64
   2 ?    1.0   8.6      0.99   2.6e+02     208     270 ..     199     265 ..     189     288 .. 0.58
   3 ?   12.1  33.8   0.00042      0.11      19     279 ..     215     465 ..     214     472 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.097
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 226 qsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeireem 278
                                       q+  +++e l+ +++++e++l+ + e  ++ l ++qek+++le+e++++r++ 
  gi|344210266|ref|YP_004786442.1| 131 QNIDSQIETLQREREQIETELTQAREA-KKRLPSVQEKVTRLENEIEDLRAKR 182
                                       555566666666666666666655543.3445666666666666666666544 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.99
                                       XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHH CS
                          Filament 208 sealrsakeeitelrrqiqsleieleslkkqkasleaqlaele....erleaeleklqeklseleee 270
                                         +l++a++e ++++ ++++le  +e  ++  +  +++l  le    + ++ +l++++e+ls++e++
  gi|344210266|ref|YP_004786442.1| 199 RRQLSQARTEQNQAKNRVERLEQSIERTEQRLSERQDALDALEipeyNDVADKLSEARESLSQVERD 265
                                       4456666666666666666666666666666666666555554222223444455555555555554 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00042
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  19 kVraLEqenkeLeakieeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekel 95 
                                       +V  LEq+ ++ e++++e+++   a +   ++   ++l+e+r+ l +++++ + lq  ++ +++ l +      + l
  gi|344210266|ref|YP_004786442.1| 215 RVERLEQSIERTEQRLSERQDALDALEIPEYNDVADKLSEARESLSQVERDAEVLQSVYSATEMVLSE------DRL 285
                                       78899999999999999999998888888899999999999999999999988888877777777665......555 PP

                                       XXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  96 nkreevEaelkalr..kdldeatlarvdLekkvesLkeelaflk...kvheeEvkelqkqvseqvlvevdaarkldL 167
                                        + +evE+++ +            +r+dL  ++++L +el  l+   + + + v+el++q      ++    rk dL
  gi|344210266|ref|YP_004786442.1| 286 DLLTEVERDIDGDTvaCWTCGSETTRADLADQLDALGNELTALRaqkETYRDTVEELETQR---EEISQARRRKADL 359
                                       5666666666554421334456678**************9887611155666666666655...678888899**** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 168 teilkeiraqyeelaeknreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkaslea 244
                                       +e ++e+    e+  ++ ++++++  +++le++q+ +e+ s+++ +a  e++++  +i+ +e+ele+   + a+le+
  gi|344210266|ref|YP_004786442.1| 360 EEDIAEL----EATLADRKQSLDAA-RNRLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADELAQLET 431
                                       *999987....66677777777776.89************************************************9 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 245 qlaeleerleaeleklqeklseleeelaeireema 279
                                       + a + ++le++le++++ l+el +   +i++e+ 
  gi|344210266|ref|YP_004786442.1| 432 RAARV-DTLETDLETVRDDLAELRNRKDRIKRETR 465
                                       99887.57999*********999998888888765 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7  10.3      0.36        94      76     164 ..     138     232 ..     124     238 .. 0.64
   2 ?    1.1   9.3       1.1   2.8e+02     100     170 ..     196     267 ..     163     278 .. 0.64
   3 ?    3.5   2.4      0.19        50     118     168 ..     326     376 ..     307     380 .. 0.74
   4 ?   14.4  12.8     9e-05     0.023      66     167 ..     351     455 ..     341     467 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.36
                            DUF745  76 avvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqva......agaqqelaektqlleaAkk 146
                                       + +q+e +++++  ++a+ a+k   ++q+++++l++ ++  +++ e++++ a      +++ ++l++ ++  ++Ak+
  gi|344210266|ref|YP_004786442.1| 138 ETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRETIDSEAgsddspESVRRQLSQARTEQNQAKN 214
                                       455666666666666666666666666666666666666666666665544411111155666666666667889** PP

                            DUF745 147 RveeLkkqlkearkdlek 164
                                       Rve+L++ ++   + l +
  gi|344210266|ref|YP_004786442.1| 215 RVERLEQSIERTEQRLSE 232
                                       *****9999988776665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.1
                            DUF745 100 kqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkk.RveeLkkqlkearkdlektkkaAy 170
                                       +++++ql++ ++  ++ak+++e++eq  +  +q l+e+++ l+a +    + +  +l+ear+ l ++++ A+
  gi|344210266|ref|YP_004786442.1| 196 ESVRRQLSQARTEQNQAKNRVERLEQSIERTEQRLSERQDALDALEIpEYNDVADKLSEARESLSQVERDAE 267
                                       455666666666677777777777777777777777777777766642566777777777777777766664 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.19
                            DUF745 118 enlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlektkka 168
                                       ++l+  +++     +el+ +++ + +A++R + L+++++e  + l++ k++
  gi|344210266|ref|YP_004786442.1| 326 TALRAQKETYRDTVEELETQREEISQARRRKADLEEDIAELEATLADRKQS 376
                                       44555566666777899999999**************99999999888876 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 9e-05
                            DUF745  66 qleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaekt...q 139
                                       q  +  ++ e+ + e ++ l+  +++++aa++  +qaq+ +e+l++ ++aa ++l+++e+  +  ++el++ +   +
  gi|344210266|ref|YP_004786442.1| 351 QARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTAdelA 427
                                       55566678888999999999999999999999999999999999999999999999999998888888877651113 PP

                            DUF745 140 lleaAkkRveeLkkqlkearkdlektkk 167
                                        le+  +Rv++L+++l+++r+dl++ ++
  gi|344210266|ref|YP_004786442.1| 428 QLETRAARVDTLETDLETVRDDLAELRN 455
                                       46777789***************99886 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 ?    2.8   8.4      0.46   1.2e+02      46      96 ..     131     180 ..     109     189 .. 0.52
   2 ?    2.8  21.9      0.49   1.3e+02      36     147 ..     145     272 ..     145     281 .. 0.82
   3 ?   15.0  16.8   8.2e-05     0.021      37     143 ..     317     426 ..     316     428 .. 0.93
   4 ?    5.3   2.8     0.081        21      37      76 ..     428     467 ..     423     479 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.46
                     Jnk-SapK_ap_N  46 eeeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqe 96 
                                       ++ ++++e l++e+eq+ete+++ +e++kr    ++e+ + +e+e ++l++
  gi|344210266|ref|YP_004786442.1| 131 QNIDSQIETLQREREQIETELTQAREAKKRLP-SVQEKVTRLENEIEDLRA 180
                                       44555666666666666666666666655543.233333333333333333 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.49
                     Jnk-SapK_ap_N  36 ElLeslasrneeeeaeleelreeleqLeteyerekelrkrae.........eeleeiedqweeerkelqekveqlee 103
                                       E++e  +++ +e + +l  ++e++++Le+e e+ +++r+  +         e + +   q + e+++ +++ve+le+
  gi|344210266|ref|YP_004786442.1| 145 EQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRETIDseagsddspESVRRQLSQARTEQNQAKNRVERLEQ 221
                                       8999999999*************************999999988999999999999999999999999999999999 PP

                     Jnk-SapK_ap_N 104 enrelelkaknaadqlsrleekeae.lkkeysklhe......retellkkl 147
                                        +++ e+++++ +d l +le  e + +  + s++ e      r+ e+l++ 
  gi|344210266|ref|YP_004786442.1| 222 SIERTEQRLSERQDALDALEIPEYNdVADKLSEAREslsqveRDAEVLQSV 272
                                       999999999999999999997654313333333333555677888888876 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 8.2e-05
                     Jnk-SapK_ap_N  37 lLeslasrneeeeaeleelreeleqLeteyerekelrkrae...eeleeiedqweeerkelqekveqleeenrelel 110
                                       +L++l ++  +  a+ e  r+++e+Let++e+  ++r+r+    e++ e+e ++ ++++ l+++ ++le+ +  +e+
  gi|344210266|ref|YP_004786442.1| 317 QLDALGNELTALRAQKETYRDTVEELETQREEISQARRRKAdleEDIAELEATLADRKQSLDAARNRLEQAQSDVEQ 393
                                       79999999999*********************999999886666******************************999 PP

                     Jnk-SapK_ap_N 111 kaknaadqlsrleekeaelkkeysklheretel 143
                                        ++ ++  +++l++ e+e k ++++l+++  el
  gi|344210266|ref|YP_004786442.1| 394 LSDHVDAAVAELSDVESEIKYREAELEDTADEL 426
                                       99***********************99988776 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.081
                     Jnk-SapK_ap_N  37 lLeslasrneeeeaeleelreeleqLeteyerekelrkra 76 
                                       +Le  a+r +  e++le +r++l +L+++++r k + ++a
  gi|344210266|ref|YP_004786442.1| 428 QLETRAARVDTLETDLETVRDDLAELRNRKDRIKRETREA 467
                                       899*************************999976655544 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       8.4   2.2e+03     200     213 ..       3      16 ..       2      56 .. 0.66
   2 ?   -0.9   8.0       2.3     6e+02     268     347 ..     133     208 ..     106     211 .. 0.52
   3 ?    5.9   5.7      0.02       5.3     234     309 ..     203     275 ..     192     293 .. 0.73
   4 ?   11.4   8.9   0.00043      0.11     233     332 ..     325     423 ..     307     433 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 8.4
                             IFT57 200 WklEleRvlpqLkv 213
                                       W++E+eR++  L  
  gi|344210266|ref|YP_004786442.1|   3 WNIEIERIAGILDG 16 
                                       *******8766654 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.3
                             IFT57 268 lnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergs.smtDgsplvkikkaltk 343
                                       ++sq+e+    ++  +e++++   + +++++++ + +++ +++++e+e++  + e   s   +D sp  +++ +l++
  gi|344210266|ref|YP_004786442.1| 133 IDSQIET----LQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRETIDSeAGSDDSP-ESVRRQLSQ 204
                                       3333333....33444444444444444444444444444444444444333333322203355555.555665555 PP

                             IFT57 344 lkkE 347
                                        ++E
  gi|344210266|ref|YP_004786442.1| 205 ARTE 208
                                       5555 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.02
                             IFT57 234 ksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelae 309
                                       ++ +++ +++k+ +++l++ i++t +++++r+  l+     ++ ey+++ ++lse++e+++q+++  + l+  ++ 
  gi|344210266|ref|YP_004786442.1| 203 SQARTEQNQAKNRVERLEQSIERTEQRLSERQDALDA---LEIPEYNDVADKLSEARESLSQVERDAEVLQSVYSA 275
                                       3444555566666777777777777777777766664...368899999999999999999999999988877765 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00043
                             IFT57 233 kksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelae 309
                                        ++++++ ++++  +++l+++ ++ +++   r   l++ + el + + + +++l++++++++q+++ v++l+++ + 
  gi|344210266|ref|YP_004786442.1| 325 LTALRAQKETYRDTVEELETQREE-ISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVDA 400
                                       456666667777777777776554.4566789999****************************************** PP

                             IFT57 310 iseelekvkqemeergssmtDgs 332
                                          el++v++e++ r++++ D++
  gi|344210266|ref|YP_004786442.1| 401 AVAELSDVESEIKYREAELEDTA 423
                                       ******************99986 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1  27.3         3   7.7e+02      30     167 ..     136     280 ..     129     291 .. 0.80
   2 ?   10.0  28.8    0.0029      0.75      71     170 ..     330     436 ..     307     470 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 3
                             ATG16  30 rtsaleaenaklekaaasaks.....sksskksakekeasasq...snskqsakiqsleqklaqlreelaelyksrg 98 
                                       ++++l++e++++e++ ++a++     +  s + + ++++++ +    + ++ ++ + +++   ++r +l+++  +++
  gi|344210266|ref|YP_004786442.1| 136 QIETLQREREQIETELTQAREakkrlP--SVQEKVTRLENEIEdlrAKRETIDSEAGSDDSPESVRRQLSQARTEQN 210
                                       789999999999999999998755331..22333333333333677667777778888899999999********** PP

                             ATG16  99 elaqrllelneelqkleeklkedeerlaelea.eraaletklkdreeelrekeklvqdlqDElsaLqlql 167
                                       + ++r+ +l++++++ e++l+e++ +l++le  e +++ +kl++ +e l + e+  + lq  +sa ++ l
  gi|344210266|ref|YP_004786442.1| 211 QAKNRVERLEQSIERTEQRLSERQDALDALEIpEYNDVADKLSEARESLSQVERDAEVLQSVYSATEMVL 280
                                       ******************************9648899999999999999999999999998888876655 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0029
                             ATG16  71 kqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraalet.......klk 140
                                       +q+++  ++ ++l ++ree +++ +++++l++ + el+++l++++++l + ++rl+++++++++l++       +l+
  gi|344210266|ref|YP_004786442.1| 330 AQKETYRDTVEELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDhvdaavaELS 406
                                       46777888888999999999999999999999999999999999998888888888888888888872222222455 PP

                             ATG16 141 dreeelrekeklvqdlqDElsaLqlqlnqa 170
                                       d e e++ +e+ ++d  DEl++L+ ++  +
  gi|344210266|ref|YP_004786442.1| 407 DVESEIKYREAELEDTADELAQLETRAARV 436
                                       666666666666667777777666554332 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 ?    4.0   0.9      0.14        37      19      42 ..     157     180 ..     135     182 .. 0.83
   2 ?    3.7   0.4      0.18        47       7      34 ..     214     241 ..     208     243 .. 0.91
   3 ?    4.3   0.0      0.12        31      15      40 ..     244     269 ..     242     272 .. 0.91
   4 ?    3.4   0.4      0.23        60      24      48 ..     430     454 ..     409     460 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHH-XXXXXXX CS
                        Vac_Fusion  19 vikcckrvnealkRlEnHleTlRk 42 
                                         k+   v+e + RlEn  e lR+
  gi|344210266|ref|YP_004786442.1| 157 AKKRLPSVQEKVTRLENEIEDLRA 180
                                       456667799************997 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        Vac_Fusion   7 erllvlekdfqlvikcckrvnealkRlE 34 
                                       +r+ +le++ + ++++ ++ ++al+ lE
  gi|344210266|ref|YP_004786442.1| 214 NRVERLEQSIERTEQRLSERQDALDALE 241
                                       79999*******************9998 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHH-XXXXX CS
                        Vac_Fusion  15 dfqlvikcckrvnealkRlEnHleTl 40 
                                       ++++v+++ ++  e+l+ +E+ +e l
  gi|344210266|ref|YP_004786442.1| 244 EYNDVADKLSEARESLSQVERDAEVL 269
                                       5899*****************99976 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHH-XXXXXXXXXXXXX CS
                        Vac_Fusion  24 krvnealkRlEnHleTlRkamlaLa 48 
                                        + + +++ lE  leT+R  + +L 
  gi|344210266|ref|YP_004786442.1| 430 ETRAARVDTLETDLETVRDDLAELR 454
                                       5666788999********9998874 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  13.1     0.018       4.7      73     176 ..     134     231 ..     130     232 .. 0.72
   2 ?   -1.4   0.0       6.4   1.7e+03     103     125 ..     248     270 ..     242     279 .. 0.57
   3 ?    7.4   6.0     0.013       3.4      65     132 ..     328     395 ..     310     401 .. 0.79
   4 ?    7.6  12.7     0.011         3       2     129 ..     343     465 ..     342     475 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.018
                           DUF4201  73 tktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdk 149
                                        +++ +l+ ++e   +  ++ +e+kk+l + +e+ ++l+ e++ ++++r+ ++ +       g + + +++ +   +
  gi|344210266|ref|YP_004786442.1| 134 DSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRETIDSEA------GSDDSPESVRRQLSQ 204
                                       55666677777777777777777777777777777777777777777776666543......344455578888899 PP

                           DUF4201 150 tkekveekrksvkkLrrkvkilemrlk 176
                                          + ++ +++v+ L++++++ e+rl+
  gi|344210266|ref|YP_004786442.1| 205 ARTEQNQAKNRVERLEQSIERTEQRLS 231
                                       99999999*****************97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6.4
                           DUF4201 103 keerlaklrkelykvklerdklr 125
                                         ++l + r++l++v+ + + l+
  gi|344210266|ref|YP_004786442.1| 248 VADKLSEARESLSQVERDAEVLQ 270
                                       44555555555555555555444 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.013
                           DUF4201  65 Lkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklk 132
                                       L + k+++ +tv +l++ +e  +  ++  ++l++++ e+e++la+ +++l  ++++ ++++ + e+l+
  gi|344210266|ref|YP_004786442.1| 328 LRAQKETYRDTVEELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLS 395
                                       55667888899999999999999999999999999999999888888888888888888887777776 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.011
                           DUF4201   2 rkkrnelsklrlklislkhqlakiqeklekkeelgegLtlidFeqlqienqalnkkIeernkeLkrlkkkttktvha 78 
                                       + +r+e+s+ r + + l++ +a++++ l  +++  ++   +  eq+q ++++l+++++   +eL+   + +++   +
  gi|344210266|ref|YP_004786442.1| 343 ETQREEISQARRRKADLEEDIAELEATLADRKQSLDA-ARNRLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAE 418
                                       5799****************************99998.6799******************************99999 PP

                           DUF4201  79 lthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqne 129
                                       l+++ + l     +l+++  + +++e++l+ +r+ l ++++++d+++++ +
  gi|344210266|ref|YP_004786442.1| 419 LEDTADELA----QLETRAARVDTLETDLETVRDDLAELRNRKDRIKRETR 465
                                       988887775....55666666777777777777777777777777777655 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 ?   11.3   1.3   0.00086      0.22     100     152 ..     131     183 ..     108     199 .. 0.88
   2 ?    2.6   1.2      0.39     1e+02     100     163 ..     200     264 ..     190     279 .. 0.54
   3 ?    1.4   0.5      0.98   2.5e+02     110     161 ..     336     387 ..     312     398 .. 0.42
   4 ?    4.1   4.2      0.14        37      88     169 ..     356     437 ..     339     442 .. 0.67
   5 ?    5.9   2.4      0.04        10      89     155 ..     385     451 ..     363     463 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00086
                                       ..........HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 100 keindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaase 152
                                       ++i++ +e+l+  r+++e+ +++++e+++ l ++ e+v++++++++++ a  e
  gi|344210266|ref|YP_004786442.1| 131 QNIDSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRE 183
                                       6788999****************************************987655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.39
                                       ..........HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 100 keindsvesleetrqrveegselveetgealkeiveavaeva.dlvqeiaaaseeqsasieevnq 163
                                       ++  ++ +  +++++rve   + +e+t++ l+e  +a + ++  + +++a   +e  +s+++v +
  gi|344210266|ref|YP_004786442.1| 200 RQLSQARTEQNQAKNRVERLEQSIERTEQRLSERQDALDALEiPEYNDVADKLSEARESLSQVER 264
                                       44445555555566666666666666666666655555544312344444444444444444444 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.98
                                       HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 110 eetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieev 161
                                        +t+++ e+  e+++++++  +++ e +ae+++++ + +++ +   + +e+ 
  gi|344210266|ref|YP_004786442.1| 336 RDTVEELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQA 387
                                       3333333333333333333333333333333333333333333333333333 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.14
                                       HHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  88 akeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqa 164
                                         ++e+ i+e+++   d  +sl+ +r+r e++ + ve+  + +   v++ ++v+++++   a  e+ +  + +  + 
  gi|344210266|ref|YP_004786442.1| 356 KADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADELAQLETR 432
                                       45566677777777777777888888888888777777777777777777777776666666666666555555555 PP

                                       HHHHH CS
                         MCPsignal 165 veeva 169
                                        ++v+
  gi|344210266|ref|YP_004786442.1| 433 AARVD 437
                                       55555 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.04
                                       HHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  89 keiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqs 155
                                       ++ ++ ++++  +++ +v+ l++++++++    + e+t+++l+++ +++a+v++l +++ +  ++++
  gi|344210266|ref|YP_004786442.1| 385 EQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADELAQLETRAARVDTLETDLETVRDDLA 451
                                       3344556666778888888888888888888888888888888888888888888888877776666 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 ?   12.8   8.4   0.00036     0.093      28      82 ..     130     184 ..     129     192 .. 0.95
   2 ?    3.9   9.7       0.2        53      53      97 ..     196     240 ..     189     242 .. 0.81
   3 ?    1.0   0.4       1.6   4.3e+02      64      84 ..     250     270 ..     239     294 .. 0.61
   4 ?    3.7  16.1      0.24        62      40      96 ..     337     393 ..     307     406 .. 0.42
   5 ?    8.1   8.6      0.01       2.6      35     101 ..     398     464 ..     391     474 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00036
                             DHR10  28 lqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeer 82 
                                       +q+++ +++ + +  e+ie+el + +eakk+l + +++++ +e+e ++l +k+e 
  gi|344210266|ref|YP_004786442.1| 130 FQNIDSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRET 184
                                       899*************************************************986 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.2
                             DHR10  53 eeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerl 97 
                                       e+++++l+++r + ++ +++++ le+ +er +++l+  ++ l+ l
  gi|344210266|ref|YP_004786442.1| 196 ESVRRQLSQARTEQNQAKNRVERLEQSIERTEQRLSERQDALDAL 240
                                       566788888888888888888888888888888888888887765 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.6
                             DHR10  64 daleekeielrelerkeerlq 84 
                                       d+l+e ++ l+++er  e lq
  gi|344210266|ref|YP_004786442.1| 250 DKLSEARESLSQVERDAEVLQ 270
                                       333333333333333333333 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.24
                             DHR10  40 klleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeekler 96 
                                       + +ee+e++ ++  +a+++ ++l++ ++e+e++l++ ++  +  + +le+a+   e+
  gi|344210266|ref|YP_004786442.1| 337 DTVEELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQ 393
                                       223333333333333333333333333333333333333333333333333333333 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.01
                             DHR10  35 lrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqa 101
                                       + ++++ l ++e+e++  e + ++ ++  ++le++ +++  le+  e ++  l+  + + +r +++ 
  gi|344210266|ref|YP_004786442.1| 398 VDAAVAELSDVESEIKYREAELEDTADELAQLETRAARVDTLETDLETVRDDLAELRNRKDRIKRET 464
                                       5555555555555555555555555555555555555555555555555555555555555555544 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 ?    4.1   3.1      0.19        50      80     130 ..     131     180 ..     128     184 .. 0.84
   2 ?    4.7   5.1      0.12        32      38     115 ..     196     277 ..     185     282 .. 0.68
   3 ?   11.7   4.2   0.00083      0.22      33     127 ..     314     400 ..     308     406 .. 0.71
   4 ?    3.0   0.2       0.4     1e+02      24      57 ..     437     470 ..     426     479 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.19
                                       HHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  80 kksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqker 130
                                       +++ +++e   +r +e+i ++ ++ r+ ++ l s ++k+++Le++i+ +++
  gi|344210266|ref|YP_004786442.1| 131 QNIDSQIE-TLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRA 180
                                       55667777.7777789999999**********************9998776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.12
                                       CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHH CS
                         Fib_alpha  38 ekleneleeisnstkeaeelvkeikdslrekqkskkdn.....dnvikksskeleeeilrlketidaqesnirvLqn 109
                                       e+++++l++++ ++++a++ v+++++s++++++  ++         i ++++  + + ++ +e++++ e+  +vLq+
  gi|344210266|ref|YP_004786442.1| 196 ESVRRQLSQARTEQNQAKNRVERLEQSIERTEQRLSERqdaldALEIPEYNDVAD-KLSEARESLSQVERDAEVLQS 271
                                       4567777777777777777777777776665555444312232344566666666.888999999999999999999 PP

                                       HHHHHH CS
                         Fib_alpha 110 vlesne 115
                                       v+++ e
  gi|344210266|ref|YP_004786442.1| 272 VYSATE 277
                                       998765 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00083
                                       CCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHH CS
                         Fib_alpha  33 vkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqn 109
                                       + ++l+ l nel+ ++ ++++ +++v+e++       ++ + + +  ++ + +lee+i++l++t+ +  +++ + +n
  gi|344210266|ref|YP_004786442.1| 314 LADQLDALGNELTALRAQKETYRDTVEELE-------TQRE-EISQARRRKADLEEDIAELEATLADRKQSLDAARN 382
                                       444444455555544444444444444443.......3333.3455667899************************* PP

                                       HHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 110 vlesneqkiqkLeqdidq 127
                                        le+ ++++++L  ++d+
  gi|344210266|ref|YP_004786442.1| 383 RLEQAQSDVEQLSDHVDA 400
                                       ************999986 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.4
                                       HCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHH CS
                         Fib_alpha  24 dlllkyekdvkkdlekleneleeisnstkeaeel 57 
                                       d+l++  ++v++dl++l+n+ ++i+++t+ea+++
  gi|344210266|ref|YP_004786442.1| 437 DTLETDLETVRDDLAELRNRKDRIKRETREAFDT 470
                                       4566666677777777777777777777776654 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 ?    3.1   7.7      0.13        34      33     117 ..      97     179 ..      94     193 .. 0.66
   2 ?    0.6  24.0      0.77     2e+02     135     259 ..     134     272 ..     129     287 .. 0.64
   3 ?   12.8  18.9   0.00015     0.039      34     172 ..     316     463 ..     306     507 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.13
                          CALCOCO1  33 qnrLeeclreraeLlqaqeaanrqrekekeeykrdreeldrerkelesrveelkeelkesrekveeleekqkelerl 109
                                       ++ L  cl er+e  +a  +   +  ++   +  d +++d++ + l+++ e++++el+++re +++l + q++++rl
  gi|344210266|ref|YP_004786442.1|  97 RAELFACLDERNEVRRA--VRTGENLEDVLLRPLDFQNIDSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRL 171
                                       56667788888887777..4444444555666677777888888888888888888888888877777777777777 PP

                          CALCOCO1 110 seelaeek 117
                                       ++e+ + +
  gi|344210266|ref|YP_004786442.1| 172 ENEIEDLR 179
                                       77665443 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.77
                          CALCOCO1 135 EeDiktltqralekEteLeRlkerak.......kalaqrkeeeaerkqlqakleq......seeelrslskelqelr 198
                                       +  i+tl +   + EteL   +e  k       k++++    e+e ++l+ak e+      s++  +s+ ++l ++r
  gi|344210266|ref|YP_004786442.1| 134 DSQIETLQREREQIETELTQAREAKKrlpsvqeKVTRL----ENEIEDLRAKRETidseagSDDSPESVRRQLSQAR 206
                                       56778888888888888888888888555544322222....22333333333330001113444577888888999 PP

                          CALCOCO1 199 nslaerdtqvlqLqdtittltqkLttAqrk.....eaenEallkelrslqerlaaSerkvegLkee 259
                                         +++ + +v +L+++i +++q+L++ q       + e   + ++l+ ++e l   er +e L++ 
  gi|344210266|ref|YP_004786442.1| 207 TEQNQAKNRVERLEQSIERTEQRLSERQDAldaleIPEYNDVADKLSEARESLSQVERDAEVLQSV 272
                                       999999999999999999999998887765111113455567888888999999999998888874 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00015
                          CALCOCO1  34 nrLeeclreraeLlqaqeaanrqrekekeeykrdreeldrerkelesrveelkeelkesre....kveeleekqkel 106
                                        +L+    e + L  ++e+ +  +e+  e  +++ ++  r++++le++++el++ l+  ++      ++le+ q ++
  gi|344210266|ref|YP_004786442.1| 316 DQLDALGNELTALRAQKETYRDTVEEL-ETQREEISQARRRKADLEEDIAELEATLADRKQsldaARNRLEQAQSDV 391
                                       456666666666666666665555544.5556666677788888888888888888887775555567788888888 PP

                          CALCOCO1 107 erlseelaeeksalleakeesearirELEeDiktltq......ralekEteLeRlkerakkalaqrkeeeae 172
                                       e+ls+++ +  + l++ + e + r  ELE+    l+q      r+ + Et+Le +++    + +++   + e
  gi|344210266|ref|YP_004786442.1| 392 EQLSDHVDAAVAELSDVESEIKYREAELEDTADELAQletraaRVDTLETDLETVRDDLAELRNRKDRIKRE 463
                                       888888888888888888888889899998777776644433355667888888888776544433322222 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.9    0.0026      0.68      49     124 ..     120     206 ..      93     208 .. 0.66
   2 ?    6.7   3.3     0.028       7.3      77     138 ..     206     270 ..     196     291 .. 0.74
   3 ?   -0.5   8.4       4.6   1.2e+03      60     107 ..     366     410 ..     298     471 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0026
                                       T.........THHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHHHHHHHHHHS--EESEEES-SSHH CS
                   Cob_adeno_trans  49 e.........eeelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveelekeideleaelpplksfilpggspa 116
                                                  +++++++e +q+e  ++ +el   ++ k++    +e+v++le+ei++l+a+ ++++s      sp+
  gi|344210266|ref|YP_004786442.1| 120 LedvllrpldFQNIDSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLRAKRETIDSEAGSDDSPE 196
                                       145666666778999*****************7553333333333677************99888877666666555 PP

                                       H..HHHHHHH CS
                   Cob_adeno_trans 117 a..aalhvaR 124
                                       +   +l+ aR
  gi|344210266|ref|YP_004786442.1| 197 SvrRQLSQAR 206
                                       5234555555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.028
                                       TCCG-S--HHHHHHHHHHHHHHHHHS--....EESEEES-SSHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Cob_adeno_trans  77 kkekkkiteeeveelekeideleaelpp....lksfilpggspaaaalhvaRtvcRraERavvela 138
                                       ++e+++  +++ve+le+ i++ e++l++    l+   +p+ + +a +l+ aR    ++ER +  l+
  gi|344210266|ref|YP_004786442.1| 206 RTEQNQA-KNRVERLEQSIERTEQRLSErqdaLDALEIPEYNDVADKLSEARESLSQVERDAEVLQ 270
                                       3333334.44599999999999999985445588899**********************9986664 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 4.6
                                       HHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHHHHHHHHHHS--EES CS
                   Cob_adeno_trans  60 iqneLfdlgaelatpekkkekkkiteeeveelekeideleaelpplks 107
                                       ++  L d  ++l    + +++ +  +++ve+l + +d+  ael+ ++s
  gi|344210266|ref|YP_004786442.1| 366 LEATLADRKQSLD---AARNRLEQAQSDVEQLSDHVDAAVAELSDVES 410
                                       2222222222221...11222222222233333333333333333322 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.2     0.016       4.1      34      83 ..     136     186 ..     132     191 .. 0.86
   2 ?    4.9   1.3      0.11        28      32      92 ..     213     265 ..     199     284 .. 0.57
   3 ?    2.9   0.1      0.45   1.2e+02      62      93 ..     315     346 ..     312     354 .. 0.91
   4 ?    2.6   1.8      0.56   1.5e+02      44      89 ..     334     380 ..     321     399 .. 0.43
   5 ?    5.7   1.6      0.06        16      39      91 ..     374     431 ..     359     434 .. 0.72
   6 ?    6.2   1.5     0.043        11      34      93 ..     404     464 ..     400     470 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.016
                           DUF2730  34 dleklaekveendkrlteletkvenLPtakd.lekLkllladlrgelkale 83 
                                       ++e+l+ + e++++ lt++    + LP+ ++ + +L+ +++dlr++ ++++
  gi|344210266|ref|YP_004786442.1| 136 QIETLQREREQIETELTQAREAKKRLPSVQEkVTRLENEIEDLRAKRETID 186
                                       57889999999****************965439************988876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.11
                           DUF2730  32 redleklaekveendkrlteletkvenL..PtakdlekLkllladlrgelkaleaevrqlshq 92 
                                       ++ +e+l++++e++++rl+e +  ++ L  P  +d+            +l++++++++q+++ 
  gi|344210266|ref|YP_004786442.1| 213 KNRVERLEQSIERTEQRLSERQDALDALeiPEYNDV----------ADKLSEARESLSQVERD 265
                                       455566666666666666666666554422444444..........44444444444444444 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.45
                           DUF2730  62 akdlekLkllladlrgelkaleaevrqlshqv 93 
                                       a++l++L  +l+ lr++ ++ + +v++l++q 
  gi|344210266|ref|YP_004786442.1| 315 ADQLDALGNELTALRAQKETYRDTVEELETQR 346
                                       578999**********************9985 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.56
                           DUF2730  44 endkrlteletkvenLPtak.dlekLkllladlrgelkaleaevrql 89 
                                       +++  ++elet+ e++  a+   ++L+ ++a+l++ l + ++++++ 
  gi|344210266|ref|YP_004786442.1| 334 TYRDTVEELETQREEISQARrRKADLEEDIAELEATLADRKQSLDAA 380
                                       44444444444444444332122334444444444443333333332 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.06
                           DUF2730  39 aekveendkrlteletkvenLPtakd.....lekLkllladlrgelkaleaevrqlsh 91 
                                       +++++  ++rl+++++ ve+L  ++d     l++++ +++  ++el++++ e++ql++
  gi|344210266|ref|YP_004786442.1| 374 KQSLDAARNRLEQAQSDVEQLSDHVDaavaeLSDVESEIKYREAELEDTADELAQLET 431
                                       4666778999999999999998776523222666677777777777777777777776 PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.043
                           DUF2730  34 dleklaekveendkrlteletkvenLPta.kdlekLkllladlrgelkaleaevrqlshqv 93 
                                       +l+ ++ +++  +  l+++  ++++L t+   +++L+++l+ +r +l +l+++ +++++ +
  gi|344210266|ref|YP_004786442.1| 404 ELSDVESEIKYREAELEDTADELAQLETRaARVDTLETDLETVRDDLAELRNRKDRIKRET 464
                                       6777888888888889999999999998725799999999999999999999999998876 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 ?    0.8   8.1       1.9   4.8e+02      28     109 ..     137     211 ..     115     212 .. 0.51
   2 ?    0.5  13.5       2.3   5.9e+02       7      93 ..     146     232 ..     141     241 .. 0.72
   3 ?    3.2   7.0      0.35        90      16      84 ..     196     273 ..     191     290 .. 0.73
   4 ?    9.2  11.8    0.0047       1.2      27     125 ..     317     408 ..     309     421 .. 0.72
   5 ?    6.6   0.4      0.03       7.7      32     100 ..     420     488 ..     401     493 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.9
                             Mod_r  28 vkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldell....qkfspdallarL 100
                                       +++l+ e+e++        e  l    + +e +++l +  e++++le+e e++ ++ +++     ++ sp++++++L
  gi|344210266|ref|YP_004786442.1| 137 IETLQREREQI--------ETELT---QAREAKKRLPSVQEKVTRLENEIEDLRAKRETIDseagSDDSPESVRRQL 202
                                       22222222222........22222...33333444444444444444444444444444435555778888888888 PP

                             Mod_r 101 qtavaeaee 109
                                        +a +e+++
  gi|344210266|ref|YP_004786442.1| 203 SQARTEQNQ 211
                                       888888776 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 2.3
                             Mod_r   7 eLqelledeeklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeq 82 
                                       +++  l++    ++++ ++ ++v +l++e e+l+a+ e + ++   + ++ e +r +l++++ e +++++++e++eq
  gi|344210266|ref|YP_004786442.1| 146 QIETELTQAREAKKRLPSVqEKVTRLENEIEDLRAKRETI-DSEAGSDDSPESVRRQLSQARTEQNQAKNRVERLEQ 221
                                       55555555555666666776889**********7776666.556666777788888888888888888888888888 PP

                             Mod_r  83 eldellqkfsp 93 
                                         ++  q++s+
  gi|344210266|ref|YP_004786442.1| 222 SIERTEQRLSE 232
                                       88777766665 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.35
                             Mod_r  16 eklealvktl.pevkqlkeekeellaeneslaeknlsl.ep........eleelrselqekleelkelekefeekeq 82 
                                       e +++ ++++  e +q k++ e l++++e++ e+ ls+ ++        e++++ ++l+e++e+l ++e+  e +++
  gi|344210266|ref|YP_004786442.1| 196 ESVRRQLSQArTEQNQAKNRVERLEQSIERT-EQRLSErQDaldaleipEYNDVADKLSEARESLSQVERDAEVLQS 271
                                       5555666666556677888888887777777.666666355999999999999999999999999999988887776 PP

                             Mod_r  83 el 84 
                                        +
  gi|344210266|ref|YP_004786442.1| 272 VY 273
                                       55 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0047
                             Mod_r  27 evkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfspdallarLqta 103
                                       ++++l +e++ l+a+ e   +   +  +ele +r+e+++++   + le+   e+e+ l  + +k s+da+++rL++a
  gi|344210266|ref|YP_004786442.1| 317 QLDALGNELTALRAQKETY-R---DTVEELETQREEISQARRRKADLEEDIAELEATL--ADRKQSLDAARNRLEQA 387
                                       4555555555554443333.2...3456899999999999999999999999999999..55788999999999999 PP

                             Mod_r 104 vaeaeeeSealaeeflegeiel 125
                                        ++ e++S+ +   +    +++
  gi|344210266|ref|YP_004786442.1| 388 QSDVEQLSDHVDAAVA-ELSDV 408
                                       9999999999655443.34444 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.03
                             Mod_r  32 keekeellaeneslaeknlslepeleelrselqekleelkelekefeek.eqeldellqkfspdallarL 100
                                       ++  +el a+ e  a +   le++le +r++l+e ++  +++++e +e   + ++++l++f+  +  arL
  gi|344210266|ref|YP_004786442.1| 420 EDTADEL-AQLETRAARVDTLETDLETVRDDLAELRNRKDRIKRETREAfDTAMKDILSRFGTGFETARL 488
                                       3333444.55555566666667799999999999999888888888776245668888888877777776 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 ?    6.0   6.6     0.072        19      23      71 ..     138     185 ..     130     197 .. 0.71
   2 ?    6.6   9.7     0.047        12      11      87 ..     198     271 ..     195     278 .. 0.87
   3 ?    6.3  11.2     0.058        15      15      93 ..     325     402 ..     309     406 .. 0.73
   4 ?    8.6  10.5     0.011       2.8      15      94 ..     349     431 ..     347     433 .. 0.90
   5 ?    6.8   2.8     0.039        10      23      74 ..     406     456 ..     400     474 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.072
                    HIP1_clath_bdg  23 eeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarl 71 
                                       e ++re++++e+el +++e ++r l   +e++ +L++e+e+ ra+ +++
  gi|344210266|ref|YP_004786442.1| 138 ETLQREREQIETELTQAREAKKR-LPSVQEKVTRLENEIEDLRAKRETI 185
                                       56899999999999998766655.4555566777888877776665555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.047
                    HIP1_clath_bdg  11 vtkqlsvarqaqeeverekkeleeelerlkeeaerkleeqkeelekLk.releakraelarlkssLesseqsgeqls 86 
                                       v +qls+ar +q++ ++  ++le+++er    +e++l+e++  l++L+  e ++  ++l+++++sL++ e+  e l+
  gi|344210266|ref|YP_004786442.1| 198 VRRQLSQARTEQNQAKNRVERLEQSIER----TEQRLSERQDALDALEiPEYNDVADKLSEARESLSQVERDAEVLQ 270
                                       679***********99999999999998....6678999999*****84599999999********99998888777 PP

                    HIP1_clath_bdg  87 s 87 
                                       s
  gi|344210266|ref|YP_004786442.1| 271 S 271
                                       6 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.058
                    HIP1_clath_bdg  15 lsvarqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaa 91 
                                       l++ r+++e    + +ele++ e++++ ++rk +  +e + +L++ l+++++ l+ +++ Le+ +   eqls +++a
  gi|344210266|ref|YP_004786442.1| 325 LTALRAQKETYRDTVEELETQREEISQARRRKAD-LEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVDA 400
                                       5566666666666777888888887777666654.455666689999999999999999999999988898888876 PP

                    HIP1_clath_bdg  92 Lq 93 
                                         
  gi|344210266|ref|YP_004786442.1| 401 AV 402
                                       55 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.011
                    HIP1_clath_bdg  15 lsvarqaqeeverekkeleeelerlkee...aerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssq 88 
                                       +s+ar  + ++e    ele +l + k++   a+++le+ ++ +e+L   + a  ael+ ++s ++ +e + e+ + +
  gi|344210266|ref|YP_004786442.1| 349 ISQARRRKADLEEDIAELEATLADRKQSldaARNRLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADE 425
                                       6899******************9988762225678889999************************************ PP

                    HIP1_clath_bdg  89 laaLqa 94 
                                       la+L++
  gi|344210266|ref|YP_004786442.1| 426 LAQLET 431
                                       ***985 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.039
                    HIP1_clath_bdg  23 eeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkss 74 
                                       ++ve e k  e ele+  +e   +le ++  +++L+++le+ r++la+l++ 
  gi|344210266|ref|YP_004786442.1| 406 SDVESEIKYREAELEDTADEL-AQLETRAARVDTLETDLETVRDDLAELRNR 456
                                       789999999999999976665.6899*********************99975 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   4.2    0.0075       1.9       7      43 ..     130     166 ..     128     171 .. 0.85
   2 ?    3.6   0.7      0.24        63      71      92 ..     161     182 ..     156     189 .. 0.48
   3 ?    5.9   3.7     0.046        12      68     101 ..     206     239 ..     195     241 .. 0.70
   4 ?    0.7   0.1       1.9   4.9e+02       6      38 ..     244     276 ..     240     290 .. 0.67
   5 ?    6.2   1.1     0.037       9.6      70      98 ..     317     345 ..     307     352 .. 0.45
   6 ?    0.2  13.2       2.8   7.2e+02       5      95 ..     323     408 ..     320     433 .. 0.58
   7 ?    4.0   0.3      0.19        48      65      94 ..     437     466 ..     429     475 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0075
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-T CS
                       Prefoldin_2   7 fqqlqqqlqqlaqqikqletqlkelelvleelellde 43 
                                       fq++ +q++ l+ +++q+et+l+ + ++++ l ++ e
  gi|344210266|ref|YP_004786442.1| 130 FQNIDSQIETLQREREQIETELTQAREAKKRLPSVQE 166
                                       8999999999999999999999999999999988877 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  71 ketlekeiktlekqleklekel 92 
                                       + ++++++++le+++e+l+++ 
  gi|344210266|ref|YP_004786442.1| 161 LPSVQEKVTRLENEIEDLRAKR 182
                                       4444455555555555544443 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.046
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                       Prefoldin_2  68 eerketlekeiktlekqleklekeleelkeelqk 101
                                        +++++++ ++++le+++e+ e++l+e ++ l +
  gi|344210266|ref|YP_004786442.1| 206 RTEQNQAKNRVERLEQSIERTEQRLSERQDALDA 239
                                       5667777777777777777777777777776654 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   6 kfqqlqqqlqqlaqqikqletqlkelelvleel 38 
                                       ++++  ++l++  + + q+e++ + l++v  + 
  gi|344210266|ref|YP_004786442.1| 244 EYNDVADKLSEARESLSQVERDAEVLQSVYSAT 276
                                       566666677777777777777776666665554 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  70 rketlekeiktlekqleklekeleelkee 98 
                                       +++ l  e+++l  q+e+ + ++eel+++
  gi|344210266|ref|YP_004786442.1| 317 QLDALGNELTALRAQKETYRDTVEELETQ 345
                                       44444444444444444444444444433 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEE..EE-HHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   5 nkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlv..kqdkeevkeeLeerketlekeik 79 
                                       n+++ l++q + +   +++letq +e+ ++     +l+ed         +l   kq+++ ++++Le+ + ++    +
  gi|344210266|ref|YP_004786442.1| 323 NELTALRAQKETYRDTVEELETQREEISQARRRKADLEED---IAELEATLAdrKQSLDAARNRLEQAQSDV----E 392
                                       6777888888888888888888888888888888888888...44444444411445555555555544333....3 PP

                                       HHHHHHHHHHHHHHHH CS
                       Prefoldin_2  80 tlekqleklekeleel 95 
                                       +l++  +   +el+++
  gi|344210266|ref|YP_004786442.1| 393 QLSDHVDAAVAELSDV 408
                                       3333333333333333 PP

  == domain 7  score: 4.0 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  65 eeLeerketlekeiktlekqleklekelee 94 
                                       ++Le+++et+   +++l ++++++++e +e
  gi|344210266|ref|YP_004786442.1| 437 DTLETDLETVRDDLAELRNRKDRIKRETRE 466
                                       566777777777777777777777666555 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 ?    3.8  15.8      0.22        58      96     197 ..     134     232 ..     126     241 .. 0.76
   2 ?    1.3   0.3       1.3   3.3e+02     149     196 ..     234     281 ..     230     283 .. 0.82
   3 ?   11.4  13.6   0.00099      0.26      87     199 .]     337     454 ..     306     454 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.22
                              End3  96 dweevrLkreLaeLeeklekveeeaekrkekereessksalvkreleqLLkYKeeqlrel.eegegkske.knlksv 170
                                       d    +L+re +++e++l++++e+++ r     + ++k + + +e+e L   K+e++ ++  +++  ++   +l++ 
  gi|344210266|ref|YP_004786442.1| 134 DSQIETLQREREQIETELTQAREAKK-R---LPSVQEKVTRLENEIEDLRA-KRETIDSEaGSDDSPESVrRQLSQA 205
                                       667789***************98776.3...34456789999******866.666665441444443344599**** PP

                              End3 171 kedietveeqVegLesylssrkeeLeq 197
                                       + + ++ ++ Ve+Le+ +++ ++ L++
  gi|344210266|ref|YP_004786442.1| 206 RTEQNQAKNRVERLEQSIERTEQRLSE 232
                                       **************9888888887764 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1.3
                              End3 149 eeqlreleegegkskeknlksvkedietveeqVegLesylssrkeeLe 196
                                       ++ l  le  e + ++++l++ +e +++ve   e+L+s  s  + +L+
  gi|344210266|ref|YP_004786442.1| 234 QDALDALEIPEYNDVADKLSEARESLSQVERDAEVLQSVYSATEMVLS 281
                                       566777777777777899*******************99988877775 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00099
                              End3  87 tdfsatkgtdweevrLkreLaeLeeklekveeeaekrkekereessksalvkreleqLLkYKeeqlreleegegksk 163
                                        ++++ +++  e  + +r  a+Lee ++++e++  +rk++ ++++++ ++ + ++eqL ++    + el++ e + k
  gi|344210266|ref|YP_004786442.1| 337 DTVEELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVDAAVAELSDVESEIK 413
                                       233444566677999**********************999999999******************9999998766555 PP

                              End3 164 e..knlksvkedietvee...qVegLesylssrkeeLeqLk 199
                                          ++l++  ++++++e+    V++Le+ l++ ++ L++L+
  gi|344210266|ref|YP_004786442.1| 414 YreAELEDTADELAQLETraaRVDTLETDLETVRDDLAELR 454
                                       43599*******9999863337************9999986 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8  18.9     0.049        13     474     582 ..     131     238 ..     119     251 .. 0.65
   2 ?    6.3  29.5    0.0084       2.2     178     386 ..     253     469 ..     243     481 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.049
                              HOOK 474 gseeekltelqelledanrrkneLetenr...lanqrileLeaqveelqkalqeqgskaed...ssllkkkleehle 544
                                       ++ + ++++lq++ e+ + ++ + ++ ++   + +++++ Le+++e+l+ + ++ +s+a +   + +++++l++   
  gi|344210266|ref|YP_004786442.1| 131 QNIDSQIETLQREREQIETELTQAREAKKrlpSVQEKVTRLENEIEDLRAKRETIDSEAGSddsPESVRRQLSQART 207
                                       566788899999999988888888776652334799************99988877776431123444555555555 PP

                              HOOK 545 klkevqeelqkkkeqleelepklssnkqkieeleeaLk 582
                                       + +++++ +++ ++ +e +e++        +e ++aL 
  gi|344210266|ref|YP_004786442.1| 208 EQNQAKNRVERLEQSIERTEQR-------LSERQDALD 238
                                       5555555555555555555555.......555444443 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0084
                              HOOK 178 qeekdelaQrcheldkqlsllqeEknaLlaenkklqerlse.lengeesgtiqltskkylelqkqleqlqeelfrlE 253
                                        e++++l+Q  ++ +   s+     ++L ++   l  ++++ ++  +  + +  +++   +l  ql++l +el  l 
  gi|344210266|ref|YP_004786442.1| 253 SEARESLSQVERDAEVLQSVYSATEMVLSEDRLDLLTEVERdIDGDTVACWTCGSETTRADLADQLDALGNELTALR 329
                                       5667777776665555555555555555555544444444304422233333334566789999************* PP

                              HOOK 254 tarddyrlkceelek...evlelqqrneeltslaeEa.qaLkDEvDvLresadkvkkleatvetykkkle....dln 322
                                       ++++ yr  +eele+   e+ + + r+ +l++  +E  ++L D    L ++ +++++ ++ ve +   ++    +l+
  gi|344210266|ref|YP_004786442.1| 330 AQKETYRDTVEELETqreEISQARRRKADLEEDIAELeATLADRKQSLDAARNRLEQAQSDVEQLSDHVDaavaELS 406
                                       *******9999999722245666789999998766652679999999999999999999999988776543333999 PP

                              HOOK 323 dLrrqvklleernaeYlqktveleeelkkanalrsqlelykkqvqelhkklseeskkadklefe 386
                                       d+  ++k  e +  +   + ++le  + ++ +l + le+++ ++ el+++ +   k+  + +f+
  gi|344210266|ref|YP_004786442.1| 407 DVESEIKYREAELEDTADELAQLETRAARVDTLETDLETVRDDLAELRNRKDR-IKRETREAFD 469
                                       *******9999999999999***************************998775.4555555555 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   1.8     0.012         3     332     408 ..     130     189 ..     112     196 .. 0.61
   2 ?    7.0  11.2    0.0074       1.9     324     411 ..     147     233 ..     141     285 .. 0.87
   3 ?    5.8   4.4     0.017       4.4     334     411 ..     313     380 ..     304     397 .. 0.65
   4 ?    2.3   1.8       0.2        52     337     411 ..     403     467 ..     381     484 .. 0.52

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.012
                              FapA 332 epelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeel 408
                                       +++++++++ l++e e++e el++ +++                  + l +++e+  +l++e+e+l+++++++++e 
  gi|344210266|ref|YP_004786442.1| 130 FQNIDSQIETLQREREQIETELTQAREAK-----------------KRLPSVQEKVTRLENEIEDLRAKRETIDSEA 189
                                       44444444444444444444444444443.................4556666677777777777777777766665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0074
                              FapA 324 teievgldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleee 400
                                       +e+e++    e+k++l  ++e++ +le+e+e+l++k + +++++ +++ ++  + ql ++++++++ k+++e le+ 
  gi|344210266|ref|YP_004786442.1| 147 IETELTQA-REAKKRLPSVQEKVTRLENEIEDLRAKRETIDSEAGSDDSPESVRRQLSQARTEQNQAKNRVERLEQS 222
                                       55666455.68899999999999999999999999999999988899999999999999999999999999999999 PP

                              FapA 401 lkelkeelesk 411
                                       +++ +++l ++
  gi|344210266|ref|YP_004786442.1| 223 IERTEQRLSER 233
                                       99999999887 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.017
                              FapA 334 elkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeles 410
                                       +l ++l++l +el +l+++ e++++++++l+           ++e++ ++++ k  l+e+++ele+ l++ k++l+ 
  gi|344210266|ref|YP_004786442.1| 313 DLADQLDALGNELTALRAQKETYRDTVEELET----------QREEISQARRRKADLEEDIAELEATLADRKQSLDA 379
                                       44555555555555555555555555555555..........56778888888888888888888888888887776 PP

                              FapA 411 k 411
                                        
  gi|344210266|ref|YP_004786442.1| 380 A 380
                                       5 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.2
                              FapA 337 eklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeelesk 411
                                       ++l+++e e++  e+ele+  +++++l+           +   ++ l++++e  +++l+el+++++++k e ++ 
  gi|344210266|ref|YP_004786442.1| 403 AELSDVESEIKYREAELEDTADELAQLET----------RAARVDTLETDLETVRDDLAELRNRKDRIKRETREA 467
                                       22233333333333333333333333333..........445666666666666666666666666666665554 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   0.7      0.39     1e+02      29      73 ..     131     174 ..     129     187 .. 0.76
   2 ?    2.6   0.5      0.64   1.7e+02      29      76 ..     224     275 ..     197     282 .. 0.64
   3 ?    1.4   0.2       1.5   3.9e+02      34      87 ..     310     366 ..     306     368 .. 0.69
   4 ?   12.2   2.2   0.00064      0.17      21      85 ..     370     434 ..     366     446 .. 0.86
   5 ?   -0.5   0.2         6   1.6e+03      27      38 ..     442     453 ..     418     476 .. 0.51

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.39
                            DUF948  29 deaaatieelekqvdpilkevedllakvnelledvneklekvdpl 73 
                                       +++ ++ie+l+++ ++i +e++++ +  ++ l  v+ek+ ++++ 
  gi|344210266|ref|YP_004786442.1| 131 QNIDSQIETLQREREQIETELTQAREAKKR-LPSVQEKVTRLENE 174
                                       567788999999999999999998666655.88999998888764 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.64
                            DUF948  29 deaaatieelekqvdpi....lkevedllakvnelledvneklekvdpltea 76 
                                       +++++++ e ++ +d++     ++v+d l++++e l++v++  e ++++ +a
  gi|344210266|ref|YP_004786442.1| 224 ERTEQRLSERQDALDALeipeYNDVADKLSEARESLSQVERDAEVLQSVYSA 275
                                       4444444444444444322224567777777777777777777777777666 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 1.5
                            DUF948  34 tieelekqvdpilkevedllakvne...lledvneklekvdplteavadlgesvsel 87 
                                       t ++l +q+d++ +e+++l a+ ++   ++e+++ + e++ +     adl e ++el
  gi|344210266|ref|YP_004786442.1| 310 TRADLADQLDALGNELTALRAQKETyrdTVEELETQREEISQARRRKADLEEDIAEL 366
                                       556788899999999988887776633355555557777777777777777777666 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00064
                            DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                       l   k+ ld+a++++e+ +++v+++++ v++++a+  ++ ++++ + ++++   +++a+l +  +
  gi|344210266|ref|YP_004786442.1| 370 LADRKQSLDAARNRLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADELAQLETRAA 434
                                       5556889*******************************999999988888888888888877655 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 6
                            DUF948  27 tldeaaatieel 38 
                                        l+ +++ ++el
  gi|344210266|ref|YP_004786442.1| 442 DLETVRDDLAEL 453
                                       223333333333 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   7.6      0.61   1.6e+02     624     709 ..     128     231 ..     116     237 .. 0.53
   2 ?    7.6   9.2     0.003      0.77     237     408 ..     241     419 ..     217     421 .. 0.68
   3 ?    9.8   7.0   0.00068      0.18     206     368 ..     309     475 ..     307     490 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.61
                          Prominin 624 vnletlaekleelanelsngkknlkqslkneaqdlrai..qqelvlplessvkklkksvkklde............. 685
                                       ++++++ +++e+l++e ++     +++l+++ +  +++   qe+v++le+++++l+ + +++d+             
  gi|344210266|ref|YP_004786442.1| 128 LDFQNIDSQIETLQREREQI----ETELTQAREAKKRLpsVQEKVTRLENEIEDLRAKRETIDSeagsddspesvrr 200
                                       55666666666666666444....33333322222222114567778888888888888888886544333333333 PP

                          Prominin 686 .......ensdlqesikkllaaveraenflk 709
                                              e+++ ++++++l +++er+e+ l 
  gi|344210266|ref|YP_004786442.1| 201 qlsqartEQNQAKNRVERLEQSIERTEQRLS 231
                                       3333333444455555555555555555554 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.003
                          Prominin 237 aLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCq..seeCskilssleiekldts 311
                                        + e + ++++l+ea+e+L+qv++  + L++  s  +  l++ + dl + ++  +   +  C++  s+++    d+ 
  gi|344210266|ref|YP_004786442.1| 241 EIPEYNDVADKLSEARESLSQVERDAEVLQSVYSATEMVLSEDRLDLLTEVERDIDgdTVACWTCGSETTR--ADLA 315
                                       556778899********************************************887756999999999977..5555 PP

                          Prominin 312 kcldqlpnvdevlealeevletnlssi......vkeglarlneipekvknqtaevvpdlkkalakgreqikklakki 382
                                        +ld+l n  + l+a +e  ++ ++++      + ++  r  +++e ++ +++ +++d k++l+ +r+ +++ ++++
  gi|344210266|ref|YP_004786442.1| 316 DQLDALGNELTALRAQKETYRDTVEELetqreeISQARRRKADLEEDIA-ELEATLADRKQSLDAARNRLEQAQSDV 391
                                       5554443333333333333333332221000003345555556666654.466677788888888888888888777 PP

                          Prominin 383 p..realdavisdlenterssktfddvv 408
                                          ++ +da + +l+++e+++k+ + ++
  gi|344210266|ref|YP_004786442.1| 392 EqlSDHVDAAVAELSDVESEIKYREAEL 419
                                       6667778888888888888888777665 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00068
                          Prominin 206 elekhvsddLddagkhlgldladtlesnvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrd 282
                                       ++++++ d+Ld  g++l   l+++ e     +++ele+  e++++a++    +++   eL  + ++ +++l +++++
  gi|344210266|ref|YP_004786442.1| 309 TTRADLADQLDALGNELTA-LRAQKETY-RDTVEELETQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNR 383
                                       6778888999999988864.44444433.578999999999999999888888888888888888888888888888 PP

                          Prominin 283 lnqalsnlCq........seeCskilssleiekldtskcldqlpnvdevlealeevletnlssivkeglarlneipe 351
                                       l+qa s++ q         +e s+++s+ +  + +++ + d+l ++++   +++++ et+l+ +v+++la+l++ ++
  gi|344210266|ref|YP_004786442.1| 384 LEQAQSDVEQlsdhvdaaVAELSDVESEIKYREAELEDTADELAQLETRAARVDTL-ETDLE-TVRDDLAELRNRKD 458
                                       88888874444566655347788888888888888888889999999999999998.89987.5779********** PP

                          Prominin 352 kvknqtaevvpdlkkal 368
                                       ++k++t+e +   +k++
  gi|344210266|ref|YP_004786442.1| 459 RIKRETREAFDTAMKDI 475
                                       ********999777665 PP

>> YscO-like  YscO-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3  19.3       3.8   9.9e+02      25     131 ..     134     245 ..     130     276 .. 0.74
   2 ?    7.0  11.0      0.02       5.3      67     151 ..     344     427 ..     307     435 .. 0.83
   3 ?    6.4   0.2     0.032       8.4      29      85 ..     441     499 ..     430     507 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHHHHHH.HHHHHHH..HHHHHHHHHHHHHHHHHH....H---HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         YscO-like  25 kdkkkaLekEkeklr.kleeerd..kvkkhkkaKvaqlreeld....kGttsdkikkmkryikvvkeelkqeekkve 94 
                                        ++++ L++E+e+ + +l ++r+  k+    ++Kv+ l +e++    k  t+d         + v+ +l+q   + +
  gi|344210266|ref|YP_004786442.1| 134 DSQIETLQREREQIEtELTQAREakKRLPSVQEKVTRLENEIEdlraKRETIDSEAGSDDSPESVRRQLSQARTEQN 210
                                       6678889999888753566666621444577888888888775222267788888999999**************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         YscO-like  95 kQkekVkvAerkvEqareelakkrkeveklekhkeew 131
                                       + k++V+  e+ +E+ ++ l +++  +++le     +
  gi|344210266|ref|YP_004786442.1| 211 QAKNRVERLEQSIERTEQRLSERQDALDALEIPE--Y 245
                                       *****************************99743..3 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.02
                                       --HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         YscO-like  67 ttsdkikkmkryikvvkeelkqeekkvekQkekVkvAerkvEqareelakkrkeveklekhkeewlkevkkeeekre 143
                                       t  ++i +++r    ++e++++ e  +++ k++  +A+ ++Eqa+ ++ +    v++   +  +   e+k+ e++ e
  gi|344210266|ref|YP_004786442.1| 344 TQREEISQARRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVDAAVAELSDVESEIKYREAELE 420
                                       5678999999999*********************************************************9887766 PP

                                       HHHHHHHH CS
                         YscO-like 144 eleqdEiG 151
                                       +   dE+ 
  gi|344210266|ref|YP_004786442.1| 421 D-TADELA 427
                                       5.456665 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHH.---HHHHHHHHHHHHHHHHH CS
                         YscO-like  29 kaLekEkeklrkleeerdkvkkhkkaKvaq.lreeldk.Gttsdkikkmkryikvvkee 85 
                                         Le  +++l++l++ +d+ k++ ++  +  ++++l + Gt+ +  +    +  vv+ +
  gi|344210266|ref|YP_004786442.1| 441 TDLETVRDDLAELRNRKDRIKRETREAFDTaMKDILSRfGTGFETARLTADFDIVVARD 499
                                       679999999**************99999988*****98799998888888887777655 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  18.7    0.0011      0.29     114     238 ..     343     469 ..     339     481 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0011
                           DUF4407 114 eeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekka 190
                                       e+q+ee++++ ++ +a+l++++aelea +a+ ++ +daa++rl++++ ++++  d    +        + + k ++a
  gi|344210266|ref|YP_004786442.1| 343 ETQREEISQA-RRRKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDH-VDAAVAELSDVESEIKYREA 417
                                       3444444444.344567********************************9966664.55555667778888888888 PP

                           DUF4407 191 qldaaqaelaelkakld....atarlaalraelaeleaerakeraasqaaaa 238
                                       +l++   ela+l+++       +++l++ r+ lael+++++++++++++a +
  gi|344210266|ref|YP_004786442.1| 418 ELEDTADELAQLETRAArvdtLETDLETVRDDLAELRNRKDRIKRETREAFD 469
                                       8888888888888886678887888888888888888888888777776554 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.7     0.028       7.4      34      85 ..     131     181 ..     130     186 .. 0.75
   2 ?    6.3   4.5     0.049        13      23      82 ..     210     269 ..     196     273 .. 0.71
   3 ?    4.2   1.1      0.22        57      31      82 ..     313     366 ..     308     372 .. 0.76
   4 ?    5.7   4.2     0.075        19      15      89 ..     377     460 ..     373     461 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.028
                   Snapin_Pallidin  34 eqldrlnekLkeleeaqe.aevlpdlkeyakKLvnikkrmsslnerlqklkkR 85 
                                       +++d++ e L+  +e ++ +  l++++e +k+L +++ ++++l++ ++ l+++
  gi|344210266|ref|YP_004786442.1| 131 QNIDSQIETLQ--REREQiETELTQAREAKKRLPSVQEKVTRLENEIEDLRAK 181
                                       56888888887..4555556778888999999999999999999888888766 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.049
                   Snapin_Pallidin  23 kelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqkl 82 
                                       ++ ++  e L ++++r  ++L e ++a +a  +p+ +  a+KL++++  +s+++   + l
  gi|344210266|ref|YP_004786442.1| 210 NQAKNRVERLEQSIERTEQRLSERQDALDALEIPEYNDVADKLSEARESLSQVERDAEVL 269
                                       44444446788888888888888888888555777778889*******999998766655 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.22
                   Snapin_Pallidin  31 eLleqldrlnekLkeleeaqe..aevlpdlkeyakKLvnikkrmsslnerlqkl 82 
                                       +L++qld l ++L+ l+  +e   +++++l++ ++ ++++++r   l+e + +l
  gi|344210266|ref|YP_004786442.1| 313 DLADQLDALGNELTALRAQKEtyRDTVEELETQREEISQARRRKADLEEDIAEL 366
                                       688888888888888877766667888888888888888888877777766655 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.075
                   Snapin_Pallidin  15 ldeldeklkelrqsQeeLleqldrlnekLkeleeaqe.........aevlpdlkeyakKLvnikkrmsslnerlqkl 82 
                                       ld+ +++l++ +   e+L++++d   ++L ++e + +         a+ l++l++ a+++ +++ +++++ + l +l
  gi|344210266|ref|YP_004786442.1| 377 LDAARNRLEQAQSDVEQLSDHVDAAVAELSDVESEIKyreaeledtADELAQLETRAARVDTLETDLETVRDDLAEL 453
                                       55555666666666666666666666666655433222200000022234466667777777777777777777666 PP

                   Snapin_Pallidin  83 kkRaekL 89 
                                       + R +++
  gi|344210266|ref|YP_004786442.1| 454 RNRKDRI 460
                                       6666665 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   9.3      0.33        87     159     279 ..     145     267 ..     118     282 .. 0.60
   2 ?    9.4   6.1    0.0023      0.61     116     277 ..     293     467 ..     283     478 .. 0.54

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.33
                             FAM76 159 skkskekskekkaskkkskkhkkrss..rlevskle.eeklaeekesnetskksldsnssdhlvavtqLkeeiaslk 232
                                       ++ ++e +++++a+k+  +  +++ +  ++e+ +l+ ++++ ++++++++s +s+  + s+   + +q k+++++l+
  gi|344210266|ref|YP_004786442.1| 145 EQIETELTQAREAKKRLPSV-QEKVTrlENEIEDLRaKRETIDSEAGSDDSPESVRRQLSQARTEQNQAKNRVERLE 220
                                       11111111111111111111.111111233333333323356666777788889*********************** PP

                             FAM76 233 kqleqkdqellekdkkitelkaellekekelreklkelekeakekie 279
                                       + +e+ +q l+e++  + +l   + +  ++  +  +e+ +++++  e
  gi|344210266|ref|YP_004786442.1| 221 QSIERTEQRLSERQDALDALEIPEYNDVADKLSEARESLSQVERDAE 267
                                       **************999998865555444444444444444444444 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0023
                             FAM76 116 kkvdGk.lLCwlCtlsykralakakeeeeekrskskkkkskskkskkskekskekkaskkkskkhkkrssrlevskl 191
                                       + +dG  + Cw C  +  ra    + +   ++ +  ++++++ ++  ++ ++   ++++ ++ + +k++ + ++++l
  gi|344210266|ref|YP_004786442.1| 293 RDIDGDtVACWTCGSETTRADLADQLDALGNELTALRAQKETYRDTVEELET---QREEISQARRRKADLEEDIAEL 366
                                       679997256********99887777665554443333333333333333333...3444444444444555555555 PP

                             FAM76 192 e.....eek.....laeekesnetskksldsnssdhlvavtqLkeeiaslkkqleqkdqellekdkkit...elkae 255
                                       e      ++     +++ +++ ++  ++l+ ++   + ++++++ ei+ ++ +le    el + +   +   +l ++
  gi|344210266|ref|YP_004786442.1| 367 EatladRKQsldaaRNRLEQA-QSDVEQLSDHVDAAVAELSDVESEIKYREAELEDTADELAQLETRAArvdTLETD 442
                                       533332222222212222222.2223355566666677888889999999999998888887776654411155555 PP

                             FAM76 256 llekek...elreklkelekeakek 277
                                       l++ +    elr++  ++++e++e 
  gi|344210266|ref|YP_004786442.1| 443 LETVRDdlaELRNRKDRIKRETREA 467
                                       5555541114455555555555544 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.6     0.012       3.1     108     156 ..     131     179 ..     126     182 .. 0.91
   2 ?    2.7   1.2      0.32        83      98     153 ..     211     267 ..     192     275 .. 0.66
   3 ?    3.1   0.0      0.24        63     101     137 ..     298     334 ..     276     352 .. 0.77
   4 ?    3.4   2.5      0.19        49     103     155 ..     356     408 ..     336     412 .. 0.76
   5 ?    4.9   2.0     0.064        17      84     151 ..     398     463 ..     388     471 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.012
                     Fzo_mitofusin 108 qqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekfe 156
                                       q++d + ++l++e +++e+e+++  e++k++  +++k ++le+e+e+ +
  gi|344210266|ref|YP_004786442.1| 131 QNIDSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDLR 179
                                       567888899***********************************99865 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.32
                     Fzo_mitofusin  98 elsstfarlcqqvdetekeleeeikelek.eiekleevqkkakllrnkaslleseLe 153
                                       + ++ ++rl+q++++te+ l+e+ ++l++ ei + ++v  k+   r+  s++e++ e
  gi|344210266|ref|YP_004786442.1| 211 QAKNRVERLEQSIERTEQRLSERQDALDAlEIPEYNDVADKLSEARESLSQVERDAE 267
                                       345567778888888888888877777654677777777766666666666665555 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.24
                     Fzo_mitofusin 101 stfarlcqqvdetekeleeeikelekeiekleevqkk 137
                                        t+a++++ +++t+++l +++++l +e+++l + +++
  gi|344210266|ref|YP_004786442.1| 298 DTVACWTCGSETTRADLADQLDALGNELTALRAQKET 334
                                       489999*******************999999776554 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.19
                     Fzo_mitofusin 103 farlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekf 155
                                        a l++++ e e++l ++ ++l++  ++le++q+  ++l ++     +eL++ 
  gi|344210266|ref|YP_004786442.1| 356 KADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQLSDHVDAAVAELSDV 408
                                       45688888889999999999999999999999999999988887777777765 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.064
                     Fzo_mitofusin  84 vsltsancshqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkasllese 151
                                       v++  a++s  v++e++   a+l+ + de  ++le++ +++++  + le+v   +  lrn+  ++++e
  gi|344210266|ref|YP_004786442.1| 398 VDAAVAELS-DVESEIKYREAELEDTADEL-AQLETRAARVDTLETDLETVRDDLAELRNRKDRIKRE 463
                                       444444443.46666666666666666654.4567777777776677777777777777777666665 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   4.5      0.27        69      25      63 ..     196     234 ..     131     240 .. 0.86
   2 ?   -0.8   0.0       5.2   1.3e+03      21      57 ..     308     347 ..     304     355 .. 0.54
   3 ?    3.5   0.3      0.25        65      14      60 ..     382     427 ..     350     435 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.27
                              ApoO  25 kslepytsavqdelnkvkskvetaeqsvtdtiasLkepp 63 
                                       +s+ +++s++  e n++k++ve +eqs+++t + L+e +
  gi|344210266|ref|YP_004786442.1| 196 ESVRRQLSQARTEQNQAKNRVERLEQSIERTEQRLSERQ 234
                                       67788999999999****************999999864 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 5.2
                              ApoO  21 rslRkslepytsavqdel...nkvkskvetaeqsvtdtia 57 
                                       +++R  l ++++a+ +el   + +k+ + ++++ ++++ +
  gi|344210266|ref|YP_004786442.1| 308 ETTRADLADQLDALGNELtalRAQKETYRDTVEELETQRE 347
                                       5666667777777776663333444444444444444443 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.25
                              ApoO  14 drLeegvrslRkslepytsavqdelnkvkskvetaeqsvtdtiasLk 60 
                                       +rLe+  + + ++l+++++a+ +el++v+s ++  e  ++dt ++L+
  gi|344210266|ref|YP_004786442.1| 382 NRLEQAQSDV-EQLSDHVDAAVAELSDVESEIKYREAELEDTADELA 427
                                       4444444444.456666666666777777777777777777776666 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 ?    7.2   2.2     0.024       6.3      37      84 ..     131     178 ..     128     188 .. 0.67
   2 ?    1.8   0.4       1.1   2.9e+02      37      56 ..     210     229 ..     192     243 .. 0.46
   3 ?    2.1   0.1      0.89   2.3e+02      35      62 ..     244     271 ..     239     282 .. 0.79
   4 ?    6.6   3.5     0.037       9.7      37      92 ..     326     385 ..     312     389 .. 0.75
   5 ?    5.2   4.0       0.1        26      38      92 ..     390     444 ..     375     447 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.024
                           BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseL 84 
                                       ++++++++ l+++ e+++ +  + ++ ++++  ++++vt+Le+ ++ L
  gi|344210266|ref|YP_004786442.1| 131 QNIDSQIETLQREREQIETELTQAREAKKRLPSVQEKVTRLENEIEDL 178
                                       556666677777777777777777777777777777777777666554 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 1.1
                           BLOC1_2  37 kklkdvaaslekkleklnek 56 
                                       ++ k++++ le+++e+++++
  gi|344210266|ref|YP_004786442.1| 210 NQAKNRVERLEQSIERTEQR 229
                                       22333333333333333332 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.89
                           BLOC1_2  35 kykklkdvaaslekkleklnekyeelqp 62 
                                       +y++++d++++++++l+++++  e lq+
  gi|344210266|ref|YP_004786442.1| 244 EYNDVADKLSEARESLSQVERDAEVLQS 271
                                       7888999999999999998887777776 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.037
                           BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeav....seLDeyskeLE 92 
                                       ++l+ + +  ++++e+l+ + ee+++  ++  ++e++++eLe++     + LD+   +LE
  gi|344210266|ref|YP_004786442.1| 326 TALRAQKETYRDTVEELETQREEISQARRRKADLEEDIAELEATLadrkQSLDAARNRLE 385
                                       556666677788999999999999999999999999999999986222234666655555 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.1
                           BLOC1_2  38 klkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                       ++++  +++ + + +l+  + e++    ++++  +++++Le+ ++++D+  ++LE
  gi|344210266|ref|YP_004786442.1| 390 DVEQLSDHVDAAVAELSDVESEIKYREAELEDTADELAQLETRAARVDTLETDLE 444
                                       3444444455555555555557888888888888888888888888887777777 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   6.1       3.5   9.2e+02       9      32 ..     157     180 ..     129     204 .. 0.51
   2 ?    2.9   7.1      0.48   1.2e+02       4      56 ..     207     270 ..     197     300 .. 0.75
   3 ?   12.6   4.7   0.00048      0.12       3      50 ..     308     358 ..     306     370 .. 0.79
   4 ?    3.6   2.3       0.3        77       5      43 ..     355     393 ..     351     403 .. 0.68
   5 ?    4.3   5.7      0.18        48      10      43 ..     402     435 ..     393     491 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 3.5
                             Spc24   9 iakelsdleselesleselaelke 32 
                                       + k l ++++++++le+e ++l++
  gi|344210266|ref|YP_004786442.1| 157 AKKRLPSVQEKVTRLENEIEDLRA 180
                                       233333333333333333333333 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.48
                             Spc24   4 nekfriakelsdleselesleselaelkeeleeleeesee.......keser......ve.detllk 56 
                                       +e+ ++ + ++ le+++e+ e++l+e ++ l+ le  + +       +   +      ve d+ +l+
  gi|344210266|ref|YP_004786442.1| 207 TEQNQAKNRVERLEQSIERTEQRLSERQDALDALEIPEYNdvadklsE---AreslsqVErDAEVLQ 270
                                       566777888999999999999999999999999999888866665431...1334556555666654 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00048
                             Spc24   3 dnekfriakelsdleselesleselaelkeeleeleeesee..keser..ve 50 
                                       ++++ ++a +l+ l +el++l+++++  ++++eele+++ee  + ++r  ++
  gi|344210266|ref|YP_004786442.1| 308 ETTRADLADQLDALGNELTALRAQKETYRDTVEELETQREEisQ-ARRrkAD 358
                                       788999***********************************852.3333322 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.3
                             Spc24   5 ekfriakelsdleselesleselaelkeeleeleeesee 43 
                                       +k ++ +++ +le++l + +++l+  +++le+ ++  e+
  gi|344210266|ref|YP_004786442.1| 355 RKADLEEDIAELEATLADRKQSLDAARNRLEQAQSDVEQ 393
                                       566777777777777777777777777777777765554 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.18
                             Spc24  10 akelsdleselesleselaelkeeleeleeesee 43 
                                       + elsd+ese++  e+el++  +el++le+   +
  gi|344210266|ref|YP_004786442.1| 402 VAELSDVESEIKYREAELEDTADELAQLETRAAR 435
                                       6789999999999999999999999999998777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2384  (0.132969); expected 358.6 (0.02)
Passed bias filter:                      850  (0.0474092); expected 358.6 (0.02)
Passed Vit filter:                       251  (0.0139997); expected 17.9 (0.001)
Passed Fwd filter:                       189  (0.0105416); 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: 2.84u 0.48s 00:00:03.32 Elapsed: 00:00:00.78
# Mc/sec: 2293.51
//
Query:       gi|344210267|ref|YP_004786443.1|  [L=198]
Description: hypothetical protein HAH_5326 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1194.26
//
Query:       gi|344210268|ref|YP_004786444.1|  [L=1054]
Description: bacterio-opsin activator-like protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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  158.4   1.2    1.2e-15   58.0   0.2    4.4  4  GAF_2         GAF domain
    8.6e-38  129.7   3.3    8.6e-38  129.7   3.3    2.1  2  BAT           GAF and HTH_10 associated domain
    4.2e-22   79.2   0.0    7.5e-07   29.9   0.0    4.5  4  GAF           GAF domain
    9.4e-20   70.9   0.0      3e-19   69.2   0.0    1.9  1  Response_reg  Response regulator receiver domain
    1.9e-19   70.3   0.0    3.1e-05   24.3   0.0    4.6  4  GAF_3         GAF domain
    1.2e-16   60.2   0.0    4.8e-16   58.3   0.0    2.1  2  HTH_10        HTH DNA binding domain
    8.9e-06   26.0   0.1    0.00015   22.0   0.0    3.0  2  OKR_DC_1_N    Orn/Lys/Arg decarboxylase, N-terminal domain
    0.00069   19.1   0.0     0.0024   17.4   0.0    2.0  1  Sigma70_r4    Sigma-70, region 4
     0.0036   17.1   0.0     0.0088   15.9   0.0    1.6  1  HTH_5         Bacterial regulatory protein, arsR family
     0.0043   17.1   0.0      0.073   13.1   0.0    2.7  2  HTH_20        Helix-turn-helix domain
     0.0088   15.6   0.0      0.038   13.5   0.0    2.1  1  GerE          Bacterial regulatory proteins, luxR family
  ------ inclusion threshold ------
      0.014   15.0   0.2       0.24   11.1   0.0    3.1  2  Sigma70_r4_2  Sigma-70, region 4
       0.22   11.7   2.0         22    5.3   0.0    3.1  3  DUF1492       Protein of unknown function (DUF1492)
       0.41   10.0   5.2        1.1    8.6   5.2    1.7  1  DUF4349       Domain of unknown function (DUF4349)


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 !   58.0   0.2   9.7e-19   1.2e-15       2     137 ..     172     315 ..     171     316 .. 0.88
   2 !   24.1   0.0   2.7e-08   3.5e-05      34     130 ..     377     474 ..     325     481 .. 0.70
   3 !   19.6   0.0   6.7e-07   0.00086       2     137 ..     504     630 ..     503     631 .. 0.76
   4 !   52.4   0.0     5e-17   6.4e-14       2     137 ..     674     816 ..     673     817 .. 0.89

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 9.7e-19
                                       HHHHHHHHHHHHHHHHSS...EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B--.....-TTHHHHHHHHTS-EEES CS
                             GAF_2   2 adleelldlvldelvelg.aalgyillvdddgglrlaawgeaeeefgaaldrpl.....geglvgealrtgrpviln 72 
                                       ++ ee+ ++v++ l+  +  ++++i++ +++g+++  a g++  e  +a  ++      ++g++g+a++tg+  + +
  gi|344210268|ref|YP_004786444.1| 172 STAEEIQEAVCEILTSSDaYQFAWIGEKNEAGDIVPTAGGGDALEYVEAMVSRYgrsvfDDGPFGHAIETGEHQVAS 248
                                       68899*********9988799************77777776666666666554444467****************** PP

                                       -GGG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  73 dleedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       d++++ + ++++  a++ g+rs++++P+ + g v  v+++ya+ p afde+++++L+elae +a  +
  gi|344210268|ref|YP_004786444.1| 249 DIRTESSVQPWHelASEYGFRSMIVLPIQYTGSVQSVISIYADTPFAFDEAEQAVLTELAEIVADGL 315
                                       ************99**************88889*****************************99866 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 2.7e-08
                                       EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GGG.-S-HHHHHHHHHTT--EEEEEE-TTS---EEEE CS
                             GAF_2  34 lrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndlee.dpdkkglpaghaglrsflavPlisegrvvGvln 109
                                       ++++    ++ + g+ +  pl+e ++++a+ + + ++ +d+++ + d ++    +  +++ l+ Pl+ +g ++G l+
  gi|344210268|ref|YP_004786444.1| 377 FEVLQTPDETIFSGGTI--PLSETPCAKAIGNEETIVMTDVDAeCGDADRDQIWGDEVNRYLGTPLTVGGSIYGTLC 451
                                       33333344444445555..88999****************666244444444556667777*******9******** PP

                                       ES........--HHHHHHHHHHH CS
                             GAF_2 110 lyankppa..fdeedlelLeela 130
                                       +y+++ ++  f++ d++l+++l+
  gi|344210268|ref|YP_004786444.1| 452 FYGSGTGGseFSDWDVTLVDLLS 474
                                       *755555556*********9997 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 6.7e-07
                                       HHHHHHHHHHHHHHHHS.S...EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GGG CS
                             GAF_2   2 adleelldlvldelvel.g.aalgyillvdddgglrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndlee 76 
                                       +++ee +++v+++ +++ g  +++ ++++ d + +r ++ +e+ee++   +    g++ v  a+ t + ++++   +
  gi|344210268|ref|YP_004786444.1| 504 TSEEEAAQIVVSRTRDIiGlPEVVLYAFDSDTNTFRPLSTTETEEQQAIPA---DGDSFVSSAFFTEETIVCDGNST 577
                                       689*************76*88899999988888877555554444443333...477789******88888766333 PP

                                       -S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  77 dpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                           + + ++    +  ++vPl   g  +Gvl  + +  ++fd + +++ e+l+++i +a 
  gi|344210268|ref|YP_004786444.1| 578 ----SKAGEDTMTDGKAVFVPL---G-DHGVLRAGDTIGGEFDTQTRRITELLGATIRTAF 630
                                       ....2333466666666*****...9.9*****86666666**************998875 PP

  == domain 4  score: 52.4 bits;  conditional E-value: 5e-17
                                       HHHHHHHHHHHHHHHHSS...EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B---TT.H..HHHHHHHTS-EEES- CS
                             GAF_2   2 adleelldlvldelvelg.aalgyillvdddgg.lrlaawgeaeeefgaaldrplgeg.l..vgealrtgrpvilnd 73 
                                        + +e+ ++v+d+lv  + +++++i++++ d++ ++ ++w++++++f ++ + p +e  +  + + +rt++ ++ n+
  gi|344210268|ref|YP_004786444.1| 674 DSRSEIEQAVCDQLVASDiCSFAWIGEYESDTDrVTPRTWAGTDRGFLEESRTPSNETpPppAVQTARTNEQTLNNN 750
                                       57899*********9999999********777747777*********99999977444433366******9999999 PP

                                       GGG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  74 leedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       +++  + kg+   + ++g++s +++Pl ++   +G+l++ya+ p+ fd   +++Lee++e+++ ai
  gi|344210268|ref|YP_004786444.1| 751 IADGLRGKGWQrrLLERGFQSVVSIPLSYQQLSYGILTVYAKTPDVFDLPTQSVLEEVSETVGYAI 816
                                       ***9999999999**************99879*********************************9 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 ?   -3.4   0.2       6.3   8.1e+03     131     131 ..     317     317 ..     282     350 .. 0.53
   2 !  129.7   3.3   6.7e-41   8.6e-38       1     155 [.     828     981 ..     828     982 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.3
                               BAT 131 e 131
                                       +
  gi|344210268|ref|YP_004786444.1| 317 S 317
                                       1 PP

  == domain 2  score: 129.7 bits;  conditional E-value: 6.7e-41
                               BAT   1 DavveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddg 77 
                                       D+ veL+le +++dd+++++a  +d ++++eg+vp++d + +vff++d   p+++++ ++ l+ +e ++++++++d+
  gi|344210268|ref|YP_004786444.1| 828 DRAVELQLEATESDDIIHRIAGVADTEITFEGIVPQGDTSCIVFFSTDA-PPDDLQACLDILPRIERLECLTDTEDT 903
                                       899********************************************97.88************************* PP

                               BAT  78 tlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrtrref 154
                                       +l+e+tvsg+ la t+ae+Gg ++ ++ ++++ ++ +evP+++d+R+++  l++++pd+eLv r++rer v+tr++f
  gi|344210268|ref|YP_004786444.1| 904 SLFEATVSGTQLALTVAEQGGAPQLIQSDGETLEIQLEVPQTVDIRQLIAELRRSCPDIELVGRHKRERGVQTRESF 980
                                       ***************************************************************************99 PP

                               BAT 155 r 155
                                       +
  gi|344210268|ref|YP_004786444.1| 981 H 981
                                       6 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.2e-08   1.5e-05      39     130 ..     222     312 ..     172     315 .. 0.81
   2 !   29.9   0.0   5.8e-10   7.5e-07       5     133 .]     348     481 ..     344     481 .. 0.80
   3 ?    6.4   0.0      0.01        13       3      67 ..     507     576 ..     505     602 .. 0.71
   4 !   11.7   0.0   0.00024       0.3      37     133 .]     721     816 ..     677     816 .. 0.61

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.2e-08
                                       EECCEEEETTSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CS CS
                               GAF  39 asrwlfmkngrgicgqvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pf 114
                                        sr+ + + ++g +g++++tg+  v +d+++++  ++  +++l++++g+rs++v+P+  +g +  +++++  +p  f
  gi|344210268|ref|YP_004786444.1| 222 VSRYGRSVFDDGPFGHAIETGEHQVASDIRTESSVQP--WHELASEYGFRSMIVLPIQYTGSVQSVISIYADTPfAF 296
                                       445555555667778**************99999999..999*****************************999888 PP

                                       HHHHHHHHHHHHHHHH CS
                               GAF 115 treelellqvladqva 130
                                       +++e ++l++la+ va
  gi|344210268|ref|YP_004786444.1| 297 DEAEQAVLTELAEIVA 312
                                       ************9877 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 5.8e-10
                                       HHHHHHHHHHHHHTESEEEEEEEEETTEEE.....CEEEEECC...EEEETTSHHHHHHHHHSSSEEESTGGTSTTH CS
                               GAF   5 lldtvveelrellgadrvalylpdydGlhy.....dipqasrw...lfmkngrgicgqvlatgqplvipdstpdprf 73 
                                         + +++  r++lg ++++l +   +G +y     ++p++  +   + +   ++ c++++ + +++v +d+ + ++ 
  gi|344210268|ref|YP_004786444.1| 348 QIADLMQVGRSVLGTEYATLSR--VNGMEYdfevlQTPDETIFsggTIPLSETP-CAKAIGNEETIVMTDV-DAECG 420
                                       5667888889999999999976..899888786664444444477455555666.99************97.55554 PP

                                       HTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS...CSHHHHHHHHHHHHHHHHHHH CS
                               GAF  74 aqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp...pftreelellqvladqvaval 133
                                        +  +rd++ + +++ +l+ Pl+++g ++G+l+++   +   +f+++++ l+  l+  ++++l
  gi|344210268|ref|YP_004786444.1| 421 DA--DRDQIWGDEVNRYLGTPLTVGGSIYGTLCFYGSGTggsEFSDWDVTLVDLLSKWIGNEL 481
                                       44..589999**************************5556689*************9999886 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHHHHHHTESEEEEEEEEETTEEE....CEEEEECCEEEETTSHHHHHHHHHSSSEEEST.G CS
                               GAF   3 eelldtvveelrellgadrvalylpdydGlhy....dipqasrwlfmkngrgicgqvlatgqplvipd.s 67 
                                       ee++++vv++ r++ g+ +v+ly  d+d +++     ++ + +   + +g++++  ++ t +++v+++ s
  gi|344210268|ref|YP_004786444.1| 507 EEAAQIVVSRTRDIIGLPEVVLYAFDSDTNTFrplsTTETEEQQAIPADGDSFVSSAFFTEETIVCDGnS 576
                                       899********************96666654444422233333345555888888888888888888633 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00024
                                       EEEECC..EEEETTSHHHHHHHHHSSSEEESTGGTSTT.HHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEES CS
                               GAF  37 pqasrw..lfmkngrgicgqvlatgqplvipdstpdpr.faqynrrdllenmgirsslvvPlvndgelwGllvlhnp 110
                                        ++sr    +++ + + ++++ ++ q+l+ + + +d+       +++ l + g++s++++Pl  ++  +G+l+++ +
  gi|344210268|ref|YP_004786444.1| 721 LEESRTpsNETP-PPPAVQTARTNEQTLNNN-I-ADGLrGK--GWQRRLLERGFQSVVSIPLSYQQLSYGILTVYAK 792
                                       333333322222.222233444555555555.4.3333122..366789999************************8 PP

                                       SS.CSHHHHHHHHHHHHHHHHHHH CS
                               GAF 111 sp.pftreelellqvladqvaval 133
                                       +p  f+     +l+++++ v+ a+
  gi|344210268|ref|YP_004786444.1| 793 TPdVFDLPTQSVLEEVSETVGYAI 816
                                       8989999999999*9999999886 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.0   2.4e-22     3e-19       1     106 [.      24     130 ..      24     136 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 2.4e-22
                                       EEEESSSHHHHHHHHHHHH..HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlle..eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpvi 75 
                                       vl+vdD   +r+ +++lle  ++ + ev ea++ ++al ++ +e++d+i+ D +mp+ dG+e+++++r+ + +lp i
  gi|344210268|ref|YP_004786444.1|  24 VLLVDDYGEFRRTTAELLEheNDRI-EVIEAASVEDALSYFGSESIDCIVSDYEMPEADGIEFVETVRQSNGDLPFI 99 
                                       89*****************844566.999************************************************ PP

                                       EEESSTSHHHHHHHHHCTESEEEESSG-HHH CS
                      Response_reg  76 iltahseeedavealkagaddflsKpfdpee 106
                                       +lt++++e+ a ea++ag+ d+ +K   pe+
  gi|344210268|ref|YP_004786444.1| 100 LLTGQGSEKLASEAVSAGVTDYFVKGGGPEQ 130
                                       *************************877765 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   9.9e-05      0.13      61     124 ..     239     312 ..     172     316 .. 0.73
   2 !   24.3   0.0   2.4e-08   3.1e-05       3     128 ..     346     482 ..     344     483 .. 0.82
   3 !   23.0   0.0   6.1e-08   7.8e-05       3     123 ..     507     626 ..     505     632 .. 0.83
   4 ?    4.6   0.0     0.031        40      80     127 ..     769     816 ..     731     818 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.9e-05
                             GAF_3  61 lssgevvsepsfaeedg..........lpdraalavPLvagrqviGvlalastkprafdaedlelleslArqia 124
                                       +++ge +++ + + e++          +  r+++++P++ +  v+ v+ ++ + p+afd+++++ l +lA  +a
  gi|344210268|ref|YP_004786444.1| 239 IETGEHQVASDIRTESSvqpwhelaseYGFRSMIVLPIQYTGSVQSVISIYADTPFAFDEAEQAVLTELAEIVA 312
                                       555555444444444332222222222678**********99****************************8777 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 2.4e-08
                             GAF_3   3 dellekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesldedsalarralssgevvsepsfaeedg.. 77 
                                        e++++l++ + ++lg+e++ l  +++++ ++ v    d+      +++  +  ++ a++ +e ++ +++++e g  
  gi|344210268|ref|YP_004786444.1| 346 REQIADLMQVGRSVLGTEYATLSRVNGMEYDFEVLQTPDETIFSGGTIPLSETPCAKAIGNEETIVMTDVDAECGda 422
                                       58999*******************************9988777777***8888888888888887776665542222 PP

                             GAF_3  78 .....lpd..raalavPLvagrqviGvlalastkpra..fdaedlelleslArqiataie 128
                                            + d  + +l  PL++g   +G+l+++ ++++   f++ d+ l++ l+ +i+++++
  gi|344210268|ref|YP_004786444.1| 423 drdqiWGDevNRYLGTPLTVGGSIYGTLCFYGSGTGGseFSDWDVTLVDLLSKWIGNELQ 482
                                       333333225478888***************988766557******************997 PP

  == domain 3  score: 23.0 bits;  conditional E-value: 6.1e-08
                             GAF_3   3 dellekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesld.edsalarralssgevvse....psfae 74 
                                       +e ++++++++ ++ g+  ++l+ +d d n++++ + ++ +++  ++++  +++  + a++++e ++     +s a+
  gi|344210268|ref|YP_004786444.1| 507 EEAAQIVVSRTRDIIGLPEVVLYAFDSDTNTFRPLSTTETEEQ--QAIPaDGDSFVSSAFFTEETIVCdgnsTSKAG 581
                                       8899********************************9955554..5999766667778888888775567777889* PP

                             GAF_3  75 edglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqi 123
                                       ed++ d++a++vPL +     Gvl ++ t +++fd ++++  e l++ i
  gi|344210268|ref|YP_004786444.1| 582 EDTMTDGKAVFVPLGD----HGVLRAGDTIGGEFDTQTRRITELLGATI 626
                                       ***************9....78898888888888888888888888776 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.031
                             GAF_3  80 draalavPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                        ++++ +PL  ++ ++G+l ++ + p  fd  +++ le+++  ++ ai
  gi|344210268|ref|YP_004786444.1| 769 FQSVVSIPLSYQQLSYGILTVYAKTPDVFDLPTQSVLEEVSETVGYAI 816
                                       588999*****99***********9999************99999888 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0         8     1e+04      18      34 ..     797     813 ..     797     818 .. 0.89
   2 !   58.3   0.0   3.8e-19   4.8e-16       1      53 []     988    1040 ..     988    1040 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8
                            HTH_10  18 FdyPRrvtlkeLAkelG 34 
                                       Fd P +  l+e++++ G
  gi|344210268|ref|YP_004786444.1| 797 FDLPTQSVLEEVSETVG 813
                                       899999999***99988 PP

  == domain 2  score: 58.3 bits;  conditional E-value: 3.8e-19
                            HTH_10    1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53  
                                        LT++q+evl +A+ +G++  PR+ t +e+A++l+Is++t+s hLr a +kl+e
  gi|344210268|ref|YP_004786444.1|  988 LTPRQFEVLLAAFYSGFYQSPRDKTGQEIADTLDISQPTFSHHLRVAVRKLLE 1040
                                        9*************************************************985 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 !   22.0   0.0   1.2e-07   0.00015      14     111 .]      44     145 ..      31     145 .. 0.77
   2 ?   -0.1   0.1      0.84   1.1e+03       4      57 ..     152     199 ..     150     208 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.2e-07
                        OKR_DC_1_N  14 ekegfevvgvtstdDllsvieqnsriaavvlsvd...deaaelldeirernedlPvFllaetrtsedvpadvlreid 87 
                                       e++ +ev++++s++D+ls+  +  +i+++v +++    +  e+++ +r+ n dlP  ll+ + +++ ++  v + ++
  gi|344210268|ref|YP_004786444.1|  44 ENDRIEVIEAASVEDALSYFGS-ESIDCIVSDYEmpeADGIEFVETVRQSNGDLPFILLTGQGSEKLASEAVSAGVT 119
                                       44789***************99.89***********9999***************8888875555555555555555 PP

                        OKR_DC_1_N  88 gfielledtpefia...rqieaaakkY 111
                                        ++ +  + pe++a   ++ie a+++Y
  gi|344210268|ref|YP_004786444.1| 120 DYF-VKGGGPEQYAvltNRIENAVESY 145
                                       444.45666666654447888888777 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.84
                        OKR_DC_1_N   4 aairelaealekegfevvgvtstdDllsvieqnsriaavvlsvddeaaelldei 57 
                                       a++ ++ + +++ +++v+++ + +      e + +++ ++ s d ++ + + e 
  gi|344210268|ref|YP_004786444.1| 152 ARLSRINSLFREINRQVLRASTAE------EIQEAVCEILTSSDAYQFAWIGEK 199
                                       67788899999999******9999......445566666666665555555555 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.9e-06    0.0024       3      48 ..     986    1038 ..     986    1040 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.9e-06
                                        HHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4    3 asLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48  
                                        a+L++r+ evl   f        ++ T +EI+++l+iS+ + + +++ A+rkL
  gi|344210268|ref|YP_004786444.1|  986 AQLTPRQFEVLLAAFysgfyqsPRDKTGQEIADTLDISQPTFSHHLRVAVRKL 1038
                                        69*****************99999*************************9998 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 !   15.9   0.0   6.9e-06    0.0088      19      38 ..    1014    1033 ..    1007    1033 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.9e-06
                                        HHHHHHHTS-HHHHHHHHHH CS
                             HTH_5   19 celaeelglsqstvShHLkk 38  
                                         e+a+ l++sq+t ShHL++
  gi|344210268|ref|YP_004786444.1| 1014 QEIADTLDISQPTFSHHLRV 1033
                                        69****************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 ?    0.1   0.0      0.68   8.7e+02      13      36 ..     332     368 ..     322     381 .. 0.63
   2 !   13.1   0.0   5.7e-05     0.073      28      47 ..    1014    1033 ..     996    1035 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.68
                                       HHHHHHHSTCTTB-HHHHHHHHT.............S CS
                            HTH_20  13 rrilraLaraegltaselaerld.............l 36 
                                       r i   +++++g+  +++a++++              
  gi|344210268|ref|YP_004786444.1| 332 RTITEVFTSRDGALREQIADLMQvgrsvlgteyatlS 368
                                       4555555999**********99633445545555533 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.7e-05
                                        HHHHHHHTS-HHHHHHHHHH CS
                            HTH_20   28 selaerldlskntlsyHLrv 47  
                                         e+a++ld+s+ t s+HLrv
  gi|344210268|ref|YP_004786444.1| 1014 QEIADTLDISQPTFSHHLRV 1033
                                        69****************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 !   13.5   0.0     3e-05     0.038       3      45 ..     988    1038 ..     986    1039 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3e-05
                                        S-HHHHHHH.HHHCTT.......S-HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE    3 LskRErevL.rllaeG.......ksnkeIAeelniSekTVkvhksnimkKL 45  
                                        L++R+ evL + +++G       k+ +eIA+ l+iS+ T + h++ + +KL
  gi|344210268|ref|YP_004786444.1|  988 LTPRQFEVLlAAFYSGfyqsprdKTGQEIADTLDISQPTFSHHLRVAVRKL 1038
                                        66666666523344442222222799************************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 ?   -2.8   0.1       4.3   5.5e+03       3      16 ..     880     893 ..     879     893 .. 0.89
   2 ?   11.1   0.0   0.00019      0.24       6      54 .]     983    1038 ..     982    1038 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.3
                                       HHHHHHTTS-HHHH CS
                      Sigma70_r4_2   3 alrealaeLperqr 16 
                                        l+++l+ Lp ++r
  gi|344210268|ref|YP_004786444.1| 880 DLQACLDILPRIER 893
                                       5899*******998 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00019
                                        HHHTTS-HHHHHHHHHHHTS--.......-HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2    6 ealaeLperqreifllrylegl.......sykEIAellgisegtVksrlsRArkkL 54  
                                        e+ a+L++rq e++l  ++ g+       + +EIA  l+is  t  ++l+ A +kL
  gi|344210268|ref|YP_004786444.1|  983 ELTAQLTPRQFEVLLAAFYSGFyqsprdkTGQEIADTLDISQPTFSHHLRVAVRKL 1038
                                        5679999999999999999986444444499******************9999997 PP

>> DUF1492  Protein of unknown function (DUF1492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       6.4   8.2e+03      30      69 ..     326     365 ..     324     380 .. 0.67
   2 ?    4.1   0.3     0.039        50      27      79 ..     639     694 ..     632     700 .. 0.84
   3 ?    5.3   0.0     0.017        22      74      99 ..    1013    1038 ..    1008    1039 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.4
                           DUF1492  30 akediekktaeaik.kklelqrlidklensdsrsvLrmvyi 69 
                                       ++e++ ++ +e+   +   l+++i++l +   rsvL   y 
  gi|344210268|ref|YP_004786444.1| 326 MREEVLRTITEVFTsRDGALREQIADLMQV-GRSVLGTEYA 365
                                       667777777777641556788888888765.4677766665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.039
                           DUF1492  27 Lvvakediekkta..eaikkklelqrli.dklensdsrsvLrmvyidkltvwqvid 79 
                                       L   + d+e++t+  e +++  el + i +++  +dsrs ++    d+l + +++ 
  gi|344210268|ref|YP_004786444.1| 639 LEDRQRDLEQQTVqlEQMNRLTELSQKIhERVLRADSRSEIEQAVCDQLVASDICS 694
                                       55567899***97558899*****9988357999******999999***9999995 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.017
                           DUF1492   74 vwqvidklnisrstyyrllrvavkeL 99  
                                         +++ d l+is+ t+   lrvav++L
  gi|344210268|ref|YP_004786444.1| 1013 GQEIADTLDISQPTFSHHLRVAVRKL 1038
                                        5689*******************987 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   5.2   0.00088       1.1     100     149 ..     613     663 ..     611     678 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00088
                           DUF4349 100 asedrllall.ekaksvedlleiereLsevqaeieslegqlryLdnqvays 149
                                       ++ +r+++ll +   ++ d l+ e+eL+++q ++e+ + ql+++++ +++s
  gi|344210268|ref|YP_004786444.1| 613 TQTRRITELLgATIRTAFDRLTYETELEDRQRDLEQQTVQLEQMNRLTELS 663
                                       577899999966688999*****************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1054 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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: 0.94u 0.32s 00:00:01.26 Elapsed: 00:00:00.52
# Mc/sec: 6117.91
//
Query:       gi|344210269|ref|YP_004786445.1|  [L=87]
Description: hypothetical protein HAH_5328 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-24   84.5   0.4      5e-24   84.3   0.4    1.0  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 !   84.3   0.4   2.8e-28     5e-24       2      75 .]      17      86 ..      16      86 .. 0.97

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 2.8e-28
                            HalOD1  2 eespstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVep 75
                                      +esps+a+v+a+aa e v  t l+pLy+ iDpdALd+L+a     ++++d+++sFty gy+V++r++ +ie++p
  gi|344210269|ref|YP_004786445.1| 17 YESPSEAIVTAIAAKESVTETSLPPLYNRIDPDALDTLVAG----QTNDDIQISFTYSGYTVRIRDSETIEITP 86
                                      69***************************************....88999**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 578.65
//
Query:       gi|344210270|ref|YP_004786446.1|  [L=184]
Description: hypothetical protein HAH_5329 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   2.0          3    7.5   0.5    2.3  2  DUF4131   Domain of unknown function (DUF4131)
       0.11   12.5   0.1       0.27   11.2   0.1    1.7  1  HTH_11    HTH domain


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 ?    4.3   0.0    0.0032        29      97     121 ..      58      82 ..      21      92 .. 0.82
   2 ?    7.5   0.5   0.00034         3       7      59 ..     125     177 ..     118     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0032
                           DUF4131  97 sagktkpvsgrvlvtvpkspaeglr 121
                                        ++ + +++ rv+v++++ +a++l+
  gi|344210270|ref|YP_004786446.1|  58 VEELSSQARKRVYVSLYQTHAPKLQ 82 
                                       56778899***********999776 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00034
                           DUF4131   7 lvllalllllllllllllrr...rprrrvllllllllllallgfalrapqpnandl 59 
                                       + ll ++lll+++ ++   +   + ++ v++l+ +  +l+l+ +++ ++++++nd+
  gi|344210270|ref|YP_004786446.1| 125 VALLNAILLLAAIVGV---SplsAISPLVIGLVVISSFLVLSIAHAVSRRRGENDK 177
                                       3333333333333333...3445999999999999999999999999999999885 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   3.1e-05      0.27       1      25 [.      25      49 ..      25      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                            HTH_11  1 RllqilelLleargpisgeeLAeeL 25
                                      R++  l  L+++++p+   +LAeeL
  gi|344210270|ref|YP_004786446.1| 25 RRRYTLYYLRQQKEPVQLTDLAEEL 49
                                      7888999*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1265.98
//
Query:       gi|344210271|ref|YP_004786447.1|  [L=39]
Description: hypothetical protein HAH_5330 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); 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: 0.35u 0.29s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 266.88
//
Query:       gi|344210272|ref|YP_004786448.1|  [L=66]
Description: hypothetical protein HAH_5331 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   13.3   0.1      0.076   13.1   0.1    1.1  1  DUF3071   Protein of unknown function (DUF3071)


Domain annotation for each model (and alignments):
>> DUF3071  Protein of unknown function (DUF3071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.2e-06     0.076       1      36 [.      24      63 ..      24      66 .] 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.2e-06
                           DUF3071  1 MreLrlvglesdgeslvleae....egeefflavddeLra 36
                                      M+eL++v++++d++ ++l ++     +eef +  +d+Lr+
  gi|344210272|ref|YP_004786448.1| 24 MEELTVVKSSTDSQLIFLPEHesqlGEEEFIVIHSDSLRD 63
                                      9*****************996678899***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); 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 0.26s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 444.33
//
Query:       gi|344210273|ref|YP_004786449.1|  [L=242]
Description: glucose-1-phosphate thymidylyltransferase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-41  141.6   0.0    3.4e-41  141.4   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    2.2e-14   54.1   0.0    2.5e-14   53.9   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    6.3e-06   26.1   0.0    1.8e-05   24.6   0.0    1.7  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 !  141.4   0.0   5.8e-45   3.4e-41       1     245 [.       2     234 ..       2     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 5.8e-45
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       kav+La G+GtRL PLt +l+k lv v +k +l+ ++l +l++ + +e  v++  ++++ + +++++ +  gv +++
  gi|344210273|ref|YP_004786449.1|   2 KAVVLAAGKGTRLQPLTDDLPKALVEVDEK-PLLTHCLDELVSLDADE-FVIVVGYRKEQIIDYYGNSY-NGVPITY 75 
                                       79****************************.*****************.66666677777778888888.699**** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       ++++e+ g+A+A+++a+  ++d++    +l+Lg++++ + ++ ++v++ +e++ ++  ++  vp++ea++yGv  ++
  gi|344210273|ref|YP_004786449.1|  76 VHQEEPAGLAHALLQAEPEIKDDF----MLMLGDNVF-RGNLDTVVQRQREQRVDCAFLVEEVPEDEASRYGVCVTN 147
                                       *********************999....788876655.55**************99********************* PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EE. CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWs. 230
                                       + g++++ vEKP+ ++ s+l+ +G Y+f + +++   +++++++rge e++d++  ++++g+   a+  ++   W+ 
  gi|344210273|ref|YP_004786449.1| 148 KYGEITDVVEKPDDPP-SNLVMTGFYTFSPAIFQAC-SQVQPSDRGEYELSDAIDLLMDSGRTIDAVRLNG---WRv 219
                                       ****************.*****************99.67*********************98887766666...754 PP

                                       EXSSHHHHHHHHHHH CS
                   NTP_transferase 231 DvGtldslleanekl 245
                                       DvG +++  +a+++l
  gi|344210273|ref|YP_004786449.1| 220 DVGYPEDKETAEQRL 234
                                       ***999988777766 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 !   53.9   0.0   4.2e-18   2.5e-14       1     112 [.       3     120 ..       3     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 4.2e-18
                                       EEEEEESS-TTTTT.....THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC....TS-EEE-T CS
                      NTP_transf_3   1 aviLAGGrSsRmgg.....dKallplggkpllervldalraagvdevvvvggd..eevlaalarl....gvrvvede 66 
                                       av+LA+G+++R++      +Kal+++++kpll ++ld l ++ +de v+v+g+  e++ +++  +    ++++v++e
  gi|344210273|ref|YP_004786449.1|   3 AVVLAAGKGTRLQPltddlPKALVEVDEKPLLTHCLDELVSLDADEFVIVVGYrkEQIIDYYGNSyngvPITYVHQE 79 
                                       79**********8444568*******************************999555666655333342267777777 PP

                                       TSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHH CS
                      NTP_transf_3  67 dpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaa 112
                                       +  +g +++l+ a  ++  +d ++++++D ++  +  +++++++ +
  gi|344210273|ref|YP_004786449.1|  80 E-PAGLAHALLQAEPEI--KDDFMLMLGDNVF--RGNLDTVVQRQR 120
                                       5.478888888888887..7999999999998..444555555544 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 !   24.6   0.0     3e-09   1.8e-05       2      54 ..       2      57 ..       1      67 [. 0.85
   2 ?   -1.7   0.0      0.33     2e+03     162     218 ..     175     233 ..     166     236 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3e-09
                                      EEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GG CS
                              IspD  2 vvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvsed 54
                                       +v+ AAG+G+R++    +lpK+++e++ ++ll+h +d l +  a + ++vv  ++
  gi|344210273|ref|YP_004786449.1|  2 KAVVLAAGKGTRLQpltDDLPKALVEVDEKPLLTHCLDELVSLDADEFVIVVGYRK 57
                                      69**********9744479***********************88888888776554 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.33
                                       EHHHHHHHHHHH..HHCT---SSHHHHHHHTT--EEEEE--TTG----SHHHHHHHHHH CS
                              IspD 162 rvdlllaahakg..eqegaeitDdaslvekiGlsvkvVeGeednlKittpeDlalAeai 218
                                       + ++++a+ + +  ++  +e +D ++l+   G ++  V  +   + + +peD  +Ae  
  gi|344210273|ref|YP_004786449.1| 175 SPAIFQACSQVQpsDRGEYELSDAIDLLMDSGRTIDAVRLNGWRVDVGYPEDKETAEQR 233
                                       55566666655443555678889999999999999999888888888888888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1643.92
//
Query:       gi|344210274|ref|YP_004786450.1|  [L=91]
Description: hypothetical protein HAH_5333 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 620.45
//
Query:       gi|344210275|ref|YP_004786451.1|  [L=268]
Description: hypothetical protein HAH_5334 [Haloarcula hispanica ATCC 33960]
Scores for 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-09   36.0   0.4    1.7e-08   34.5   0.3    1.9  1  Glycos_transf_2  Glycosyl transferase family 2
    3.9e-06   26.9   0.6    0.00048   20.1   0.6    2.6  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    9.9e-06   25.1   0.8    1.7e-05   24.4   0.8    1.5  1  Glyco_transf_7C  N-terminal domain of galactosyltransferase
    2.5e-05   23.9   0.0       0.12   11.9   0.0    2.3  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
    2.5e-05   24.3   0.0    3.7e-05   23.7   0.0    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
     0.0092   15.5   0.0      0.032   13.7   0.0    1.9  1  Glyco_transf_21  Glycosyl transferase family 21
  ------ inclusion threshold ------
      0.096   12.3   0.0       0.16   11.6   0.0    1.3  1  PrpR_N           Propionate catabolism activator


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 !   34.5   0.3   6.5e-12   1.7e-08      47     169 ..      24     131 ..      12     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 6.5e-12
                                       GGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCC CS
                   Glycos_transf_2  47 eelakedprvrvirreenvGkagalnaglraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifget 123
                                       +e+a  ++++ vi  +e     +a+n+g+++a++d i+flD+D+ p p++l+k  e le  +a  ++++r  +++++
  gi|344210275|ref|YP_004786451.1|  24 KEHA--FDDFEVIVCDES-PVTRARNEGIKQASTDKIVFLDDDSRPRPEYLQKADELLET-EA--AYAGRTIHPVDD 94 
                                       4444..677778888866.8899*******************************999999.77..677777777777 PP

                                       CCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEEEEHHHHHC CS
                   Glycos_transf_2 124 deiernkrvgenerlyfkerkrslkgnlsfeigsaallrrealeel 169
                                        + ++         + +    + ++  + +++g++++++r++++ +
  gi|344210275|ref|YP_004786451.1|  95 VFARH---------FTTHYDWGDDPCYVNHFWGCNMGVHRDVFKAV 131
                                       77775.........45789999999999999999999999999765 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 !   20.1   0.6   1.9e-07   0.00048      68     222 ..      36     178 ..       4     184 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.9e-07
                   Glyco_tranf_2_3  68 rnlgstgksralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaer 144
                                       ++ ++ +  ra ne+++++++d ++++DdD++  P++l+++  +++t+   a+++ +  +  + +        fa++
  gi|344210275|ref|YP_004786451.1|  36 CDESPVT--RARNEGIKQASTDKIVFLDDDSRPRPEYLQKADELLETE---AAYAGRTIHPVDDV--------FARH 99 
                                       3345533..456****************************99999333...44444444433332........3344 PP

                   Glyco_tranf_2_3 145 hlrflaarralg.vltlnGsgslirrevlkelegldplfllt.dDyelglrlrragfrtayvpgaavrevfpsslka 219
                                       ++ +    +    v  + G  + + r+v+k+ +g+d++   + + +el++r+r a+f++ y p+++v +   ss+++
  gi|344210275|ref|YP_004786451.1| 100 FTTHYDWGDDPCyVNHFWGCNMGVHRDVFKAVGGWDEQMGWGhEEKELARRVR-AEFDIRYDPELIVDHPYASSITE 175
                                       44333322222225555566677778888888888884333358888888764.67888888888877777777666 PP

                   Glyco_tranf_2_3 220 yik 222
                                       y+k
  gi|344210275|ref|YP_004786451.1| 176 YWK 178
                                       666 PP

>> Glyco_transf_7C  N-terminal domain of galactosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.8   6.5e-09   1.7e-05       1      57 [.      98     153 ..      98     182 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 6.5e-09
                   Glyco_transf_7C   1 rhlsveidkfgyklpyekyfgGvlalrkedfekiNGfsntfwgWGgEDdelyaRlak 57 
                                       rh+++++d  +     +++ g+++ + ++ f++++G +++ +gWG E +el++R+++
  gi|344210275|ref|YP_004786451.1|  98 RHFTTHYDWGDDPCYVNHFWGCNMGVHRDVFKAVGGWDEQ-MGWGHEEKELARRVRA 153
                                       6888888888888889**********************98.6************865 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 !   11.9   0.0   4.5e-05      0.12      69     102 ..      41      74 ..       5      84 .. 0.72
   2 !    9.9   0.0   0.00018      0.45     168     202 ..     121     154 ..     110     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.5e-05
                   Glyco_tranf_2_2  69 laaarNrGaskaesdlvlFlDaDcfissDkfeki 102
                                        ++arN G+++a +d ++FlD D    ++ ++k 
  gi|344210275|ref|YP_004786451.1|  41 VTRARNEGIKQASTDKIVFLDDDSRPRPEYLQKA 74 
                                       579*******************987777777665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00018
                   Glyco_tranf_2_2 168 ilinrraflevGGyDErfrGhgaEDfdlllRlaka 202
                                       + ++r  f  vGG+DE++ G g E+ +l  R+ + 
  gi|344210275|ref|YP_004786451.1| 121 MGVHRDVFKAVGGWDEQM-GWGHEEKELARRVRAE 154
                                       567899************.********99998765 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 !   23.7   0.0   1.5e-08   3.7e-05       2     107 ..      57     151 ..      56     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.5e-08
                   Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelaspevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsgaf 78 
                                       i++lD+D+++ p++l ++ ++l++ e+a + g ++  +v ++++++ ++++++  g d +       v  ++G ++ 
  gi|344210275|ref|YP_004786451.1|  57 IVFLDDDSRPRPEYLQKADELLET-EAA-YAGRTI-HPVDDVFARHFTTHYDW--G-DDPCY-----VNHFWGCNMG 122
                                       99****************999987.433.444444.34679999999999963..3.44554.....4459****** PP

                   Glyco_trans_2_3  79 lrrsalqevggwdgdessvsEDfdmglrl 107
                                       ++r+++++vggwd   +   E ++++ r 
  gi|344210275|ref|YP_004786451.1| 123 VHRDVFKAVGGWDEQMGWGHEEKELARRV 151
                                       *************6655666666666655 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 !   13.7   0.0   1.3e-05     0.032      24     137 ..      47     152 ..      31     184 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                   Glyco_transf_21  24 qaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagvlqaklsglgf 100
                                        ++++a +d +v++D+d r +p+yL++  + le+        + ++ ++ +   ++ a +++t++ + +     ++ 
  gi|344210275|ref|YP_004786451.1|  47 EGIKQASTDKIVFLDDDSRPRPEYLQKADELLET-------EAAYAGRTIHPVDDVFARHFTTHYDWGDD-PCYVNH 115
                                       68899**********************8888885.......44444444444444555666777777777.677788 PP

                   Glyco_transf_21 101 avGksmalrreaLeaiGGfealadeLAeDyalgkllr 137
                                        +G  m ++r++++a+GG  +   +  e  +l++++r
  gi|344210275|ref|YP_004786451.1| 116 FWGCNMGVHRDVFKAVGGWDEQMGWGHEEKELARRVR 152
                                       8888888888888888887776666666666666665 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.1e-05      0.16      97     139 ..       8      50 ..       1      55 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.1e-05
                            PrpR_N  97 ieiytinseeeaeaavkelkaegvevvvGdgvvadlAekaGlk 139
                                       i + + ++e ea +++ke + + +ev+v+d+  ++ A++ G+k
  gi|344210275|ref|YP_004786451.1|   8 IATLKPRDEIEAIQCLKEHAFDDFEVIVCDESPVTRARNEGIK 50 
                                       44444555556889***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1648.09
//
Query:       gi|344210276|ref|YP_004786452.1|  [L=48]
Description: hypothetical protein HAH_5335 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   0.0       0.12   11.9   0.0    1.0  1  PMT       Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.9e-06      0.12     158     186 ..       4      32 ..       1      34 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.9e-06
                               PMT 158 apfsrswwlwllltgvalglavsvKwvgl 186
                                       ++ +r+ +l+l++tg++ g+av+ K  +l
  gi|344210276|ref|YP_004786452.1|   4 EQATRRTILSLVATGLSFGVAVLLKREIL 32 
                                       57899*******************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 318.24
//
Query:       gi|344210277|ref|YP_004786453.1|  [L=378]
Description: glucose-fructose oxidoreductase [Haloarcula hispanica ATCC 33960]
Scores for complete 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   72.8   0.0    6.8e-20   72.1   0.0    1.4  1  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
  ------ inclusion threshold ------
      0.061   13.8   0.1       0.19   12.2   0.1    1.9  1  CoA_binding_2  CoA binding domain
      0.066   12.9   0.1       0.13   12.0   0.1    1.4  1  DUF1349        Protein of unknown function (DUF1349)


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 !   72.1   0.0   1.1e-23   6.8e-20      11     119 ..      23     136 ..       4     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 1.1e-23
                                       H.HHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE...EESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHH CS
                      GFO_IDH_MocA  11 i.gskhlrplnesqrleevvalldpdaeraeavaesfgve...aysdleelladpeidavivatpngtheelakaal 83 
                                       + +++h+ ++++  +  e++a  d  +e+a+++ e+++++   +y+d e++l+  e+d+v+v++p++ h+ +++ ++
  gi|344210277|ref|YP_004786453.1|  23 AmAYRHAGAYRRL-DSCELTACADVVPENARNFGEQWNLPdgnVYTDTEKMLTAVEPDIVSVCVPPHIHAPVVMTCA 98 
                                       3489999888888.888************************************************************ PP

                                       HTT-..EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE CS
                      GFO_IDH_MocA  84 eagk..hvllEKPlattveeakelvelaekkgklvsvg 119
                                       e g+  ++ +EKP+at +e++++++ +++++g +++ +
  gi|344210277|ref|YP_004786453.1|  99 ESGVmdAIHCEKPMATRWEDCQKMASACKRAGIQLTFN 136
                                       ******************************99887765 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.2e-05      0.19      45     104 ..      65     132 ..       3     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.2e-05
                                       S----T......T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT......---HHHHHHHHHTT-E CS
                     CoA_binding_2  45 vyaslae.d.pepvdlvdvftppeatpeivkealalgakavwlqpg......sedeeaaelaeeagir 104
                                       vy ++++     ++d+v+v++pp++ +++v  +++ g+  ++  +       +  +++a+++++agi+
  gi|344210277|ref|YP_004786453.1|  65 VYTDTEKmLtAVEPDIVSVCVPPHIHAPVVMTCAESGVMDAIHCEKpmatrwEDCQKMASACKRAGIQ 132
                                       6777775336899***********************97766666666776666667777777777776 PP

>> DUF1349  Protein of unknown function (DUF1349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.1e-05      0.13      61     103 ..     175     218 ..     168     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.1e-05
                                       -STT-EEEEEEEEETTEEEEEEEEE-SSSEEEEEEEEE.SSEEE CS
                           DUF1349  61 kelyDqaGlmlrvdeenWlKagieyndgaprlgsVvtn.gysDw 103
                                       ++l+D +G +  +  ++W+ agiey+++  ++g+   n  +  w
  gi|344210277|ref|YP_004786453.1| 175 SHLFDLCGYFTDQAMSKWVMAGIEYSEENVQFGAHNENqAIAQW 218
                                       589**********************9988888887766555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.64u 0.37s 00:00:01.01 Elapsed: 00:00:00.58
# Mc/sec: 1962.31
//
Query:       gi|344210278|ref|YP_004786454.1|  [L=501]
Description: export protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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-76  255.9   4.8    4.5e-76  255.9   4.8    1.8  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    9.9e-31  107.1   7.3    9.9e-31  107.1   7.3    2.4  2  Polysacc_synt    Polysaccharide biosynthesis protein
    4.7e-14   52.6  19.1    4.7e-14   52.6  19.1    3.1  3  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
       0.14   12.3   3.2       0.88    9.7   1.8    2.9  2  Insulin_TMD      Insulin receptor trans-membrane segment


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 !  255.9   4.8     1e-79   4.5e-76       1     293 []      47     340 ..      47     340 .. 0.99
   2 ?   -3.5   2.4         1   4.7e+03     116     116 ..     450     450 ..     374     489 .. 0.57

  Alignments for each domain:
  == domain 1  score: 255.9 bits;  conditional E-value: 1e-79
                   Polysacc_synt_3   1 vLARLLspedFGvvaialvvislanlfvdmGlssaliqke.dlteedlstvftfnlvlgllialvlfllapliasfy 76 
                                       ++A LLsp + G+++ial+ +s ++ f+++G++saliq e d+ + +l+t++t++ + g++ia++lfl ap+ias++
  gi|344210278|ref|YP_004786454.1|  47 IVASLLSPRAVGLMGIALLTLSSLKKFSELGIKSALIQAEeDNVDDELNTAWTIETARGTVIAVILFLGAPFIASLF 123
                                       7899***********************************9899999******************************* PP

                   Polysacc_synt_3  77 nqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllsslls 153
                                       n+p + +++rv+al++++ gl +    +++++l+F k f++++ + v++++v++ +Al   +v+AL+ig ++ ++ +
  gi|344210278|ref|YP_004786454.1| 124 NEPAATDLFRVIALSPFIVGLRNPAVVYFQKSLDFHKEFVYRVSGAVAYFVVTVGIALYDPTVYALAIGYIAGDAAR 200
                                       ***************************************************************************** PP

                   Polysacc_synt_3 154 lvllwlaskwrprlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaeits 230
                                       +++++la  +rp ++f+++++k+  sfg++++++++l +l+++ d+ ++G++l ++aLG+Y+ a+rl+++p +eit+
  gi|344210278|ref|YP_004786454.1| 201 FLVSYLADGYRPWPSFDIDVAKKRYSFGKWVTANSILYFLYSRGDDAFVGWALMASALGFYQLAYRLSNAPATEITQ 277
                                       ***************************************************************************** PP

                   Polysacc_synt_3 231 viakVlfPalSrlqddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqWleavp 293
                                       +i++V+f+a+S++q+d +klr+ y+++lr+++l ++P+a+g+a+va  +v+ +++ +W++++p
  gi|344210278|ref|YP_004786454.1| 278 TISSVTFSAYSKVQNDVEKLRSGYFQTLRMTTLASFPAAMGIAAVAPAFVEAFFTPEWQPMIP 340
                                       ************************************************************986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1
                   Polysacc_synt_3 116 k 116
                                       +
  gi|344210278|ref|YP_004786454.1| 450 V 450
                                       1 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.1   7.3   2.2e-34   9.9e-31       2     271 ..      24     288 ..      23     291 .. 0.95
   2 ?   -7.0   8.1         4   1.8e+04     120     162 ..     439     481 ..     375     487 .. 0.50

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 2.2e-34
                     Polysacc_synt   2 lkgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslil 78 
                                       +k   +  +++++ ++l ++ lv++a +l+p  +Gl+ +al +++ l  +++lG+  al+++ +++ ++ el + ++
  gi|344210278|ref|YP_004786454.1|  24 VKSGVWVGVMNVTERGLELLLLVIVASLLSPRAVGLMGIALLTLSSLKKFSELGIKSALIQAEEDNVDD-ELNTAWT 99 
                                       57788999************************************************************6.******* PP

                     Polysacc_synt  79 lnvllvllvlvllfllllliaaflglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvil 155
                                       +++  +++++v+lfl +++ia ++++p+++ l +++al+  ++   +  ++ +++ l + k ++ +++  +  +v++
  gi|344210278|ref|YP_004786454.1| 100 IETARGTVIAVILFLGAPFIASLFNEPAATDLFRVIALSPFIVGLRNPAVVYFQKSLDFHKEFVYRVSGAVAYFVVT 176
                                       ***************************************************************************** PP

                     Polysacc_synt 156 vliavflfldivaavlgavlaalvggivslavlrkkf..rprfvilslklvrellsfsapltisslaillytyidsi 230
                                       v+ia++ +  ++a+++g+ ++  ++ +vs++     +  +p+f i      ++  sf+ ++t++s++  ly + d  
  gi|344210278|ref|YP_004786454.1| 177 VGIALYDPT-VYALAIGYIAGDAARFLVSYLADG--YrpWPSFDID---VAKKRYSFGKWVTANSILYFLYSRGDDA 247
                                       *********.999999999999999999999988..6336888888...99************************** PP

                     Polysacc_synt 231 llglllgaeavGiYnaayqllvaisgllapivtaalfPvfs 271
                                       + g+ l a+a+G+Y++ay+l++a+   ++  +++++f + s
  gi|344210278|ref|YP_004786454.1| 248 FVGWALMASALGFYQLAYRLSNAPATEITQTISSVTFSAYS 288
                                       *****************************999999885555 PP

  == domain 2  score: -7.0 bits;  conditional E-value: 4
                     Polysacc_synt 120 llvgvasfrrglfqglermkyaavsqvveqlsrvilvliavfl 162
                                         +g+a+ ++  +q +    +++   ++  +++ ++v++a+ l
  gi|344210278|ref|YP_004786454.1| 439 ASLGMAAAVTYVYQTVTLTGPVLEFILLVLVGIGVYVALALAL 481
                                       3444455555555555555555555555555555555555544 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 ?   -1.4   0.3       0.5   2.2e+03      41      65 ..      44      69 ..      28      73 .. 0.70
   2 ?   -2.1   2.2      0.82   3.7e+03      94     138 ..     139     176 ..      97     193 .. 0.47
   3 !   52.6  19.1   1.1e-17   4.7e-14       1     141 [.     341     481 ..     341     482 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.5
                   Polysacc_synt_C 41 vklilnllliplf.givGaaiatvla 65
                                      + +i+  ll p+  g++G+a+ t+ +
  gi|344210278|ref|YP_004786454.1| 44 LLVIVASLLSPRAvGLMGIALLTLSS 69
                                      44555556665444888888777765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.82
                   Polysacc_synt_C  94 pllaalvmgivvylllllllgllllaalalllavlvgalvYllll 138
                                       p++++l   +vvy+  +l +        +++  v  ga++Y++++
  gi|344210278|ref|YP_004786454.1| 139 PFIVGLRNPAVVYFQKSLDFHK------EFVYRV-SGAVAYFVVT 176
                                       3333333333333222222211......223333.3333333333 PP

  == domain 3  score: 52.6 bits;  conditional E-value: 1.1e-17
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivG.aaiatvlallvvavlnlya 76 
                                       v+++la++ ++ s+  +++ +  ++gr+++++k +++ +++  ++ ++ + ++gi G aa+ t +  + ++ +  y+
  gi|344210278|ref|YP_004786454.1| 341 VMQLLAIYGLLRSMGATMGPVWKAVGRPDYIAKLSAVRVALIAVFIYPVTMMYGIEGtAALITGIYIFPMMPIDTYL 417
                                       79*************************************************************************** PP

                   Polysacc_synt_C  77 lrrllgikl.ellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllll 141
                                       + r++++++  ++r +  pl+a+l+m+++v+++++ +  + +   l+++l vlvg+ vY++l+l+l
  gi|344210278|ref|YP_004786454.1| 418 IARTINVSPvRVFREVSYPLVASLGMAAAVTYVYQTVTLTGP--VLEFILLVLVGIGVYVALALAL 481
                                       **********88*****************9988888877666..45****************9976 PP

>> Insulin_TMD  Insulin receptor trans-membrane segment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.33   1.5e+03       7      29 ..      92     114 ..      90     120 .. 0.72
   2 ?    9.7   1.8    0.0002      0.88      19      38 ..     457     476 ..     450     478 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.33
                       Insulin_TMD   7 dyldpsnivkIvigPviciilll 29 
                                       d l++   +    g vi +il l
  gi|344210278|ref|YP_004786454.1|  92 DELNTAWTIETARGTVIAVILFL 114
                                       55566666666779999999987 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0002
                       Insulin_TMD  19 igPviciillllvigavfvv 38 
                                        gPv  +ill+lv+ +v+v 
  gi|344210278|ref|YP_004786454.1| 457 TGPVLEFILLVLVGIGVYVA 476
                                       69****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2938.81
//
Query:       gi|344210279|ref|YP_004786455.1|  [L=166]
Description: hypothetical protein HAH_5338 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1037.75
//
Query:       gi|344210280|ref|YP_004786456.1|  [L=722]
Description: carbohydrate binding module (family 6) protein [Haloarcula hispanica ATCC 33960]
Scores for 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-69  228.8  13.7    6.9e-24   84.1   0.8    3.6  3  DUF5010_C        DUF5010 C-terminal domain
      2e-52  176.8  21.8    4.2e-19   69.1   2.4    4.3  4  CBM_6            Carbohydrate binding module (family 6)
    7.7e-05   22.1   3.6       0.58    9.4   0.0    3.3  3  Glyco_hydro_114  Glycoside-hydrolase family GH114
    0.00022   21.6   0.2       0.74   10.1   0.0    4.3  4  Endotoxin_C      delta endotoxin
  ------ inclusion threshold ------
      0.017   14.6   0.0        5.8    6.5   0.0    3.6  3  TcfC             E-set like domain
        1.2    8.7   8.5        1.5    8.5   0.3    3.1  3  Neuraminidase    Neuraminidase-like domain
        4.6    6.8  10.4        9.6    5.7  10.4    1.4  1  NESP55           Neuroendocrine-specific golgi protein P55 (N


Domain annotation for each model (and alignments):
>> DUF5010_C  DUF5010 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.3     5e-24   1.3e-20       1     111 [.     239     348 ..     239     349 .. 0.97
   2 !   84.1   0.8   2.7e-27   6.9e-24       1     111 [.     397     506 ..     397     507 .. 0.97
   3 !   78.4   1.3   1.6e-25   4.2e-22       1     111 [.     553     662 ..     553     663 .. 0.96

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 5e-24
                         DUF5010_C   1 rsgnldikktdDvnggwnvtsteaGewlewkeipfkaGavtlkvryattkeaakvrfvidgtagpsvelpaTgglqe 77 
                                       r+ ++di++t+D+ g +n++  +aGewle+   ++++G++ ++vr+a++ ++ ++ + +++++  +v +p+Tg++  
  gi|344210280|ref|YP_004786456.1| 239 RDTDVDIRPTEDKSGKYNIGYFQAGEWLEYT-TDVSPGTYDIRVRVASALSDGRLELSLGDRTLTTVAVPNTGDWTS 314
                                       67899*************************7.69******************************************* PP

                         DUF5010_C  78 wetvdagtlkieakgyhtvkleiveGnidlnylt 111
                                       wetv +  ++ie +   t+++e  + ++++n+l+
  gi|344210280|ref|YP_004786456.1| 315 WETVTVEDIEIESEQQSTLRVEALDSGVEFNWLE 348
                                       ********************************86 PP

  == domain 2  score: 84.1 bits;  conditional E-value: 2.7e-27
                         DUF5010_C   1 rsgnldikktdDvnggwnvtsteaGewlewkeipfkaGavtlkvryattkeaakvrfvidgtagpsvelpaTgglqe 77 
                                       r+ ++di++t+D  g++n++  e Gewle++  ++++G++ lkvr+att++++++rf++++++  +v++p+Tgg+ +
  gi|344210280|ref|YP_004786456.1| 397 RDTDVDIRQTQDDSGEYNIGYFEDGEWLEYS-ADVSPGQYDLKVRVATTQDDRQLRFHLGDRELGTVDVPNTGGWTT 472
                                       67899*************************6.7******************************************** PP

                         DUF5010_C  78 wetvdagtlkieakgyhtvkleiveGnidlnylt 111
                                       wet+ a  ++i+a+g + +++e +  +id+n+++
  gi|344210280|ref|YP_004786456.1| 473 WETAVAEDVTIDADGQQVLRVEAIGSGIDFNWAE 506
                                       ********************************86 PP

  == domain 3  score: 78.4 bits;  conditional E-value: 1.6e-25
                         DUF5010_C   1 rsgnldikktdDvnggwnvtsteaGewlewkeipfkaGavtlkvryattkeaakvrfvidgtagpsvelpaTgglqe 77 
                                       r+ ++di++t+D  g +nv+  e Gewle+   ++ aG++ + vr+att+++++++f +dg +  +v++p+Tgg+ +
  gi|344210280|ref|YP_004786456.1| 553 RDSDVDIRETQDNSGKYNVGYFEDGEWLEYTA-EVPAGTYDIDVRVATTRDNRQLQFSLDGEQLGTVDVPNTGGWTT 628
                                       67899*************************74.6779**************************************** PP

                         DUF5010_C  78 wetvdagtlkieakgyhtvkleiveGnidlnylt 111
                                       wet+ +  ++++ +g h ++++ v  +id+n+++
  gi|344210280|ref|YP_004786456.1| 629 WETATLPDVTVQDGGEHVIQVKAVGSGIDFNWFE 662
                                       ********************************97 PP

>> CBM_6  Carbohydrate binding module (family 6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       6.7   1.7e+04      53      69 ..     177     193 ..     168     202 .. 0.64
   2 !   57.9   0.3   4.8e-19   1.2e-15       6     124 ..     238     350 ..     236     351 .. 0.86
   3 !   60.2   3.4   8.9e-20   2.3e-16       8     124 ..     398     508 ..     371     509 .. 0.93
   4 !   69.1   2.4   1.6e-22   4.2e-19       8     124 ..     554     664 ..     538     665 .. 0.92

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 6.7
                                       EEESSSEEEEEEEESST CS
                             CBM_6  53 vasgaaggsielrldsa 69 
                                       v+ +++  s+++++ds 
  gi|344210280|ref|YP_004786456.1| 177 VSRSGGDYSLTISTDST 193
                                       55555556777777772 PP

  == domain 2  score: 57.9 bits;  conditional E-value: 4.8e-19
                                       SEEES-EEEE--STTTSEEEE---TT-EEEEEEEEESSTEEEEEEEEEEESSSEEEEEEEESSTTSSEEEEEEE--- CS
                             CBM_6   6 dkqsgvslekataagggkavgyinnGdwlaYkdvdfgsggaysvearvasgaaggsielrldsatgtlvgtvsvpst 82 
                                       +++++v++ ++ +++g++++gy+++G+wl+Y+  d+ s g+y++++rvas+ + g++el+l++   + + tv+vp+t
  gi|344210280|ref|YP_004786456.1| 238 NRDTDVDIRPTEDKSGKYNIGYFQAGEWLEYT-TDV-SPGTYDIRVRVASALSDGRLELSLGD---RTLTTVAVPNT 309
                                       67899********99*****************.995.66777*********************...9999******* PP

                                       SSTTEEEEEEEEEEE-SEEEEEEEEEECSST---EEEEEEEE CS
                             CBM_6  83 ggwqtyvtvsanvtlptGvhdlylvftggaeylfnldwfkft 124
                                       g+w++++tv+ +  +   +++  l++ + +   + ++w++f+
  gi|344210280|ref|YP_004786456.1| 310 GDWTSWETVTVEDIEIESEQQSTLRVEALD-SGVEFNWLEFD 350
                                       ******999987666667777777777754.55888888886 PP

  == domain 3  score: 60.2 bits;  conditional E-value: 8.9e-20
                                       EES-EEEE--STTTSEEEE---TT-EEEEEEEEESSTEEEEEEEEEEESSSEEEEEEEESSTTSSEEEEEEE---SS CS
                             CBM_6   8 qsgvslekataagggkavgyinnGdwlaYkdvdfgsggaysvearvasgaaggsielrldsatgtlvgtvsvpstgg 84 
                                       +++v++ ++++ +g +++gy+++G+wl+Y+  d+   g+y++++rva++    ++ ++l++   + +gtv vp+tgg
  gi|344210280|ref|YP_004786456.1| 398 DTDVDIRQTQDDSGEYNIGYFEDGEWLEYS-ADVS-PGQYDLKVRVATTQDDRQLRFHLGD---RELGTVDVPNTGG 469
                                       48999*9999999*****************.9965.5666*********************...************* PP

                                       TTEE.EEEEEEEEE-S.EEEEEEEEEECSST---EEEEEEEE CS
                             CBM_6  85 wqty.vtvsanvtlpt.Gvhdlylvftggaeylfnldwfkft 124
                                       w+t+ + v + vt  + G++ l++++ g++   ++++w +f+
  gi|344210280|ref|YP_004786456.1| 470 WTTWeTAVAEDVTIDAdGQQVLRVEAIGSG---IDFNWAEFE 508
                                       ****777999******************87...999999996 PP

  == domain 4  score: 69.1 bits;  conditional E-value: 1.6e-22
                                       EES-EEEE--STTTSEEEE---TT-EEEEEEEEESSTEEEEEEEEEEESSSEEEEEEEESSTTSSEEEEEEE---SS CS
                             CBM_6   8 qsgvslekataagggkavgyinnGdwlaYkdvdfgsggaysvearvasgaaggsielrldsatgtlvgtvsvpstgg 84 
                                       +s+v++ ++++ +g+++vgy+++G+wl+Y+  ++++g   ++ +rva++  + +++++ld+   + +gtv vp+tgg
  gi|344210280|ref|YP_004786456.1| 554 DSDVDIRETQDNSGKYNVGYFEDGEWLEYT-AEVPAGTY-DIDVRVATTRDNRQLQFSLDG---EQLGTVDVPNTGG 625
                                       599********89*****************.99987666.*********************...9************ PP

                                       TTEEEEEE.EEEEE-S.EEEEEEEEEECSST---EEEEEEEE CS
                             CBM_6  85 wqtyvtvs.anvtlpt.Gvhdlylvftggaeylfnldwfkft 124
                                       w+t++t +   vt +  G+h +++++ g++   ++++wf+f 
  gi|344210280|ref|YP_004786456.1| 626 WTTWETATlPDVTVQDgGEHVIQVKAVGSG---IDFNWFEFR 664
                                       ****7766257888889***********87...*******97 PP

>> Glyco_hydro_114  Glycoside-hydrolase family GH114
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00023      0.58      26      57 ..     240     271 ..     215     331 .. 0.80
   2 !    5.8   0.3    0.0029       7.3      19      57 ..     391     429 ..     371     452 .. 0.76
   3 !    6.1   0.1    0.0023       5.9      18      56 ..     546     584 ..     529     617 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00023
                   Glyco_hydro_114  26 dtsaatiaalkakgkkviCYfsaGevedwrpd 57 
                                       dt+++   +  ++gk++i Yf aGe+ ++ +d
  gi|344210280|ref|YP_004786456.1| 240 DTDVDIRPTEDKSGKYNIGYFQAGEWLEYTTD 271
                                       44455333445789************988875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0029
                   Glyco_hydro_114  19 vydiDlfdtsaatiaalkakgkkviCYfsaGevedwrpd 57 
                                        yd  + dt+++  ++  ++g ++i Yf+ Ge+ ++ +d
  gi|344210280|ref|YP_004786456.1| 391 EYDTSYRDTDVDIRQTQDDSGEYNIGYFEDGEWLEYSAD 429
                                       577777788888666677789************888775 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0023
                   Glyco_hydro_114  18 dvydiDlfdtsaatiaalkakgkkviCYfsaGevedwrp 56 
                                       + yd+ + d++++  ++  ++gk+++ Yf+ Ge+ ++ +
  gi|344210280|ref|YP_004786456.1| 546 SEYDLGYRDSDVDIRETQDNSGKYNVGYFEDGEWLEYTA 584
                                       5688777888888777788899************88876 PP

>> Endotoxin_C  delta endotoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00029      0.74      48     122 ..     271     336 ..     231     352 .. 0.80
   2 ?    3.5   0.0     0.033        85      50      86 ..     431     467 ..     415     471 .. 0.80
   3 ?    2.3   0.0     0.079     2e+02      51      86 ..     588     623 ..     564     641 .. 0.81
   4 ?   -2.5   0.3       2.3     6e+03      61      85 ..     666     689 ..     644     708 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00029
                                       CSS-EEEEEEEEEEE.SS-EEEEEEEEETTCCCEEEE---TT-GGGCC-SCCCEEEEEEEE-EEEECC-CEEEEEE CS
                       Endotoxin_C  48 nstsqrYriRiRYAs.nsdtklsvsignssinaqvnlpstmsggenltlkyesFkyvefsttftfseseeetltls 122
                                       + +  +Y iR+R+As  sd++l++s+g+++ + +v +p+t +     t    s+++v++++ +++++++++tl+++
  gi|344210280|ref|YP_004786456.1| 271 DVSPGTYDIRVRVASaLSDGRLELSLGDRTLT-TVAVPNTGDW----T----SWETVTVED-IEIESEQQSTLRVE 336
                                       566789*********6799************9.9999999877....3....566666654.66666665666665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.033
                                       S-EEEEEEEEEEESS.-EEEEEEEEETTCCCEEEE--- CS
                       Endotoxin_C  50 tsqrYriRiRYAsns.dtklsvsignssinaqvnlpst 86 
                                       +  +Y +++R+A+++ d +l++++g+++   +v++p+t
  gi|344210280|ref|YP_004786456.1| 431 SPGQYDLKVRVATTQdDRQLRFHLGDRELG-TVDVPNT 467
                                       5679********965167899999999887.7777776 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.079
                                       -EEEEEEEEEEESS-.EEEEEEEEETTCCCEEEE--- CS
                       Endotoxin_C  51 sqrYriRiRYAsnsd.tklsvsignssinaqvnlpst 86 
                                       + +Y i +R+A+++d  +l++s+++++   +v++p+t
  gi|344210280|ref|YP_004786456.1| 588 AGTYDIDVRVATTRDnRQLQFSLDGEQLG-TVDVPNT 623
                                       568*********76515788888888776.7777766 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 2.3
                                       EESS-EEEEEEEEETTCCCEEEE-- CS
                       Endotoxin_C  61 Asnsdtklsvsignssinaqvnlps 85 
                                       A++++t+++ +++ ++++ + ++p+
  gi|344210280|ref|YP_004786456.1| 666 AAETETSTETETATQTST-ETETPT 689
                                       444444444444444444.333333 PP

>> TcfC  E-set like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.024        61      38      54 ..     269     285 ..     256     292 .. 0.79
   2 ?   -0.9   0.0      0.47   1.2e+03      43      54 ..     432     443 ..     427     451 .. 0.80
   3 ?    6.5   0.0    0.0023       5.8      38      54 ..     583     599 ..     570     607 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.024
                              TcfC  38 tssLPsGiYeveirvye 54 
                                       t++   G+Y++++rv +
  gi|344210280|ref|YP_004786456.1| 269 TTDVSPGTYDIRVRVAS 285
                                       778889********976 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.47
                              TcfC  43 sGiYeveirvye 54 
                                        G Y++++rv  
  gi|344210280|ref|YP_004786456.1| 432 PGQYDLKVRVAT 443
                                       699******986 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0023
                              TcfC  38 tssLPsGiYeveirvye 54 
                                       t + P G+Y++++rv  
  gi|344210280|ref|YP_004786456.1| 583 TAEVPAGTYDIDVRVAT 599
                                       6789***********76 PP

>> Neuraminidase  Neuraminidase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.7     0.015        37      34      80 ..     299     350 ..     298     454 .. 0.69
   2 ?   -1.0   0.0      0.48   1.2e+03      41      68 ..     464     495 ..     448     583 .. 0.67
   3 ?    8.5   0.3   0.00058       1.5      40     104 ..     619     688 ..     602     704 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.015
                     Neuraminidase  34 RtldlegelsanaWspWekidldi.....kegeyvrpvvangRlylfwpefe 80 
                                       Rtl++    + + W+ We ++++      ++++++r     + +   w+ef+
  gi|344210280|ref|YP_004786456.1| 299 RTLTTVAVPNTGDWTSWETVTVEDieiesEQQSTLRVEALDSGVEFNWLEFD 350
                                       666666677899********98533666655566777666667777777776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.48
                     Neuraminidase  41 elsanaWspWek.....idldikegeyvrpvva 68 
                                         + + W+ We      +++d  +g++v+ v a
  gi|344210280|ref|YP_004786456.1| 464 VPNTGGWTTWETavaedVTIDA-DGQQVLRVEA 495
                                       5567788888752111133333.6666666654 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00058
                     Neuraminidase  40 gelsanaWspWekidldi...keg.eyvrpvvang.Rlylfwpefeekakskektvddlgdqttgssees 104
                                       +  + + W+ We  +l+    ++g e+v+ v a g  +   w+ef e+a+++++t +++++qt +++e++
  gi|344210280|ref|YP_004786456.1| 619 DVPNTGGWTTWETATLPDvtvQDGgEHVIQVKAVGsGIDFNWFEFREAAETETSTETETATQTSTETETP 688
                                       6678899*******99877995555*****99888467788*****666666666555555554443333 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 ?    5.7  10.4    0.0037       9.6     110     149 ..     666     705 ..     652     714 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0037
                            NESP55 110 eyetetdseteseseieseteietepetesetapttepet 149
                                         etet +ete+ ++  +ete  te et +et   te  t
  gi|344210280|ref|YP_004786456.1| 666 AAETETSTETETATQTSTETETPTETETATETEIMTESST 705
                                       3345555555555555555555444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (722 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 4300.80
//
Query:       gi|344210281|ref|YP_004786457.1|  [L=419]
Description: hypothetical protein HAH_5340 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   16.6   0.1      0.025   14.6   0.1    2.1  2  Mtd_N     Major tropism determinant N-terminal domain


Domain annotation for each model (and alignments):
>> Mtd_N  Major tropism determinant N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   1.4e-06     0.025      24      36 ..      52      64 ..      33      65 .. 0.78
   2 ?   -1.5   0.0      0.15   2.6e+03      13      31 ..     114     132 ..     108     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-06
                                      ETTTTEEEEEESS CS
                             Mtd_N 24 dTDtkelkvGDGs 36
                                       TDt+++++GDGs
  gi|344210281|ref|YP_004786457.1| 52 ATDTGTVYIGDGS 64
                                      6***********9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.15
                                       T----TTEEEEETTTTEEE CS
                             Mtd_N  13 npvLaaGElgfdTDtkelk 31 
                                       ++ L  GE  f +Dt +lk
  gi|344210281|ref|YP_004786457.1| 114 TVKLVSGENYFPSDTIKLK 132
                                       578999**99999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2707.49
//
Query:       gi|344210282|ref|YP_004786458.1|  [L=432]
Description: hypothetical protein HAH_5341 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2721.80
//
Query:       gi|344210283|ref|YP_004786459.1|  [L=393]
Description: group 1 glycosyl transferase [Haloarcula hispanica ATCC 33960]
Scores for complete 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   0.0      2e-34  118.6   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    7.2e-31  107.4   0.0    1.3e-30  106.6   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    4.1e-11   43.2   0.0    7.7e-11   42.3   0.0    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
      4e-09   37.1   0.0    1.7e-08   35.1   0.0    1.9  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    2.8e-07   30.8   0.0    5.3e-07   29.9   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 !  118.6   0.0   5.6e-38     2e-34       3     169 ..     191     354 ..     189     357 .. 0.96

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 5.6e-38
                                       HHHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEE CS
                   Glycos_transf_1   3 ekkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflg 79 
                                        + r +l ++++  ++ +vgrl+++Kg+  l++a++++  +  p+++lv++G+g+++++l +++++l+  d v+flg
  gi|344210283|ref|YP_004786459.1| 191 AELRSELDIPTGATVVGTVGRLVERKGHFDLLDAWPTIVSE-IPDAHLVFVGDGADRERLTERVDSLGCADSVHFLG 266
                                       577889999*****************************987.*********************************** PP

                                       CCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHH CS
                   Glycos_transf_1  80 evsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkll 156
                                            d+++ll + d+f++ps++Eg++ +++EAmaa lp++a+ + g +++++++ tGl+v+   ++++a a ++l 
  gi|344210283|ref|YP_004786459.1| 267 TRQ--DVPALLGAMDVFAFPSHYEGLPGAVIEAMAAELPIVATPVDGTSDLLENYRTGLFVDVQAPDEIAWATIRLH 341
                                       **9..************************************************************************ PP

                                       HSHHHHHHHHHHH CS
                   Glycos_transf_1 157 edeelrerlgena 169
                                       + ++l+e lg +a
  gi|344210283|ref|YP_004786459.1| 342 QHQPLAETLGTAA 354
                                       ****999999887 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 !  106.6   0.0   3.5e-34   1.3e-30       3     133 ..     205     342 ..     203     343 .. 0.92

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 3.5e-34
                                       EEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---THHHHHHHH-S CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfvedlaellaaad 74 
                                       v+++vGrl+ ++kg+  ll+a+p + ++  d++lv+vGdg  r e+l e+++  g +++v+f+G ++d+++ll a+d
  gi|344210283|ref|YP_004786459.1| 205 VVGTVGRLV-ERKGHFDLLDAWPTIVSEipDAHLVFVGDGAdR-ERLTERVDslGCADSVHFLGTRQDVPALLGAMD 279
                                       7899****6.55**************88855*********955.69*9999779999******************** PP

                                       EEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  75 vfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLle 133
                                       vf +Ps  eg++ +++Eamaa+lp+Vat+v g+++++   ++gl v+ + p+++a a +rL +
  gi|344210283|ref|YP_004786459.1| 280 VFAFPShyEGLPGAVIEAMAAELPIVATPVDGTSDLLenYRTGLFVDVQAPDEIAWATIRLHQ 342
                                       ***********************************998559*******9***********976 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   2.2e-14   7.7e-11       1     169 [.      17     183 ..      17     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 2.2e-14
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev.........elvvrvprvplpllkrllrslaflrrlrrll 68 
                                       vGG+er + +La++     ++Vt+ t  +  ple e           +  rv    + + + +l +l +++++   +
  gi|344210283|ref|YP_004786459.1|  17 VGGAERTLIDLANEVNGEEYDVTIWTIFSTNPLETELspevtvrslTDAGRVANGAIEGVESPLVYLLAPLKFCLTA 93 
                                       7************************99999999999999988877755556666666677788899999999999** PP

                    Glyco_transf_4  69 krekpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrl.lrradrviavSeat 144
                                       +re+pD++ +  ++  + a la      + +++ +              ++++++r++  r+ ++ +d ++ +S a 
  gi|344210283|ref|YP_004786459.1|  94 RREQPDLIQSFLFYDNVIARLAGVF-CSATIITGIREVP----------NEEPFVRRVIDRMtISLSDVIVSNSTAG 159
                                       ***************9999887776.6777777777776..........45555555544444************** PP

                    Glyco_transf_4 145 adelrerygvppekitVipnGvDle 169
                                       +d+ ++  g ++e+++V++nG ++e
  gi|344210283|ref|YP_004786459.1| 160 RDYAVK-RGAEEENVAVVYNGRNIE 183
                                       ******.**************8876 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 !   35.1   0.0   4.7e-12   1.7e-08       1     160 []      18     179 ..      18     179 .. 0.76
   2 ?   -0.7   0.1      0.48   1.7e+03      85     106 ..     289     311 ..     240     360 .. 0.66

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 4.7e-12
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlp.vprrp........spladlaalralrrllr 68 
                                       gG++r   +la +   + ++Vt++t   +++ + +  + v+v++l  ++r          spl  l a+  +  +  
  gi|344210283|ref|YP_004786459.1|  18 GGAERTLIDLANEVNGEEYDVTIWTIFSTNPLETELSPEVTVRSLTdAGRVAngaiegveSPLVYLLAPLKFCLTA- 93 
                                       8************************555666665667778887774344332222322224555566666666666. PP

                   Glyco_trans_4_4  69 qrrerpdvvhahsptaglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeelr 145
                                        rre+pd+++++ ++ + +arla +  ++ ++  +++   + + ++vrr++   +r +++  d+++++s+a +++++
  gi|344210283|ref|YP_004786459.1|  94 -RREQPDLIQSFLFYDNVIARLAGVFCSATIITGIREV--PNEEPFVRRVI---DRMTISLSDVIVSNSTAGRDYAV 164
                                       .*************999999999966677777767664..33345665555...777999***************** PP

                   Glyco_trans_4_4 146 algvpadrvvvvpng 160
                                        +g+  ++v+vv ng
  gi|344210283|ref|YP_004786459.1| 165 KRGAEEENVAVVYNG 179
                                       **************8 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.48
                   Glyco_trans_4_4  85 glaarlar.rrrgiplvvtlhgl 106
                                       gl+++++  +++ +p+v t+ + 
  gi|344210283|ref|YP_004786459.1| 289 GLPGAVIEaMAAELPIVATPVDG 311
                                       33333332246778888888642 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 !   29.9   0.0   1.5e-10   5.3e-07       3      88 ..     282     369 ..     280     373 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.5e-10
                   Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarerv 77 
                                        +ps++e++ + + Ea+a+  ++++++ +g  +l+++ +++++++   ++e+a +  +l+++  +++ +++aa +r+
  gi|344210283|ref|YP_004786459.1| 282 AFPSHYEGLPGAVIEAMAAELPIVATPVDGTSDLLENYRTGLFVDvqAPDEIAWATIRLHQHQPLAETLGTAAGQRA 358
                                       57999*********************99************************************************* PP

                   Glyco_trans_1_2  78 laehtydhrae 88 
                                        +e+t +  ++
  gi|344210283|ref|YP_004786459.1| 359 ASEFTIESMVD 369
                                       *****987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2419.54
//
Query:       gi|344210284|ref|YP_004786460.1|  [L=398]
Description: N-acetylgalactosamine-4-sulfatase [Haloarcula hispanica ATCC 33960]
Scores for complete 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   0.2    1.1e-13   51.2   0.1    2.3  2  Sulfatase     Sulfatase
     0.0018   17.9   0.3      0.046   13.3   0.0    2.1  2  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
      0.003   16.2   0.0     0.0036   16.0   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 !    4.1   0.0    0.0044        26      30      69 ..      23      61 ..       9      85 .. 0.80
   2 !   51.2   0.1   1.9e-17   1.1e-13     172     307 ..     111     247 ..      91     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0044
                                      HHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSS CS
                         Sulfatase 30 drlaeeglrftnfysaaplcspsraalltgryphnsgvas 69
                                      d+lae g + +   +a++++  s  +lltg+ p+ns++ s
  gi|344210284|ref|YP_004786460.1| 23 DDLAELGQTHKTI-AASTHTPTSFGSLLTGLLPPNSNIHS 61
                                      6778888888777.5778*****************99654 PP

  == domain 2  score: 51.2 bits;  conditional E-value: 1.9e-17
                                       SEEEEEEE-TTSSST....CTCGGHTCCGSTTTTCCCCCCH...HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGE CS
                         Sulfatase 172 pfflylatlapHapp....eapdeyakkyatffddgseaar...qlleaylnsveyvDdligrvlaaLeenglldnt 241
                                       pf+ +    + Hap+    + + ey +++a   + ++   +    ++  y+n v +  +  +rvl++Le+ gl+++t
  gi|344210284|ref|YP_004786460.1| 111 PFVHVARRPGGHAPYdgfdWDDYEYRNETA--LEYLWRVSSdpeTARKDYYNGVDRSFEEFKRVLQTLERRGLREDT 185
                                       666666677888877664444444444433..33455554477799******************************* PP

                                       EEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTSHCEEECSEEEGGGHHHHHHHHT CS
                         Sulfatase 242 lvvftSDhgasleesngplrggkganayeggtrvPllvwwpgekaprvseelvshiDlfptildla 307
                                       lv++tSDhg+ l+e   +   g ++ a+++ + vP+    p+  ++  +++l +h+D++pt+++++
  gi|344210284|ref|YP_004786460.1| 186 LVIYTSDHGEVLGE---YGYFGHTHLATPEVVYVPTSFIHPELDSS-GENGLLHHVDILPTVASAM 247
                                       ************66...55555554677777777776666666666.99**************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 !    3.4   0.1    0.0076        46      43     128 ..      39     148 ..      30     168 .. 0.63
   2 !   13.3   0.0   7.8e-06     0.046     197     234 ..     155     195 ..     143     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0076
                                       -SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEEEEEETTTTGG...................GGGCTT......S- CS
                      Phosphodiest  43 tlTfpnhaslvTGlyPgeHGivgNtfydrktgeyvvfvtededa...................prwwqg......ep 94 
                                       t+T+++  sl+TGl P +  i +++   +++ +  vf++e++++                   p           ep
  gi|344210284|ref|YP_004786460.1|  39 THTPTSFGSLLTGLLPPNSNIHSFKHSVPANVRS-VFDIESHEVsiaaqggmnhsiaemfanpP----RkpiddvEP 110
                                       89************************99999997.88888888767777776655544444431....033444544 PP

                                       HHHHHHHTH.TTC.EEEESETTTTSEBTTCT.SC.....T CS
                      Phosphodiest  95 iwdtaakar.glk.aaalfwpgsevdystyyylvs....e 128
                                        ++++a+   g++  + + w   + +y+++ +l++    +
  gi|344210284|ref|YP_004786460.1| 111 PFVHVARRPgGHApYDGFDWD--DYEYRNETALEYlwrvS 148
                                       444444444455533344443..44455555555455554 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 7.8e-06
                                       HHHHHHHHHHHHHHH...HHHHHHTTGTTTEEEEEEES--- CS
                      Phosphodiest 197 vedalrrvDkaigdL...lealderglsaetniilvSDHGm 234
                                        +d++  vD+  +++   l+ l++rgl+++t +i +SDHG 
  gi|344210284|ref|YP_004786460.1| 155 RKDYYNGVDRSFEEFkrvLQTLERRGLREDTLVIYTSDHGE 195
                                       667788888776543333999*******************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 !   16.0   0.0   6.1e-07    0.0036     301     349 ..     152     200 ..     133     280 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.1e-07
                            DUF229 301 nslshdkfnllealDedllkylkklekkgllentlvlllsDHGlrfgkl 349
                                       ++   d++n + +  e++ ++l++le++gl e+tlv+  sDHG   g++
  gi|344210284|ref|YP_004786460.1| 152 ETARKDYYNGVDRSFEEFKRVLQTLERRGLREDTLVIYTSDHGEVLGEY 200
                                       5567899999999999***************************766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.34s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2387.66
//
Query:       gi|344210285|ref|YP_004786461.1|  [L=326]
Description: glycosyltransferase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-27   94.9   0.1    7.2e-27   94.3   0.1    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    2.6e-17   63.5   0.0    3.2e-17   63.2   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    5.9e-11   42.4   0.0    8.5e-11   41.8   0.0    1.4  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.051   13.0   0.0      0.092   12.1   0.0    1.3  1  Rhamno_transf    Putative rhamnosyl transferase
       0.56   10.6   2.9         20    5.6   0.3    2.6  2  Atu4866          Agrobacterium tumefaciens protein Atu4866


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 !   94.3   0.1     2e-30   7.2e-27       1     131 [.      15     143 ..      15     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 2e-30
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       svv pty +++ l+ + +s+++q +yp++e+iv+DD S+  +++ l     ++  v  +r+ en+G   a+n+g+++
  gi|344210285|ref|YP_004786461.1|  15 SVVLPTYKRPDRLRSAARSVAEQ-TYPNIELIVIDDHSPQPAADTLAGEPLRGIEVNCVRHQENRGANQARNTGIER 90 
                                       8**********************.**************88887777777679************************* PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-S CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkr 131
                                       a g+yi++lD+Dd++d +++ + v ++ +  ad v +    ++++ + ++r   
  gi|344210285|ref|YP_004786461.1|  91 AEGEYIALLDDDDAWDSEKIARQVTEMAE-SADSVGVVYTGCEYDYGDYTRDVI 143
                                       *****************************.**************9999998754 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 !   63.2   0.0     9e-21   3.2e-17       4     132 ..      14     139 ..      10     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 9e-21
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       ++v+ pt++++d+l++  +s++ q+yp++e++v++d s + +++++ +  ++l +++v++v+ ++n   +g+ +a n
  gi|344210285|ref|YP_004786461.1|  14 VSVVLPTYKRPDRLRSAARSVAEQTYPNIELIVIDDHSPQPAADTLAG--EPLRGIEVNCVRHQEN---RGANQARN 85 
                                       89*******************************************965..99*********88885...6899999* PP

                   Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqff..ltpkvgavgtpvfllnrstl 132
                                        +++++++++++l+DdD+ ++ + ++r+++ +   +++vg+v+t  + ++++++
  gi|344210285|ref|YP_004786461.1|  86 TGIERAEGEYIALLDDDDAWDSEKIARQVTEMaeSADSVGVVYTGCEYDYGDYT 139
                                       ********************999999998888766669****998888877766 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 !   41.8   0.0   2.4e-14   8.5e-11       1     217 [.      15     212 ..      15     261 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 2.4e-14
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllv.ylkdeddkayslaaarNrG 76 
                                       svv+p ++  +r  ++   +  a +  ++ieliv+dd S+++ ++ +        +v  +++  ++  +  +arN G
  gi|344210285|ref|YP_004786461.1|  15 SVVLPTYKRPDR--LRSAARSVAEQTYPNIELIVIDDHSPQPAADTLAGEPLRGIEVnCVRH--QENRGANQARNTG 87 
                                       577777777777..6666667777777***************99999875554455533344..56779999***** PP

                   Glyco_tranf_2_2  77 askaesdlvlFlDaDcfissDkfekilklitikklrenidaa.vvlpvvdlnkedsevlkdvedltassrvledlla 152
                                       +++ae++++  lD D+ + s+k+++++      ++ e  d+  vv++  ++   d   + +    ta+++v +dll 
  gi|344210285|ref|YP_004786461.1|  88 IERAEGEYIALLDDDDAWDSEKIARQVT-----EMAESADSVgVVYTGCEYDYGD---YTRDVIFTAEGDVTKDLLL 156
                                       ********************99999988.....9999888753788765554333...3333456889999999998 PP

                   Glyco_tranf_2_2 153 akstlvkffapssssilinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellyka 217
                                             + f + s ++++    + + G  D+rf  ++  D + l+Rl ++ ++  + p  l+y++
  gi|344210285|ref|YP_004786461.1| 157 -----GESFGEFS-TLMVSADIIPQAGLPDDRF--PSWQDREWLIRLSLHSEFR-VIPEVLTYRN 212
                                       .....66677665.5667788888999999999..9999999999999987765.9999999986 PP

>> Rhamno_transf  Putative rhamnosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.6e-05     0.092      49     138 ..      32     116 ..      29     131 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
                     Rhamno_transf  49 pslraQtdqdFtllvligdtlPekfrerladlladlpqvrlivvppmehrealrevlreareaseaevlqfRlDdDD 125
                                       +s+++Qt ++ +l+ +i+d++P++  + la   + l  + +  v  +e+r a ++   + ++a+ ++++   lDdDD
  gi|344210285|ref|YP_004786461.1|  32 RSVAEQTYPNIELI-VIDDHSPQPAADTLAG--EPLRGIEVNCVRHQENRGANQARNTGIERAEGEYIA--LLDDDD 103
                                       79**********86.68***********985..667777777777777777766663455555555554..49**** PP

                     Rhamno_transf 126 avsvdyvarlrra 138
                                       a +++ +ar  ++
  gi|344210285|ref|YP_004786461.1| 104 AWDSEKIARQVTE 116
                                       ****999886554 PP

>> Atu4866  Agrobacterium tumefaciens protein Atu4866
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.012        42      24      56 ..      73     105 ..      68     120 .. 0.87
   2 ?    5.6   0.3    0.0056        20      45      67 ..     134     156 ..     117     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.012
                           Atu4866  24 RYdEaRgeresAyqGryevtgdeidYlDDtGFt 56 
                                       R +E Rg  +   +G  + +g+ i+ lDD   +
  gi|344210285|ref|YP_004786461.1|  73 RHQENRGANQARNTGIERAEGEYIALLDDDDAW 105
                                       899*************************97655 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0056
                           Atu4866  45 deidYlDDtGFtAdGefvddvLh 67 
                                       d  dY+ D+ FtA+G+++ d L 
  gi|344210285|ref|YP_004786461.1| 134 DYGDYTRDVIFTAEGDVTKDLLL 156
                                       5668999***********99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2065.22
//
Query:       gi|344210286|ref|YP_004786462.1|  [L=596]
Description: hypothetical protein HAH_5345 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   8.2     0.0012   19.1   8.2    3.2  3  PMT_2         Dolichyl-phosphate-mannose-protein mannosyltran
  ------ inclusion threshold ------
      0.048   12.0  20.4       0.34    9.2  20.4    2.0  1  PTPS_related  6-pyruvoyl-tetrahydropterin synthase related do
        1.7    9.5   7.7         13    6.6   0.3    3.4  4  TMEM220       Transmembrane family 220, helix
        5.1    6.7   9.0       0.42   10.3   1.6    2.6  2  DUF4956       Domain of unknown function (DUF4956)
        5.4    7.8  24.7       0.46   11.3   3.5    4.1  4  Tmemb_14      Transmembrane proteins 14C


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 ?   -3.0   0.4       2.1   7.5e+03      29      35 ..      74      80 ..      53     105 .. 0.51
   2 !   19.1   8.2   3.4e-07    0.0012      18     128 ..     156     268 ..     143     306 .. 0.75
   3 ?    1.0   5.5      0.13   4.5e+02      28      96 ..     393     460 ..     381     466 .. 0.55

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.1
                             PMT_2 29 alagvlt 35
                                      +l  + +
  gi|344210286|ref|YP_004786462.1| 74 ILTLIAA 80
                                      2222222 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3.4e-07
                             PMT_2  18 gf.selairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftp..daplvllwalalylllr 91 
                                       g   +   +lv+ l++ l i+++  l+++l gkr +l+a l +  ++++++  + + p  ++++v+ ++l+l  l+r
  gi|344210286|ref|YP_004786462.1| 156 GVpIDAMPYLVALLFTTLQIIGIGVLVKTLSGKRGSLAAGLAAGSTLIYTTFHLSNHPamNSFMVVPVLLTLTELYR 232
                                       665667789***********************999999999888888666666644433388888888888888888 PP

                             PMT_2  92 aleknklkywllagvlfGlgflsKytaallliaall.y 128
                                          +n+  y+ll+ ++  ++++s++   l+++++ll  
  gi|344210286|ref|YP_004786462.1| 233 RSNDNE--YLLLILLVGLFIIYSHPMTTLFMLGILLlT 268
                                       877776..666666666678899998888888777642 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.13
                             PMT_2  28 salagvltilllyllarrlfgkraallaalllavvplfvalsa.lftpdaplvllwalalylllralekn 96 
                                        a + +l++l++  ++r  +++ a l+aa+l+ + ++  a+ +  +t+ a+ vl+++ a+++   a e n
  gi|344210286|ref|YP_004786462.1| 393 IAAIFLLSNLIVKGIIR--VNRYALLFAAVLVGMALIHSATKRnSVTTVALTVLVLLGACLAASAAYEPN 460
                                       33333333333333333..367777777777777777777777555555666666666777766666655 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 ?    9.2  20.4   9.5e-05      0.34      72     312 ..     207     457 ..     148     477 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 9.5e-05
                      PTPS_related  72 fseGniprvlaiaLvpllllallvfvdkrekrslvalallmslialshamvalivglaifvflLllevlrkrflenl 148
                                       f   n p +++++ vp+ll  + ++ +  ++ +l+ + l+   i++sh+m +l +   +++  + ++ l +r+  ++
  gi|344210286|ref|YP_004786462.1| 207 FHLSNHPAMNSFMVVPVLLTLTELYRRSNDNEYLLLILLVGLFIIYSHPMTTLFMLGILLLTSV-YSGLFGRLSLSS 282
                                       555799**********999888888889998999999999999*******99877666666666.79999******* PP

                      PTPS_related 149 valvaialgialssfWlvPllkggltsldsgsvsevlksltvpltvaLdPllrl..snggfyfGlaivllilagvll 223
                                       +  ++  lg+a      +Pll  +lt + +   + ++k  +v ++  ++P+ r   + g++ f+++ +   ++ +  
  gi|344210286|ref|YP_004786462.1| 283 TPQLSPRLGVA-----FLPLLFAWLTNFGQTRQA-IIK--VVAAQDDMNPAAREvqRAGSVQFSPLQLAEKFITLYG 351
                                       ***********.....99**********995555.777..6777788899888778566666665544333333322 PP

                      PTPS_related 224 akkrktpg....................lvaliiylvltvgialall.kllPlsqllldiRflpfaavlllllvall 279
                                       ++                           +++ + +v ++gia   l + l + +++   R+   a +++++lv+++
  gi|344210286|ref|YP_004786462.1| 352 STTIYFTIagtfvlltlywflsermrydWGFGSVHFVAGLGIAAIFLlSNLIVKGII---RVNRYALLFAAVLVGMA 425
                                       22222111234555666666666666668999********99765550555555555...77777888899999999 PP

                      PTPS_related 280 lwkvlkr.....avavllalllailivdslisfnyvgy 312
                                       l  +  +           ++l +++++++ ++ +  +y
  gi|344210286|ref|YP_004786462.1| 426 LIHSATKrnsvtT-----VALTVLVLLGACLA-ASAAY 457
                                       9988888344332.....33333333333332.22334 PP

>> TMEM220  Transmembrane family 220, helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0061        22      16      59 ..      61     104 ..      59     130 .. 0.70
   2 ?   -2.0   0.1       1.7   6.2e+03      71      71 ..     210     210 ..     161     258 .. 0.54
   3 ?   -2.3   0.1       2.2   7.8e+03      45      57 ..     242     250 ..     215     275 .. 0.45
   4 ?    6.6   0.3    0.0035        13      23      60 ..     416     457 ..     410     494 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0061
                           TMEM220  16 elWvtvYl..laallcllaalgaavkesslaralalllllaallla 59 
                                       ++W+t+Y   ++++l+l+aa+ +  ++++++  l+l+l+ +al ++
  gi|344210286|ref|YP_004786462.1|  61 LFWFTFYSvmIGGILTLIAAAIT--QTRYWRHGLGLVLSNYALYFF 104
                                       69*****8324445555444444..489999999999998888766 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                           TMEM220  71 l 71 
                                        
  gi|344210286|ref|YP_004786462.1| 210 S 210
                                       1 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.2
                           TMEM220  45 ralalllllaall 57 
                                       ++l +    + ++
  gi|344210286|ref|YP_004786462.1| 242 LILLV----GLFI 250
                                       22221....1111 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0035
                           TMEM220  23 llaallcllaalgaavkesslaralalllllaallla....l 60 
                                       l+aa+l ++a+++ a+k++s+ +++ ++l+l+ ++la    +
  gi|344210286|ref|YP_004786462.1| 416 LFAAVLVGMALIHSATKRNSVTTVALTVLVLLGACLAasaaY 457
                                       57999999****999887777776666666666666623330 PP

>> DUF4956  Domain of unknown function (DUF4956)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   1.0      0.24   8.7e+02       6      35 ..     223     252 ..     219     280 .. 0.61
   2 ?   10.3   1.6   0.00012      0.42      47     128 ..     387     471 ..     350     485 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.24
                           DUF4956   6 lilvrglYykrhrrrdlvftflllnvgvfa 35 
                                       ++l+ +  y+r++++++++ +ll++++++ 
  gi|344210286|ref|YP_004786462.1| 223 VLLTLTELYRRSNDNEYLLLILLVGLFIIY 252
                                       555556667788888999988888888764 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00012
                           DUF4956  47 iglglGLfgvlsilRlRse.eisvrevtYlFvaialg..linglaslslvellvlnvlivlvlallesprllkkerr 120
                                         +glG+ +++ +  l  +  i v+  + lF+a+ +g  li+++++ + v++++l+vl++l  +l+ s     + + 
  gi|344210286|ref|YP_004786462.1| 387 FVAGLGIAAIFLLSNLIVKgIIRVNRYALLFAAVLVGmaLIHSATKRNSVTTVALTVLVLLGACLAASAAYEPNRHM 463
                                       45678888888887776551567888899999887762257789999********************9998888888 PP

                           DUF4956 121 klvtldri 128
                                       +  ++d  
  gi|344210286|ref|YP_004786462.1| 464 TYAEYDGS 471
                                       88888864 PP

>> Tmemb_14  Transmembrane proteins 14C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2     0.088   3.2e+02      32      67 ..      71     106 ..      64     117 .. 0.75
   2 ?   11.3   3.5   0.00013      0.46      19      82 ..     184     246 ..     166     275 .. 0.72
   3 ?   -1.8   0.1       1.5   5.4e+03      13      44 ..     272     303 ..     258     319 .. 0.49
   4 ?    3.2   6.7     0.041   1.5e+02      27      89 ..     387     449 ..     383     454 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.088
                          Tmemb_14  32 llGallllagyllsknkkakelslvislvlllvmgk 67 
                                       + G+l l+a+ +++++ +++ l lv+s   l+++++
  gi|344210286|ref|YP_004786462.1|  71 IGGILTLIAAAITQTRYWRHGLGLVLSNYALYFFLP 106
                                       557778888888888888899999988776666655 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00013
                          Tmemb_14  19 lkagSvpSLiaGlllGallllagyllsknkkakelslvislvlllvmgkrllktrkfmpaglva 82 
                                         +g   SL+aGl+ G  l+++ + ls+++  ++  +v+ ++l+l++++r  + +  +  +l++
  gi|344210286|ref|YP_004786462.1| 184 TLSGKRGSLAAGLAAGSTLIYTTFHLSNHPAMNS-FMVVPVLLTLTELYRRSNDNEYLLLILLV 246
                                       5677888*******************77776554.45566677777777766666554444442 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.5
                          Tmemb_14  13 GGilgYlkagSvpSLiaGlllGallllagyll 44 
                                        G++g l   S+p L   l++++l ll ++l+
  gi|344210286|ref|YP_004786462.1| 272 SGLFGRLSLSSTPQLSPRLGVAFLPLLFAWLT 303
                                       34444444555555555555555555555544 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.041
                          Tmemb_14  27 LiaGlllGallllagyllsknkkakelslvislvlllvmgkrllktrkfmpaglvavlsalml 89 
                                       ++aGl+++a++ll+  +++   + ++ +l+ ++vl+++ ++  + +r ++ ++ ++vl +l +
  gi|344210286|ref|YP_004786462.1| 387 FVAGLGIAAIFLLSNLIVKGIIRVNRYALLFAAVLVGMALIHSATKRNSVTTVALTVLVLLGA 449
                                       589**********99999877788*************99998888887776666655555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); 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:                        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: 0.74u 0.33s 00:00:01.07 Elapsed: 00:00:00.51
# Mc/sec: 3515.25
//
Query:       gi|344210287|ref|YP_004786463.1|  [L=396]
Description: LPS biosynthesis protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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  112.6   0.0    2.4e-32  111.8   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    9.7e-31  107.0   0.0    7.4e-30  104.1   0.0    2.2  2  Glyco_trans_1_4  Glycosyl transferases group 1
    1.8e-27   96.4   0.1    2.9e-27   95.7   0.1    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
    4.6e-21   75.9   0.0    8.8e-21   75.0   0.0    1.5  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    3.1e-09   37.1   0.0    5.8e-09   36.2   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
    5.9e-05   23.1   0.0    9.9e-05   22.4   0.0    1.3  1  Glyco_trans_4_2  Glycosyl transferase 4-like
     0.0053   16.5   0.2      0.017   14.8   0.2    1.8  1  Glyco_transf_5   Starch synthase catalytic 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 !  111.8   0.0   9.3e-36   2.4e-32      16     170 ..     196     347 ..     187     349 .. 0.94

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 9.3e-36
                                       EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHC CS
                   Glycos_transf_1  16 kiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellkn 92 
                                         i++vgrl+  K+++ ++ af++++++  p++ l ++G+g+ +++l++ ++  +l d v+flg+v+++++++++++
  gi|344210287|ref|YP_004786463.1| 196 QAIVFVGRLVDGKRPQDVLAAFDTVRER-CPDASLFFCGDGPLRDSLESTVADEGLTDAVEFLGRVPYQKMPSVFRA 271
                                       6799*********************998.************************************************ PP

                                       ESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHH CS
                   Glycos_transf_1  93 adifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgena 169
                                       ad+fvlps++Egf+ +++EA+a+ +pv+as+ +  +++v+  +tG  v+ +n+e +a ai +ll+d+    +lg+ +
  gi|344210287|ref|YP_004786463.1| 272 ADLFVLPSRTEGFPRTVIEALACETPVVASDLEQTSKIVN--QTGETVQVGNVEGFATAISDLLSDQRGLSELGKHG 346
                                       *******************************999999996..57799********************8777777777 PP

                                       H CS
                   Glycos_transf_1 170 r 170
                                       r
  gi|344210287|ref|YP_004786463.1| 347 R 347
                                       6 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 !  104.1   0.0   2.9e-33   7.4e-30       3     134 .]     197     335 ..     195     335 .. 0.93
   2 ?    0.0   0.0      0.41     1e+03      92     115 ..     344     367 ..     339     379 .. 0.74

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 2.9e-33
                                       EEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaa 72 
                                        i+fvGrl++  k+ + +l a+  +r++  d+ l ++Gdgp r ++le+ +a  gl++ vef+G+v  ++++++++a
  gi|344210287|ref|YP_004786463.1| 197 AIVFVGRLVDG-KRPQDVLAAFDTVRERcpDASLFFCGDGPlR-DSLESTVAdeGLTDAVEFLGRVpyQKMPSVFRA 271
                                       69******766.**************99855**********66.59*9988669************9999******* PP

                                       -SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  73 advfvaPs..egfglkllEamaaglpvVatdvggiaevvgengllvppgdpealaeailrLled 134
                                       ad+fv+Ps  egf+ +++Ea+a+++pvVa+d++ ++++v+++g  v+ g++e +a ai +Ll+d
  gi|344210287|ref|YP_004786463.1| 272 ADLFVLPSrtEGFPRTVIEALACETPVVASDLEQTSKIVNQTGETVQVGNVEGFATAISDLLSD 335
                                       ********999*********************998999999*********************98 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.41
                                       HTT-EEEE-TGGGTTT--.TTSSEE CS
                   Glyco_trans_1_4  92 aaglpvVatdvggiaevv.gengll 115
                                        +g+++V+t+   ++e+v +++ +l
  gi|344210287|ref|YP_004786463.1| 344 KHGRAIVTTRY-NWEETVqETTEIL 367
                                       58999****99.7799996666655 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   0.1   1.1e-30   2.9e-27       1     170 []      15     179 ..      15     179 .. 0.90

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 1.1e-30
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev.elvvrvprvplpllkrllrslaflrrlrrllkrekpDvv 76 
                                       vGG+  h++ L+r  a++GheVtv+t + + +++e    +++ +++ p+ l     +++a+     r l+  ++Dvv
  gi|344210287|ref|YP_004786463.1|  15 VGGAPYHIHALSRDQAAMGHEVTVLTVSEEVEEREVTdQDGYTLIKQPPKLELLGNQIFANTVGDLRGLE--DFDVV 89 
                                       7*************************99988888888999999999999999999999999988888887..9**** PP

                    Glyco_transf_4  77 Hahs..paalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrer 151
                                       H+hs  +++  +a+l++r+  +ip+ +t+Hgl      ++  ++ ++ lr l ++++++ad +++ ++ ++  lr+ 
  gi|344210287|ref|YP_004786463.1|  90 HTHShlFFSSNVAALYCRM-ANIPIAITCHGLN---SQRGPFWFSRAHLRTLGKWTYDSADVTLCYTDVEQSKLRD- 161
                                       6665116666789999998.*************...577888999999999*************************. PP

                    Glyco_transf_4 152 ygvppekitVipnGvDler 170
                                       +gv+ ++i+V+ nG+D++r
  gi|344210287|ref|YP_004786463.1| 162 LGVD-ADIAVVNNGIDTNR 179
                                       ****.7***********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 !   75.0   0.0   3.4e-24   8.8e-21       1     160 []      16     174 ..      16     174 .. 0.87
   2 ?   -3.6   0.0       5.1   1.3e+04     126     139 ..     268     281 ..     253     283 .. 0.81

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 3.4e-24
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvv 77 
                                       gG+  ++++l+r +aa GheVtvlt ++  +++ ++ d+  ++ ++ p++ ++l++  ++  + +l     e +dvv
  gi|344210287|ref|YP_004786463.1|  16 GGAPYHIHALSRDQAAMGHEVTVLTVSEEVEER-EVTDQDGYTLIKQPPKLELLGNQIFANTVGDLR--GLEDFDVV 89 
                                       89999********************98877777.666777778899**********99999999998..99****** PP

                   Glyco_trans_4_4  78 hahspt...aglaarlarrrrgiplvvtlhglllrrgsgavrrly.ralerrllrradavlvvseaeaeelralgvp 150
                                       h+hs +   ++ aa+  r  ++ip+ +t+hgl  +rg  +  r+  r+l ++++ +ad+ l+ ++ e  +lr+lgv+
  gi|344210287|ref|YP_004786463.1|  90 HTHSHLffsSNVAALYCR-MANIPIAITCHGLNSQRGPFWFSRAHlRTLGKWTYDSADVTLCYTDVEQSKLRDLGVD 165
                                       ****44464666666666.99***********9999977755554499****************************9 PP

                   Glyco_trans_4_4 151 adrvvvvpng 160
                                        ++++vv ng
  gi|344210287|ref|YP_004786463.1| 166 -ADIAVVNNG 174
                                       .599999998 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.1
                   Glyco_trans_4_4 126 llrradavlvvsea 139
                                       ++r ad+++ +s+ 
  gi|344210287|ref|YP_004786463.1| 268 VFRAADLFVLPSRT 281
                                       67889999999886 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 !   36.2   0.0   2.3e-12   5.8e-09       3      89 ..     276     362 ..     274     365 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 2.3e-12
                   Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervla 79 
                                       + psr e++   + Ea+ac ++++++d e+  ++++   e + + ++e +a +i  ll++    +++++++r+ v +
  gi|344210287|ref|YP_004786463.1| 276 VLPSRTEGFPRTVIEALACETPVVASDLEQTSKIVNQTGETVQVGNVEGFATAISDLLSDQRGLSELGKHGRAIVTT 352
                                       669******************************998888999999******************************** PP

                   Glyco_trans_1_2  80 ehtydhraeq 89 
                                       +++++  +++
  gi|344210287|ref|YP_004786463.1| 353 RYNWEETVQE 362
                                       ****998876 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   3.9e-08   9.9e-05      19     118 ..      28     129 ..      15     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.9e-08
                   Glyco_trans_4_2  19 eLakrgyeVhvitp.kkga.kdeleaegihvhrlkvdrkgpleylkafklkklikkikPDvvhahya..kpygllgs 91 
                                         a+ g+eV+v+t  ++ +  +++ ++g+++++ + + +   + + a+++ +l   + +Dvvh+h     + ++ ++
  gi|344210287|ref|YP_004786463.1|  28 DQAAMGHEVTVLTVsEEVEeREVTDQDGYTLIKQPPKLELLGNQIFANTVGDLRGLEDFDVVHTHSHlfFSSNV-AA 103
                                       44566********95555467888899999999984455566666689*****************986644454.66 PP

                   Glyco_trans_4_2  92 laarlsgvipvvlsvwGldvlkfpkks 118
                                       l +r+++ ip++++ +Gl   ++p+  
  gi|344210287|ref|YP_004786463.1| 104 LYCRMAN-IPIAITCHGLNSQRGPFWF 129
                                       999***9.**********876666544 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   6.6e-06     0.017       1     103 [.       2     107 ..       2     150 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.6e-06
                    Glyco_transf_5   1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPrygaikeek..keleevaelskaaedevevev.... 71 
                                       +il va  ++p   +GG   +++aL++  a++gh+v+v++ + +  ++e   ++  +++++        ++e+    
  gi|344210287|ref|YP_004786463.1|   2 HILRVAQDIFP-ETVGGAPYHIHALSRDQAAMGHEVTVLTVSEEVEEREVtdQDGYTLIKQP---P---KLELlgnq 71 
                                       6999*******.****************************9995555554332222222222...1...22211112 PP

                    Glyco_transf_5  72 ...ekvkvaklkkdgvdvyfldnpeffdreg..lYgd 103
                                          ++v+  +   ++ dv+  + + ff+ +   lY+ 
  gi|344210287|ref|YP_004786463.1|  72 ifaNTVGDLRGL-EDFDVVHTHSHLFFSSNVaaLYCR 107
                                       223444444443.588888888888886433457765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2435.55
//
Query:       gi|344210288|ref|YP_004786464.1|  [L=608]
Description: asparagine synthase [Haloarcula hispanica ATCC 33960]
Scores for complete 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  311.5   0.6    1.4e-92  311.2   0.6    1.1  1  Asn_synthase  Asparagine synthase
    8.2e-46  154.9   0.0    1.4e-45  154.1   0.0    1.4  1  GATase_7      Glutamine amidotransferase domain
    2.4e-42  144.3   0.0    4.7e-42  143.4   0.0    1.5  1  GATase_6      Glutamine amidotransferase domain
  ------ inclusion threshold ------
      0.021   14.3   0.0      0.043   13.3   0.0    1.4  1  QueC          Queuosine biosynthesis protein QueC
      0.023   14.2   0.0      0.046   13.2   0.0    1.5  1  DUF3700       Aluminium induced protein
       0.18   10.9   0.0       0.33   10.0   0.0    1.4  1  NAD_synthase  NAD 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 !  311.2   0.6   4.5e-96   1.4e-92       2     353 ..     216     597 ..     215     599 .. 0.89

  Alignments for each domain:
  == domain 1  score: 311.2 bits;  conditional E-value: 4.5e-96
                      Asn_synthase   2 lrelLedaVkrrlradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelv 78 
                                       lr+l+e aV++rl+adv +Ga+LSGG+DS++i+ ++a+ ++ p+ktF++gf+++++de+ +a+eva  ++t+h+e+ 
  gi|344210288|ref|YP_004786464.1| 216 LRSLVESAVEKRLMADVDLGAFLSGGIDSTIIVGTMAQLLDDPVKTFTVGFNQDRFDESWAAREVASFHNTDHHEIT 292
                                       89*************************************************99************************ PP

                      Asn_synthase  79 lteeelldalpdviyhleepfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaalsrsrefeklp.. 153
                                       lt++++ + +pdv+  l epfad++ +p y +sr+  r +vkv+LsG+GaDElf+GY+  y+ + s s++ ++lp  
  gi|344210288|ref|YP_004786464.1| 293 LTANDVRESVPDVLNKLGEPFADPALMPSYAVSRAT-RNNVKVALSGDGADELFAGYD-KYRVE-SLSKYYRALPaq 366
                                       ************************************.788******************.77755.667888888889 PP

                      Asn_synthase 154 ...........larslrasllarklrklaellelaeardl.eelaelyrlkasdsae.................... 198
                                                  +  ++r   +++ + k  ++ +   +r++ e++ +l+r   ++                       
  gi|344210288|ref|YP_004786464.1| 367 irkyavepavnALPASRGTAVGDAVYKGQWFINRSGERSVpERHFDLMRVSDDQ--Aiqsvtnvdpieagqtalrtq 441
                                       999999999995555555555555555555555444444404444443333333..134777888888888888999 PP

                      Asn_synthase 199 .....aelegedelhrelyldlktllpgdllrk.DrasmahglEaRvPflDhrlvevalrlppelklrggieKyiLR 269
                                             el++++ l r++ +d++  lp+++l+k D+asm ++lE+RvPflD ++ve+al+lp ++kl+g+  K++L+
  gi|344210288|ref|YP_004786464.1| 442 haaisPELADRESLARIQAVDTRLSLPDQMLTKvDQASMYNSLEVRVPFLDTDVVEYALSLPTDHKLTGRDRKRVLK 518
                                       999999*********************************************************************** PP

                      Asn_synthase 270 ealegylPeeileRpKegfsapvgewklkgelrelaeellsdsrlakeglldreaveelleeheagkrnesrqlwsl 346
                                       +a++++lPe+il+R K gf +p+gew +k   +e+a+e +s  r+++ g+ld++a+ el++eh +g++++sr lw++
  gi|344210288|ref|YP_004786464.1| 519 RAFDDVLPESILQRNKHGFDMPIGEW-FK---HEFADEFVSMVRATDLGILDTAAILELFDEHLDGNHDHSRFLWTV 591
                                       **************************.99...99******************************************* PP

                      Asn_synthase 347 llsleaw 353
                                          ++ w
  gi|344210288|ref|YP_004786464.1| 592 Y-VFKHW 597
                                       9.99999 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.1   0.0   4.8e-49   1.4e-45       1     121 [.      25     142 ..      25     144 .. 0.97

  Alignments for each domain:
  == domain 1  score: 154.1 bits;  conditional E-value: 4.8e-49
                          GATase_7   1 hrrlsiidseagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllalleaewgeealerlnGm 77 
                                       hrrlsiid+e+g QP++ +edg+++++fnGeiyNy  l+e+L+++ghrf+t++Dtevl++l+e+  g +++++l+Gm
  gi|344210288|ref|YP_004786464.1|  25 HRRLSIIDPENGGQPIH-NEDGTVTVIFNGEIYNYGALKERLTSAGHRFTTQTDTEVLVHLYEE-EGPSFVDELDGM 99 
                                       99***************.79******************************************98.9*********** PP

                          GATase_7  78 fAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkal 121
                                       fAfa+wd+e++rlllaRD++GikPL ++e++ d+l+faSel +l
  gi|344210288|ref|YP_004786464.1| 100 FAFALWDSERERLLLARDPMGIKPLVLAETD-DKLAFASELPSL 142
                                       ******************************6.8********988 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.4   0.0   1.6e-45   4.7e-42       1     134 []      10     138 ..      10     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 143.4 bits;  conditional E-value: 1.6e-45
                          GATase_6   1 pdasglaslvedevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevl 77 
                                       pd++g+  + +++v+laH+Rl+i++ +  +g qP+++edg++++++NGeiyny++l+e+l + +g++f +++Dtevl
  gi|344210288|ref|YP_004786464.1|  10 PDDDGV--FRDGSVGLAHRRLSIIDPE--NGGQPIHNEDGTVTVIFNGEIYNYGALKERLTS-AGHRFTTQTDTEVL 81 
                                       688888..88999*************7..888******************************.************** PP

                          GATase_6  78 lalleelGeevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                       ++l+ee G+  +++l+Gmfafa+wd+++++l lard +g+kpl+ a+++++lafase
  gi|344210288|ref|YP_004786464.1|  82 VHLYEEEGPSFVDELDGMFAFALWDSERERLLLARDPMGIKPLVLAETDDKLAFASE 138
                                       ********************************************************8 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.4e-05     0.043       5      62 ..     237     294 ..     236     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                                       E--SSHHHHHHHHHHHHH-.SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-G CS
                              QueC   5 llSGGlDSttvlalakkeg.kevealtfdYgqrhkkeleaakkiakelgveehkildld 62 
                                        lSGG+DSt+++ ++ +   + v++ t+ ++q +  e  aa+++a+ ++  +h+ ++l+
  gi|344210288|ref|YP_004786464.1| 237 FLSGGIDSTIIVGTMAQLLdDPVKTFTVGFNQDRFDESWAAREVASFHNT-DHHEITLT 294
                                       59*******9997766665378************************9999.88887776 PP

>> DUF3700  Aluminium induced protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.5e-05     0.046     125     169 ..      92     135 ..      44     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                           DUF3700 125 vvkdleGkfafvlydskaktvfvaldadgsvplyWGiaadgsvvi 169
                                        v +l+G faf l+ds+ + +++a+d  g  pl    ++d ++++
  gi|344210288|ref|YP_004786464.1|  92 FVDELDGMFAFALWDSERERLLLARDPMGIKPLVLA-ETDDKLAF 135
                                       6889***********************999998764.44555555 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00011      0.33       5      50 ..     216     264 ..     212     308 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHCTTSEEEEE..E-SSHHHHH.HHHHHHHHHTCGEEEEE CS
                      NAD_synthase   5 lvdflkeyvkkagakgvvlG..lSGGvDSsl.vaalavkalgkenvlal 50 
                                       l   +++ v+k+ +  v lG  lSGG+DS++ v+++a+ + ++ + +++
  gi|344210288|ref|YP_004786464.1| 216 LRSLVESAVEKRLMADVDLGafLSGGIDSTIiVGTMAQLLDDPVKTFTV 264
                                       56778999999999999999999******96378898866555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (608 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); 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:                         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 0.30s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 3763.92
//
Query:       gi|344210289|ref|YP_004786465.1|  [L=389]
Description: group 1 glycosyl transferase [Haloarcula hispanica ATCC 33960]
Scores for complete 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  111.0   0.0    7.3e-32  110.3   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    1.4e-28   99.9   0.0    6.2e-28   97.9   0.0    1.9  2  Glyco_trans_1_4  Glycosyl transferases group 1
    1.6e-22   80.3   0.0    2.7e-22   79.6   0.0    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
    7.7e-18   65.4   0.2    3.8e-17   63.2   0.0    1.9  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    8.7e-06   26.1   0.0    2.2e-05   24.8   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
     0.0013   18.8   0.0      0.002   18.1   0.0    1.3  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
        0.1   12.9   0.0       0.24   11.7   0.0    1.6  1  NTP_transf_2     Nucleotidyltransferase 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 !  110.3   0.0   2.9e-35   7.3e-32      17     169 ..     201     351 ..     195     358 .. 0.94

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 2.9e-35
                                       EEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCE CS
                   Glycos_transf_1  17 iilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellkna 93 
                                       ++l vgrle+ K++  +++af+++ ++ +p+++ +i+G g++++el+ la+el++ + v f g+v+  +   ++  +
  gi|344210289|ref|YP_004786465.1| 201 VVLGVGRLERAKNFGSFLRAFEQVHAA-RPDTRAIIVGRGSKRAELETLAAELGIDAAVSFPGFVD--NPYGYMAGS 274
                                       7899********************998.*************************************9..9******** PP

                                       SEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHH CS
                   Glycos_transf_1  94 difvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdgetGllvkpnnaealaeairklledeelrerlgena 169
                                       d+++++s  Eg+++vl+EA+a+g+pv++++  +gpae++kdge G lv+  ++e la+air  l+++  ++ l+e+a
  gi|344210289|ref|YP_004786465.1| 275 DVLAMSSVHEGLPTVLIEALACGCPVVSTDcPSGPAEILKDGEYGPLVDVDDDEGLAAAIRTTLDEPLPSDILIERA 351
                                       *****************************************************************995555555554 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.84   2.2e+03      68      89 ..     139     160 ..      92     167 .. 0.79
   2 !   97.9   0.0   2.4e-31   6.2e-28       3     133 ..     201     339 ..     200     340 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.84
                                       HHHHH-SEEEE-----SHHHHH CS
                   Glyco_trans_1_4  68 ellaaadvfvaPsegfglkllE 89 
                                       +l  ++d fva seg+  +++E
  gi|344210289|ref|YP_004786465.1| 139 RLAGQSDQFVAVSEGVAKSIVE 160
                                       4667889999999998888887 PP

  == domain 2  score: 97.9 bits;  conditional E-value: 2.4e-31
                                       EEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---..HHHHHHHT..T-T.TEEEE---THHHHHHHH-SE CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgprpeeleelaa..gleerveftGfvedlaellaaadv 75 
                                       v+l vGrl e+ k++  +l+a+++++++ +  r +ivG+g++++ele laa  g+++ v+f Gfv++   ++a +dv
  gi|344210289|ref|YP_004786465.1| 201 VVLGVGRL-ERAKNFGSFLRAFEQVHAArPdTRAIIVGRGSKRAELETLAAelGIDAAVSFPGFVDNPYGYMAGSDV 276
                                       6788****.778**************77536********99556**99886699*999*******99********** PP

                                       EEE--..---SHHHHHHHHTT-EEEE-TGG.GTTT--..TTSSEE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  76 fvaPs..egfglkllEamaaglpvVatdvg.giaevv..gengllvppgdpealaeailrLle 133
                                       + + s  eg++ +l+Ea+a+g+pvV+td++ g+ae++  ge g lv+ +d e la+ai + l+
  gi|344210289|ref|YP_004786465.1| 277 LAMSSvhEGLPTVLIEALACGCPVVSTDCPsGPAEILkdGEYGPLVDVDDDEGLAAAIRTTLD 339
                                       *****************************889***99*99******************99886 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.0     1e-25   2.7e-22       1     169 [.      16     179 ..      16     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 1e-25
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpl.lkrllrslaflrrlrrllkrekpDvv 76 
                                       vGG+er+++ +a++L +rG++V++v++  +g+++  v    +v  v l   + +   + a++++l r l+r+ p ++
  gi|344210289|ref|YP_004786465.1|  16 VGGAERVTVSVANGLSKRGYDVDLVVSYNEGDFRTDV-A-GSVNVVDLGTqRIPGIGIGASVPALVRYLRRQSPQIL 90 
                                       7************************999999999994.2.223333333303333455678899************* PP

                    Glyco_transf_4  77 Hahspaalgaallalrr.rlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrery 152
                                        +++ +a    ++   +   +   + t+H++      +     +++l+++l rrl+ ++d+++avSe +a+ ++e+ 
  gi|344210289|ref|YP_004786465.1|  91 FSQMTYANDMHMISQILsGADTTAISTIHNTL-----GMQEESKEKLVQWLQRRLAGQSDQFVAVSEGVAKSIVEHV 162
                                       ****999988888888889*************.....8999999********************************* PP

                    Glyco_transf_4 153 gvppekitVipnGvDle 169
                                       gv++ek+ V++n++ ++
  gi|344210289|ref|YP_004786465.1| 163 GVDREKVSVLHNPIPVD 179
                                       **************887 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 !   63.2   0.0   1.5e-20   3.8e-17       1     159 [.      17     174 ..      17     175 .. 0.90
   2 ?   -0.1   0.0      0.43   1.1e+03      58      95 ..     216     252 ..     181     289 .. 0.64

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 1.5e-20
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvv 77 
                                       gG++r++  +a +L +rG++V+++++   ++ +  +++ v v+ l + r p + +  a+++al r+l  rr+ p ++
  gi|344210289|ref|YP_004786465.1|  17 GGAERVTVSVANGLSKRGYDVDLVVSYNEGDFRTDVAGSVNVVDLGTQRIP-GIGIGASVPALVRYL--RRQSPQIL 90 
                                       8************************95555555577888*********999.69999**********..******** PP

                   Glyco_trans_4_4  78 hahspt...aglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeelra.lgvp 150
                                        ++  +     ++  +++ ++++  + t+h++l+ ++   +  l+++l+rrl+ + d++++vse++a+ +++  gv+
  gi|344210289|ref|YP_004786465.1|  91 FSQMTYandMHMISQILS-GADTTAISTIHNTLGMQE-ESKEKLVQWLQRRLAGQSDQFVAVSEGVAKSIVEhVGVD 165
                                       ***977244458888888.99**********988766.56779*****************************99*** PP

                   Glyco_trans_4_4 151 adrvvvvpn 159
                                       +++v v++n
  gi|344210289|ref|YP_004786465.1| 166 REKVSVLHN 174
                                       *******99 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.43
                   Glyco_trans_4_4  58 aalralrrllrqrrerpd...vvhahsptaglaarlarrrr 95 
                                       ++lra+++   +++ rpd   +++  +++ + +  la+   
  gi|344210289|ref|YP_004786465.1| 216 SFLRAFEQ---VHAARPDtraIIVGRGSKRAELETLAA-EL 252
                                       23334444...367777766566666666555555555.55 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 !   24.8   0.0   8.5e-09   2.2e-05       6      63 ..     281     341 ..     276     353 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 8.5e-09
                   Glyco_trans_1_2   6 srsespnlrlfEaaacGafaltdda.egleelftpgkevilfe..dleelaekiryllanp 63 
                                       s +e++ ++l Ea+acG++++++d  +g++e++++g+ + l++  d e la++ir  l++p
  gi|344210289|ref|YP_004786465.1| 281 SVHEGLPTVLIEALACGCPVVSTDCpSGPAEILKDGEYGPLVDvdDDEGLAAAIRTTLDEP 341
                                       56688999***************999***********99999998999*******999877 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 !   18.1   0.0   7.9e-07     0.002      12     133 ..      22     145 ..      14     151 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7.9e-07
                   Glyco_trans_4_2  12 htlrlakeLakrgyeVhvitp.kkgakdeleaegihvhrlkvdrkg.pleylk.afklkklikkikPDvvh..ahya 83 
                                       +t+ +a++L+krgy+V+++ + ++g  + ++a  ++v +l    ++  ++  + + +l++ +++++P+++   + ya
  gi|344210289|ref|YP_004786465.1|  22 VTVSVANGLSKRGYDVDLVVSyNEGDFRTDVAGSVNVVDLG-TQRIpGIGIGAsVPALVRYLRRQSPQILFsqMTYA 97 
                                       68999***************977777888888889999996.34442444445266**************7436788 PP

                   Glyco_trans_4_2  84 kpygllgslaarlsgvipvvlsvwGldvlkfpkksklkklllklalkkat 133
                                       +++ ++ ++++        + +++ +  ++++ k kl ++l + ++ +++
  gi|344210289|ref|YP_004786465.1|  98 NDMHMISQILSGAD--TTAISTIHNTLGMQEESKEKLVQWLQRRLAGQSD 145
                                       9**99999985554..7899999988779999888888887776665555 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.5e-05      0.24      22      46 ..      25      49 ..      23      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.5e-05
                                      HHHCTTSCTTSSEEEEEEESTTCHH CS
                      NTP_transf_2 22 SyarGtalkgSDiDllvvlpeevsr 46
                                      S+a+G+ ++g D+Dl+v ++e   r
  gi|344210289|ref|YP_004786465.1| 25 SVANGLSKRGYDVDLVVSYNEGDFR 49
                                      99******************99655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2295.76
//
Query:       gi|344210290|ref|YP_004786466.1|  [L=311]
Description: hypothetical protein HAH_5349 [Haloarcula hispanica ATCC 33960]
Scores for complete 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-72  243.7   3.8    2.9e-72  243.5   3.8    1.0  1  DUF1616        Protein of unknown function (DUF1616)
     0.0071   16.2   3.6     0.0071   16.2   3.6    1.7  1  Bax1-I         Inhibitor of apoptosis-promoting Bax1
  ------ inclusion threshold ------
      0.022   14.3   0.7      0.037   13.5   0.7    1.4  1  DUF1129        Protein of unknown function (DUF1129)
       0.21   11.4   1.4          9    6.2   0.3    3.3  4  TMEM132D_C     Mature oligodendrocyte transmembrane protein, 
        7.4    6.4   8.7        1.6    8.6   4.6    1.9  2  7TMR-DISM_7TM  7TM diverse intracellular signalling


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 !  243.5   3.8   8.1e-76   2.9e-72       6     293 .]      20     309 ..      14     309 .. 0.92

  Alignments for each domain:
  == domain 1  score: 243.5 bits;  conditional E-value: 8.1e-76
                           DUF1616   6 lllllailvpvlnetplRivlglplvLflPGYaliaaLFPe......krdidgieRlaLSfglSiaivpliglvlnv 76 
                                        ++++++++    e +l ++++lp++Lf+PGYa++aaLFP       ++++ ++eR++ S+++Si+++ ++g+ l++
  gi|344210290|ref|YP_004786466.1|  20 YTAVVLFATLSSLEGVLLTAIALPFLLFVPGYAVVAALFPIrnpedeHHRLITTERMLYSVVASICLAIIVGVNLEF 96 
                                       4566777777788999************************9999999999*************************** PP

                           DUF1616  77 tpwgirlepilvslslftlllalvAivrRsrlpeeerfsvplral.ieslkeeleeksesrldkalnvlLvvsivla 152
                                       tpw ir++p++++l+++t++++ +A++rR++  +    +    ++ + + +++    s+ +  ++ +v++ v+i++ 
  gi|344210290|ref|YP_004786466.1|  97 TPWPIRPTPVVTALAIVTVVATGIAWYRRYKRTQTGLSQT---SMpFGNSRAASGG-SDGEGVQLGTVVVGVAILVT 169
                                       *****************************99877765443...3435556655555.34456799************ PP

                           DUF1616 153 vaalgyavvaPkegekfTelyllgedgd.elvaenypteltagesqevivgieNhEheevnYtvvvllqevtdeeev 228
                                       +a+++ ++++P++ge++Te+ ll+e+++ +l a++yp+++++ge+++++ +++NhE e+++Y vvv++ +  ++ ++
  gi|344210290|ref|YP_004786466.1| 170 FASVALVAAQPQRGEAYTEFGLLTENETgDLEASGYPEQIALGEPEQMYFTVTNHEMETTEYVVVVQMAR--TAPTG 244
                                       *********************************************************************9..66779 PP

                           DUF1616 229 evlerteldrrevtladnetweqelevepeatgenlrleflLYkdevpeeptteeayrslhlwVn 293
                                       ev+er +ld+ + + a++++w q+++v+p  +ge+lrl++lLY+++ p++pt+e+ayr+ h+wV+
  gi|344210290|ref|YP_004786466.1| 245 EVIERIRLDTYSNRTAAGDRWLQRHTVTPVLEGERLRLTYLLYRGSQPDQPTAENAYREAHIWVD 309
                                       999*************************************************************6 PP

>> Bax1-I  Inhibitor of apoptosis-promoting Bax1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   3.6     2e-06    0.0071      13     119 ..      16     129 ..      11     141 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2e-06
                            Bax1-I  13 lgllltalvaavvlsspaqlflslhivlflvvilaplalvflslsaarlkkkssalalallllftlleGlslspill 89 
                                       ++++ ta+v +++lss  + +l + i+l +++++ + a+v +++  +  ++ ++ l ++  +l++++++++l++i+ 
  gi|344210290|ref|YP_004786466.1|  16 VTVGYTAVVLFATLSSL-EGVLLTAIALPFLLFVPGYAVVAALFPIRNPEDEHHRLITTERMLYSVVASICLAIIVG 91 
                                       44555666666666655.56666667777776666666664333332333344445588899*************** PP

                            Bax1-I  90 vyt........gaiilqaflltaaifgglslyalttkr 119
                                       v          ++ +++a+++ +++  g++ y  +++ 
  gi|344210290|ref|YP_004786466.1|  92 VNLeftpwpirPTPVVTALAIVTVVATGIAWYRRYKRT 129
                                       *99********99******9999999999999777665 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.7     1e-05     0.037     114     200 ..      40     127 ..       6     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1e-05
                           DUF1129 114 itlllvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvvw.lvlftlvallpaviNpvLpplvliiigvi 189
                                       i+l ++ +v G+a v     + + +++++r  + +r+l+++++ + + +++ + +++ p  i p+    +l+i+ v+
  gi|344210290|ref|YP_004786466.1|  40 IALPFLLFVPGYAVVAALFPIRNPEDEHHRLITTERMLYSVVASICLaIIVGVNLEFTPWPIRPTPVVTALAIVTVV 116
                                       4444566778888888888887779999**9999999998877666514555667789******************* PP

                           DUF1129 190 afvvryylkkk 200
                                       a ++ +y + k
  gi|344210290|ref|YP_004786466.1| 117 ATGIAWYRRYK 127
                                       *******8866 PP

>> TMEM132D_C  Mature oligodendrocyte transmembrane protein, TMEM132D, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.77   2.8e+03      37      60 ..      35      58 ..      23      71 .. 0.73
   2 ?    6.2   0.3    0.0025         9      24      48 ..      66      90 ..      59      93 .. 0.83
   3 ?    1.8   0.0     0.058   2.1e+02      41      69 ..     107     135 ..     106     148 .. 0.83
   4 ?   -1.5   0.0      0.59   2.1e+03      42      62 ..     162     182 ..     157     233 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.77
                        TMEM132D_C 37 aLlgvfClAilvflincvvyalkf 60
                                      +Ll++  l  l f+   +v+a+ f
  gi|344210290|ref|YP_004786466.1| 35 VLLTAIALPFLLFVPGYAVVAALF 58
                                      789999999999887777776655 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0025
                        TMEM132D_C 24 asraltdLEiGmYaLlgvfClAilv 48
                                      ++++l   E  +Y +++  ClAi+v
  gi|344210290|ref|YP_004786466.1| 66 EHHRLITTERMLYSVVASICLAIIV 90
                                      566777788899***********98 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.058
                        TMEM132D_C  41 vfClAilvflincvvyalkfrrkkvpveg 69 
                                       v+ lAi+ ++   ++   +++r ++ +++
  gi|344210290|ref|YP_004786466.1| 107 VTALAIVTVVATGIAWYRRYKRTQTGLSQ 135
                                       789***********999999999988776 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.59
                        TMEM132D_C  42 fClAilvflincvvyalkfrr 62 
                                         +Ailv   + + +a++ +r
  gi|344210290|ref|YP_004786466.1| 162 VGVAILVTFASVALVAAQPQR 182
                                       556777766666666655544 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 ?    8.6   4.6   0.00044       1.6      74     149 ..      38     127 ..      14     133 .. 0.55
   2 ?   -2.4   0.1         1   3.7e+03     189     202 ..     162     175 ..     155     182 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00044
                     7TMR-DISM_7TM  74 llllilfllFarsf......lelkkkp........rllklllllavlls....llllllpllpyteslslaqllall 132
                                       + +++ fllF+  +      + + ++p               +l+ +++    ++++ ++l ++++ ++   ++++l
  gi|344210290|ref|YP_004786466.1|  38 TAIALPFLLFVPGYavvaalFPI-RNPedehhrliT---TERMLYSVVAsiclAIIVGVNLEFTPWPIRPTPVVTAL 110
                                       33333444455555444454333.322344554442...333333333300003333344458899999999***** PP

                     7TMR-DISM_7TM 133 villllligikawrkgn 149
                                       +i++++++gi+++r+ +
  gi|344210290|ref|YP_004786466.1| 111 AIVTVVATGIAWYRRYK 127
                                       **********9996644 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1
                     7TMR-DISM_7TM 189 igvllevlllslaL 202
                                       +gv++ v + s+aL
  gi|344210290|ref|YP_004786466.1| 162 VGVAILVTFASVAL 175
                                       45555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1815.59
//
Query:       gi|344210291|ref|YP_004786467.1|  [L=280]
Description: dolichyl-phosphate beta-D-mannosyltransferase [Haloarcula hispanica ATCC 33960]
Scores for complete 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-18   65.6   0.2    3.8e-16   59.4   0.2    2.1  1  Glycos_transf_2  Glycosyl transferase family 2
    4.4e-05   23.5   0.1      0.053   13.4   0.0    2.1  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0023   18.4   0.0     0.0078   16.7   0.0    1.9  2  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.2   6.3e-20   3.8e-16       2     156 ..       9     193 ..       8     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 6.3e-20
                                       EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH........................... CS
                   Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak........................... 51 
                                       vv+p++Nee  + e+++sl +      ++++v+DD+StD+t+  ++e+++                           
  gi|344210291|ref|YP_004786467.1|   9 VVVPAHNEEGFIGEVIDSLPEY----VDQVFVIDDCSTDGTWTEIKEYVDtevkpasvtgdsaqqivvadgagtmvs 81 
                                       8******************999....*************************************************** PP

                                       .....C-TTEEEEEESSS-HHHHHHHHHHHH--SS...EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEE CS
                   Glycos_transf_2  52 .....edprvrvirreenvGkagalnaglraatgd...yilflDaDdepdpdwleklvealekdgadvvlgqrprif 120
                                             d+r+  +r+  n G ++a+ +g + a       +++lD D ++dp+ l +++++  +++ad + g+r  ++
  gi|344210291|ref|YP_004786467.1|  82 esqtfLDKRIVPVRHQTNGGRGAAVQTGYELALMSgmdTVAVLDGDGQMDPNILDEILDPVVEGDADYAKGNRLISR 158
                                       ****************************9998766667***********************************9998 PP

                                       CCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCST CS
                   Glycos_transf_2 121 getdeiernkrvgenerlyfkerkrslkgnlsfeig 156
                                        + ++++  +  + n  l   ++  s  +++ +   
  gi|344210291|ref|YP_004786467.1| 159 RHCTQMSNWRL-FGNALLTMLTKIASGHWQMRDPQN 193
                                       88888775333.455555555555555555555555 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 !    8.3   0.0   0.00032       1.9       4      52 ..       7      52 ..       4      67 .. 0.86
   2 !   13.4   0.0   8.9e-06     0.053      55     148 ..      85     190 ..      60     204 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00032
                   Glyco_tranf_2_3  4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeel 52
                                      + v+Vp+ nee  +gev++sl  +    ++v+v++d s+++t  +++e 
  gi|344210291|ref|YP_004786467.1|  7 VGVVVPAHNEEGFIGEVIDSLPEY---VDQVFVIDDCSTDGTWTEIKEY 52
                                      88******************9986...8999999999999998888874 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8.9e-06
                   Glyco_tranf_2_3  55 alpdvrvrvvvnarnlgstgksralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrs. 130
                                       ++ d r++ v+ + n+g++++++  +e   +   d v+++D+D   +P++l+ +l  +   +++ + ++++  +r  
  gi|344210291|ref|YP_004786467.1|  85 TFLDKRIVPVRHQTNGGRGAAVQTGYELALMSGMDTVAVLDGDGQMDPNILDEILDPVVEGDADYAKGNRLISRRHc 161
                                       4556689999999999977776655555555559*********************9994445566666665544443 PP

                   Glyco_tranf_2_3 131 .tl..........vsalgalefaerhlrf 148
                                         +          +++l+++  +++++r 
  gi|344210291|ref|YP_004786467.1| 162 tQMsnwrlfgnalLTMLTKIASGHWQMRD 190
                                       21122244444448888888888888875 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 !   16.7   0.0   1.3e-06    0.0078       1      49 [.      14      61 ..      14      91 .. 0.85
   2 ?   -1.4   0.0      0.56   3.4e+03      61      80 ..     207     227 ..     156     239 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-06
                   Glyco_tranf_2_4  1 rneadiLpeflahhlalgfdrilvydndstDgtrailkelpevkllhvd 49
                                      +ne+ +++e+++ + ++ +d+++v+d+ stDgt++ +ke+ + ++ +  
  gi|344210291|ref|YP_004786467.1| 14 HNEEGFIGEVIDSLPEY-VDQVFVIDDCSTDGTWTEIKEYVDTEVKPAS 61
                                      59***************.********************99876665544 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.56
                   Glyco_tranf_2_4  61 llkallarya.eadwvlvvDa 80 
                                        l+ l+++y+  +d ++++Da
  gi|344210291|ref|YP_004786467.1| 207 SLNDLFDDYGfLNDMLIHLDA 227
                                       445555566423577777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 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:                        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: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1745.01
//
Query:       gi|344210292|ref|YP_004786468.1|  [L=613]
Description: hypothetical protein HAH_5351 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   54.4  24.7      5e-05   23.5   0.3    4.5  4  CARDB         CARDB
    0.00022   21.3   3.4          1    9.6   0.0    4.7  5  Fn3-like      Fibronectin type III-like domain
    0.00047   20.2   1.1        1.9    8.6   0.0    4.8  5  Cupredoxin_1  Cupredoxin-like domain
    0.00048   20.0   6.1       0.69    9.7   0.0    3.6  3  DUF4832       Domain of unknown function (DUF4832)
     0.0037   17.1   1.3          4    7.3   0.0    3.7  3  A2M           Alpha-2-macroglobulin family
      0.007   15.8   0.2      0.007   15.8   0.2    4.2  6  DUF1616       Protein of unknown function (DUF1616)
  ------ inclusion threshold ------
      0.041   13.7   0.5         11    5.8   0.0    4.0  4  DUF3872       Domain of unknown function, B. Theta Gene descr
       0.13   13.0   2.5       0.77   10.5   0.1    3.4  5  N_BRCA1_IG    Ig-like domain from next to BRCA1 gene
        1.2    9.9  36.9        0.3   11.9   4.2    5.0  5  Big_7         Bacterial Ig domain
        2.5    6.0   4.4        4.4    5.2   4.4    1.3  1  Dicty_REP     Dictyostelium (Slime Mold) REP protein
        5.1    7.3   7.1        3.5    7.8   0.0    3.6  4  Ig_GlcNase    Exo-beta-D-glucosaminidase Ig-fold domain


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 !   23.5   0.3   3.1e-08     5e-05       4      85 ..      48     133 ..      45     141 .. 0.81
   2 !   12.6   2.9   7.5e-05      0.12       4      86 ..     152     242 ..     148     246 .. 0.83
   3 !   13.6   5.4   3.7e-05      0.06       5      79 ..     258     332 ..     254     349 .. 0.77
   4 !   14.8   0.0   1.5e-05     0.025       5      76 ..     354     429 ..     350     438 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.1e-08
                                       EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-.EEEEEEEEEETTEEEEEEEE..SEE-CTEEEEEEEEEE-S.-S-C CS
                             CARDB   4 LtvtntlnpseafvgeentitvtvkNqGtaa.sgatkvalyldgelvgtvtv..psLaagesttvsftwtte.ateg 76 
                                       L++ + ++p+e  ++e ++++++++N G+++  +++ ++l  dg++ +tv     +++a e ++v+f + ++ +++g
  gi|344210292|ref|YP_004786468.1|  48 LEIRTVQSPTEIRPNEPLRVQLQITNAGSETtTQQVALRLNRDGQSPETVATkqVKVSAAEPADVTFAVEPDqISPG 124
                                       8888999***********************9788888888888888855555222566777778888888889**** PP

                                       EEEEEEEES CS
                             CARDB  77 evtltvvvD 85 
                                       e+t+ v v 
  gi|344210292|ref|YP_004786468.1| 125 EYTYAVAVG 133
                                       ***999875 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7.5e-05
                                       EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-.EEEEEEEEEETTEEE......EEEEESEE-CTEEEEEEEEEE-S. CS
                             CARDB   4 LtvtntlnpseafvgeentitvtvkNqGtaa.sgatkvalyldgelv......gtvtvpsLaagesttvsftwtte. 72 
                                       +++  t++ ++ + g++ +i+++++N G     +++++a+ +d++ +       + +v sLa g+s   ++t+ t+ 
  gi|344210292|ref|YP_004786468.1| 152 FVLADTTENATIVRGTNASIRANLTNVGAYRgVQTVQIAVDADQNGQysdaetLNESVHSLAGGQSQMSTATVRTAd 228
                                       5557788899999***************988788888888888877787554444556*****************99 PP

                                       -S-CEEEEEEEEST CS
                             CARDB  73 ategevtltvvvDp 86 
                                       +++g ++++v ++ 
  gi|344210292|ref|YP_004786468.1| 229 LEPGGYQYRVATEN 242
                                       *********99876 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 3.7e-05
                                       EE.EEEC-SEEETTSEEEEEEEEEE-SSS-.EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S.-S-CEEE CS
                             CARDB   5 tvtntlnpseafvgeentitvtvkNqGtaa.sgatkvalyldgelvgtvtvpsLaagesttvsftwtte.ategevt 79 
                                        v+nt++p++++ ge+ ++++ v+N G+ +     +v+l  d  +++ +   sLaa+e+ttvs+ + t+ ++ g++ 
  gi|344210292|ref|YP_004786468.1| 258 RVQNTTAPANVTRGETANVSAVVENVGDVDgLD--NVTLRSDSMNTTYSRTVSLAANETTTVSIDVNTTnLSRGTHN 332
                                       689*************************99445..455556666654445559***********9999865555554 PP

  == domain 4  score: 14.8 bits;  conditional E-value: 1.5e-05
                                       EE.EEEC-SEEETTSEEEEEEEEEE-SSS-.EEEEEEEEEETTEEE.EEEEE...SEE-CTEEEEEEEEEE-S-S-C CS
                             CARDB   5 tvtntlnpseafvgeentitvtvkNqGtaa.sgatkvalyldgelv.gtvtv...psLaagesttvsftwtteateg 76 
                                       +v+  ++p+ ++vg++  +++ v+N+G+ +  ++++ ++  d++   +   v     La+gest v+f + ++  + 
  gi|344210292|ref|YP_004786468.1| 354 EVSDLAGPNVLYVGDTAVFSADVTNTGETTgTQSIQHRIDSDDDDRpEAYGVdrnVTLAPGESTRVRFEVEYT-VTD 429
                                       677888999********************9888999999999998874445555569***********99988.333 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 ?    0.7   0.1      0.36   5.8e+02      44      71 .]     110     136 ..      95     136 .. 0.46
   2 ?   -1.4   0.0       1.6   2.7e+03      27      46 ..     209     229 ..     207     241 .. 0.72
   3 !    7.2   0.0    0.0032       5.2      26      47 ..     306     327 ..     302     333 .. 0.89
   4 ?   -3.6   0.0         8   1.3e+04      36      51 ..     343     358 ..     341     370 .. 0.75
   5 !    9.6   0.0   0.00061         1      26      44 ..     408     426 ..     407     448 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.36
                                       GGG-EEETTTTEEE--SCE..EEEEEESSS CS
                          Fn3-like  44 kdlsvwdeekqkwvvepGe..ytvlvgtss 71 
                                        d+ +  e  ++  + pGe  y v vg+ss
  gi|344210292|ref|YP_004786468.1| 110 ADVTFAVEP-DQ--ISPGEytYAVAVGESS 136
                                       444444443.22..3344422667777776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.6
                                       EE.E-TT-EEEEEEEEECGGG CS
                          Fn3-like  27 ve.LapGesktvtftldrkdl 46 
                                       v+ La G+s+  t t+   dl
  gi|344210292|ref|YP_004786468.1| 209 VHsLAGGQSQMSTATVRTADL 229
                                       666778888877777776665 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0032
                                       EEEE-TT-EEEEEEEEECGGG- CS
                          Fn3-like  26 kveLapGesktvtftldrkdls 47 
                                        v+La+ e++tv+++++ ++ls
  gi|344210292|ref|YP_004786468.1| 306 TVSLAANETTTVSIDVNTTNLS 327
                                       578**************99998 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 8
                                       EEEEEEECGGG-EEET CS
                          Fn3-like  36 tvtftldrkdlsvwde 51 
                                       tv++t++ +++ v d 
  gi|344210292|ref|YP_004786468.1| 343 TVSMTVQDSHFEVSDL 358
                                       7888888888887765 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.00061
                                       EEEE-TT-EEEEEEEEECG CS
                          Fn3-like  26 kveLapGesktvtftldrk 44 
                                        v+LapGes++v+f+++ +
  gi|344210292|ref|YP_004786468.1| 408 NVTLAPGESTRVRFEVEYT 426
                                       599************9865 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.2     2e+03      56      86 ..      45      75 ..      38      77 .. 0.79
   2 !    8.6   0.0    0.0012       1.9      43      91 ..      81     129 ..      76     138 .. 0.92
   3 ?   -2.6   0.0       3.7     6e+03      74      90 ..     185     201 ..     174     211 .. 0.80
   4 ?   -0.7   0.0      0.94   1.5e+03      74     102 ..     220     249 ..     216     251 .. 0.79
   5 ?    5.1   0.0     0.015        24      16      81 ..     334     422 ..     306     430 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.2
                      Cupredoxin_1 56 peefesedlgeekvlapgktttitiaplkpG 86
                                        e+e++ ++  +++ p++  +++++  ++G
  gi|344210292|ref|YP_004786468.1| 45 EDELEIRTVQSPTEIRPNEPLRVQLQITNAG 75
                                      4788999999999999999999988888877 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0012
                      Cupredoxin_1  43 ekvklkiknkdktpeefesedlgeekvlapgktttitiaplkpGeYeft 91 
                                       ++v l++++++++pe++  ++++++   + + t+ ++  + +pGeY+++
  gi|344210292|ref|YP_004786468.1|  81 QQVALRLNRDGQSPETVATKQVKVSAAEPADVTFAVEPDQISPGEYTYA 129
                                       6899***********************9******************987 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.7
                      Cupredoxin_1  74 ktttitiaplkpGeYef 90 
                                       +t +i + +++ G+Y+ 
  gi|344210292|ref|YP_004786468.1| 185 QTVQIAVDADQNGQYSD 201
                                       57788899999999975 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.94
                      Cupredoxin_1  74 ktttitiaplkpGeYeftcdmhmd.akGkl 102
                                       +t+t+  a l+pG Y++     ++ + G+l
  gi|344210292|ref|YP_004786468.1| 220 STATVRTADLEPGGYQYRVATENTtTTGTL 249
                                       5677888999******99888887778877 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.015
                      Cupredoxin_1  16 a...aaaektveitvkdggfe......Pskievkagekvklkiknkdkt......peefesed........lgeekv 69 
                                       +   a++ +tv++tv+d +fe      P+++ v     ++  ++n+++t       + + s+d        ++++ +
  gi|344210292|ref|YP_004786468.1| 334 SlgtADDIDTVSMTVQDSHFEvsdlagPNVLYVGDTAVFSADVTNTGETtgtqsiQHRIDSDDddrpeaygVDRNVT 410
                                       14547888999999999988744444477777888888888899999996666554888888899999998999999 PP

                      Cupredoxin_1  70 lapgktttitia 81 
                                       lapg++t++ ++
  gi|344210292|ref|YP_004786468.1| 411 LAPGESTRVRFE 422
                                       999999999885 PP

>> DUF4832  Domain of unknown function (DUF4832)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00042      0.69     107     200 ..      48     135 ..      47     144 .. 0.73
   2 !    8.4   0.2    0.0011       1.8     107     196 ..     152     239 ..     151     251 .. 0.76
   3 ?    3.0   0.3     0.049        80     107     134 ..     257     284 ..     256     350 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00042
                           DUF4832 107 fvlessslskkvkaggtlsleltlkNeGfAalynerkvelvlrdeegeekyklkldadprkwlpgttttitiklklp 183
                                       ++++ ++ ++++++++ l+++l+++N G  +    ++v l l ++ ++ ++  + ++ ++   p + +t+ ++   p
  gi|344210292|ref|YP_004786468.1|  48 LEIRTVQSPTEIRPNEPLRVQLQITNAGSETTT--QQVALRLNRDGQSPETVATKQVKVSAAEPAD-VTFAVE---P 118
                                       5788899999******************76665..5666666444444444555666666666655.444444...7 PP

                           DUF4832 184 selakGkykvyLnlpdp 200
                                       ++++ G+y+  +++ + 
  gi|344210292|ref|YP_004786468.1| 119 DQISPGEYTYAVAVGES 135
                                       9*****99998887665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0011
                           DUF4832 107 fvlessslskkvkaggtlsleltlkNeGfAalynerkvelvlrdeegeekyklk.ldadprkwlpgttttitiklkl 182
                                       fvl +++ ++++ +g ++s++ +l+N+G  +    ++v++ +  +++++++  + l++++ ++++g+++  t+++ +
  gi|344210292|ref|YP_004786468.1| 152 FVLADTTENATIVRGTNASIRANLTNVGAYRG--VQTVQIAVDADQNGQYSDAEtLNESVHSLAGGQSQMSTATVRT 226
                                       8999999999*****************95554..5567777777777774444349**********97666666544 PP

                           DUF4832 183 pselakGkykvyLn 196
                                        ++l+ G y+  ++
  gi|344210292|ref|YP_004786468.1| 227 -ADLEPGGYQYRVA 239
                                       .6999998876655 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.049
                           DUF4832 107 fvlessslskkvkaggtlsleltlkNeG 134
                                       f +++++ +++v++g+t++++  ++N+G
  gi|344210292|ref|YP_004786468.1| 257 FRVQNTTAPANVTRGETANVSAVVENVG 284
                                       7899**********************99 PP

>> A2M  Alpha-2-macroglobulin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0066        11      59      91 ..      52      84 ..      35      86 .. 0.84
   2 !    7.3   0.0    0.0025         4      59      83 ..     261     285 ..     238     294 .. 0.80
   3 ?   -0.6   0.0      0.74   1.2e+03      59      85 ..     357     383 ..     300     389 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0066
                                      EEE--SEEETTSEEEEEEEEEE-SSS-EEEEEE CS
                               A2M 59 dlnlPysvrrgeqveikavvfNyldkeikvrve 91
                                      +++ P+ +r +e ++++  + N  +++ + +v 
  gi|344210292|ref|YP_004786468.1| 52 TVQSPTEIRPNEPLRVQLQITNAGSETTTQQVA 84
                                      4689*******************9998887775 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0025
                                       EEE--SEEETTSEEEEEEEEEE-SS CS
                               A2M  59 dlnlPysvrrgeqveikavvfNyld 83 
                                       +++ P  v+rge+ +++avv N  d
  gi|344210292|ref|YP_004786468.1| 261 NTTAPANVTRGETANVSAVVENVGD 285
                                       4689******************865 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.74
                                       EEE--SEEETTSEEEEEEEEEE-SSS- CS
                               A2M  59 dlnlPysvrrgeqveikavvfNyldke 85 
                                       dl  P  +  g++   +a v N  +++
  gi|344210292|ref|YP_004786468.1| 357 DLAGPNVLYVGDTAVFSADVTNTGETT 383
                                       577888888888888888888886665 PP

>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   4.3e-06     0.007     151     259 ..      20     120 ..       7     143 .. 0.78
   2 ?    0.4   0.1      0.21   3.4e+02     163     256 ..     135     225 ..     121     235 .. 0.74
   3 ?    2.0   1.8     0.067   1.1e+02     185     257 ..     206     278 ..     184     287 .. 0.83
   4 ?    1.5   1.0     0.097   1.6e+02     187     258 ..     264     324 ..     252     333 .. 0.70
   5 ?   -2.2   0.1       1.3   2.1e+03     186     216 ..     406     436 ..     366     460 .. 0.72
   6 ?    0.2   0.1      0.23   3.8e+02     161     196 ..     543     575 ..     538     579 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.3e-06
                           DUF1616 151 lavaalgyavvaPkegekfTelyllgedgdelvaenypteltagesqevivgieNhEheevnYtvvvllqevtdeee 227
                                       + +a+lg  +   ++g + Te  +  ++  e  + + pte+  +e+ +v+++i+N + e+++ +v ++l++      
  gi|344210292|ref|YP_004786468.1|  20 IGGATLGLGIGGFADGPADTETTVSEDEL-EIRTVQSPTEIRPNEPLRVQLQITNAGSETTTQQVALRLNRD----- 90 
                                       45556666666656666667777766665.8888999********************************982..... PP

                           DUF1616 228 vevlerteldrrevtladnetweqelevepea 259
                                       +  ++ +++ +++v++++ e    +  vep++
  gi|344210292|ref|YP_004786468.1|  91 G--QSPETVATKQVKVSAAEPADVTFAVEPDQ 120
                                       2..35678888889999888888888888876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.21
                           DUF1616 163 PkegekfTelyllgedgdelvaenypteltagesqevivgieNhEheevnYtvvvllqevtdeeevevlerteldrr 239
                                        +  e+  ++++l++    l  +  + ++ +g++ ++    +N +  +   tv+++++     ++++  + ++l++ 
  gi|344210292|ref|YP_004786468.1| 135 SSAPESTGNVAVLTPPTFVLADTTENATIVRGTNASIRANLTNVGAYRGVQTVQIAVDA---DQNGQYSDAETLNES 208
                                       55566777777777776333344445678899999999999999999999999999997...456666789999999 PP

                           DUF1616 240 evtladnetweqeleve 256
                                         +la ++++ ++ +v+
  gi|344210292|ref|YP_004786468.1| 209 VHSLAGGQSQMSTATVR 225
                                       99999999988887775 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.067
                           DUF1616 185 enypteltagesqevivgieNhEheevnYtvvvllqevtdeeevevlerteldrrevtladnetweqelevep 257
                                       ++   +l+ g+sq  + ++     e+  Y+ +v+++++t++ +++v++  + + +++t  +n t  ++ +v+ 
  gi|344210292|ref|YP_004786468.1| 206 NESVHSLAGGQSQMSTATVRTADLEPGGYQYRVATENTTTTGTLHVQQPATFRVQNTTAPANVTRGETANVSA 278
                                       445567888999999999999999*************999999999999999999999999999888877764 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.097
                           DUF1616 187 ypteltagesqevivgieNhEheevnYtvvvllqevtdeeevevlerteldrrevtladnetweqelevepe 258
                                        p ++t+ge+ +v  ++eN +  +   +v ++ +            +++  +r+v+la+net++ +++v+ +
  gi|344210292|ref|YP_004786468.1| 264 APANVTRGETANVSAVVENVGDVDGLDNVTLRSDS-----------MNTTYSRTVSLAANETTTVSIDVNTT 324
                                       56777777777777777777766666666666653...........56667888888888888877777655 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 1.3
                           DUF1616 186 nypteltagesqevivgieNhEheevnYtvv 216
                                       + + +l+ ges++v   +e    ++++Y v+
  gi|344210292|ref|YP_004786468.1| 406 DRNVTLAPGESTRVRFEVEYTVTDSTDYPVE 436
                                       4445667788888888888887777777776 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 0.23
                           DUF1616 161 vaPkegekfTelyllgedgdelvaenypteltages 196
                                       v+P e+ +fT l++ ++++   v++++  ++++++ 
  gi|344210292|ref|YP_004786468.1| 543 VKPGEKFNFTGLEIETQQK---VEADFDAQFQTDSG 575
                                       67999999**********9...99999999988765 PP

>> DUF3872  Domain of unknown function, B. Theta Gene description (DUF3872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.2   1.9e+03      30      60 ..      48      78 ..      44      92 .. 0.80
   2 ?    2.2   0.0     0.088   1.4e+02      39      63 ..     161     185 ..     151     206 .. 0.71
   3 ?    5.8   0.0    0.0068        11      21      58 ..     248     285 ..     238     293 .. 0.87
   4 ?   -1.6   0.0       1.3   2.2e+03      92     109 ..     489     506 ..     475     514 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.2
                                      -EEEE----SS--TT-EEEEEEEEE-SS--S CS
                           DUF3872 30 FtvetmpvqkeiakgetvEiRlelkregeye 60
                                       ++ t+  ++ei  +e   + l++++ g+ +
  gi|344210292|ref|YP_004786468.1| 48 LEIRTVQSPTEIRPNEPLRVQLQITNAGSET 78
                                      5788889999999999999999999888654 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.088
                                       SS--TT-EEEEEEEEE-SS--SS-- CS
                           DUF3872  39 keiakgetvEiRlelkregeyedte 63 
                                        +i++g  + iR +l++ g y++ +
  gi|344210292|ref|YP_004786468.1| 161 ATIVRGTNASIRANLTNVGAYRGVQ 185
                                       6788899999999999999998765 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0068
                                       T---------EEEE----SS--TT-EEEEEEEEE-SS- CS
                           DUF3872  21 eldvqqeypFtvetmpvqkeiakgetvEiRlelkrege 58 
                                        l vqq   F v+    + ++++get+ +   +++ g+
  gi|344210292|ref|YP_004786468.1| 248 TLHVQQPATFRVQNTTAPANVTRGETANVSAVVENVGD 285
                                       799************************99887777665 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 1.3
                                       E-S-SEEEEEEE---SS- CS
                           DUF3872  92 llekekFrLyYtsesees 109
                                       +++++k+ LyY   s e+
  gi|344210292|ref|YP_004786468.1| 489 EITQDKYGLYYDEVSGET 506
                                       4568999****9988443 PP

>> N_BRCA1_IG  Ig-like domain from next to BRCA1 gene
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00047      0.77       1      70 [.      52     121 ..      52     146 .. 0.68
   2 ?   -1.3   0.1       2.3   3.7e+03      48      74 ..     240     267 ..     207     282 .. 0.63
   3 ?   -0.8   0.1       1.5   2.5e+03      21      69 ..     281     321 ..     255     333 .. 0.58
   4 ?   -2.8   0.0       6.7   1.1e+04      20      39 ..     376     395 ..     351     424 .. 0.59
   5 ?   -2.3   0.0       4.6   7.5e+03      53      79 ..     552     578 ..     528     592 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00047
                        N_BRCA1_IG   1 tipdgtvvppgteftktWrlrNtGseaWpagtklvfvg.Gdkmgsasaeessvsvpavap.geevevsvelk 70 
                                       t++  t++ p++  + + +++N Gse+ +++++l++   G++  + +  +++v+v+a++p + ++ v+ + +
  gi|344210292|ref|YP_004786468.1|  52 TVQSPTEIRPNEPLRVQLQITNAGSETTTQQVALRLNRdGQSP-E-TVATKQVKVSAAEPaDVTFAVEPDQI 121
                                       678889*****************************88734444.2.33445566666555222333333333 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.3
                        N_BRCA1_IG  48 eessvsvpavapgeevevsv.elkaPsk 74 
                                       +e++ ++  ++ ++ +++ v + +aP++
  gi|344210292|ref|YP_004786468.1| 240 TENTTTTGTLHVQQPATFRVqNTTAPAN 267
                                       4444455555555555555544455543 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.5
                        N_BRCA1_IG  21 rNtGseaWpagtklvfvgGdkmgsasaeessvs.vpavapgeevevsvel 69 
                                       +N G+++  ++++l+ ++   m      ++++s + ++a++e+++vs+++
  gi|344210292|ref|YP_004786468.1| 281 ENVGDVDGLDNVTLRSDS---M------NTTYSrTVSLAANETTTVSIDV 321
                                       444444433334433333...3......2333335567777777777765 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 6.7
                        N_BRCA1_IG  20 lrNtGseaWpagtklvfvgG 39 
                                       ++NtG+++ +++++ ++++ 
  gi|344210292|ref|YP_004786468.1| 376 VTNTGETTGTQSIQHRIDSD 395
                                       44555554444444444443 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 4.6
                        N_BRCA1_IG  53 svpavapgeevevsvelkaPskpgryi 79 
                                       +  +++ +++ve+  + +  +  g  i
  gi|344210292|ref|YP_004786468.1| 552 TGLEIETQQKVEADFDAQFQTDSGDRI 578
                                       233344444444444444444555555 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2     0.077   1.3e+02      13      70 .]      58     130 ..      50     130 .. 0.76
   2 ?   11.9   4.2   0.00018       0.3       1      70 []     150     238 ..     150     249 .. 0.86
   3 ?   11.2   6.5    0.0003      0.49       6      67 ..     263     332 ..     257     334 .. 0.84
   4 ?    1.3   1.0      0.38   6.2e+02      31      68 ..     341     388 ..     336     389 .. 0.74
   5 ?   -2.0   0.2         4   6.6e+03      12      42 ..     417     448 ..     409     479 .. 0.55

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.077
                                       -EB.TSEEEEEEEEE-S...S-EEEEEEEET..TEE..........EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7  13 tvs.ggtvtisasAsdd...ggvskVefyvd..gtl.g........lgtdtsapysltwtttaltagthtltV 70 
                                       ++  ++++ ++ + +++   ++ ++V ++++  g++ +        +++   a  ++++ +++ + g++t  V
  gi|344210292|ref|YP_004786468.1|  58 EIRpNEPLRVQLQITNAgseTTTQQVALRLNrdGQSpEtvatkqvkVSAAEPADVTFAVEPDQISPGEYTYAV 130
                                       566677888888888887778889999987755776668878886666666688999999999******9876 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00018
                                       XEEEEEE--TT--EB.TSEEEEEEEEE-S...S-EEEEEEEETTEE................EEEE-SSSEEEEEE- CS
                             Big_7   1 PtvtitsPangatvs.ggtvtisasAsdd...ggvskVefyvdgtl.g..............lgtdtsapysltwtt 58 
                                       Pt  +   +++at+  g++ +i+a+ ++     gv++V++ vd  + g              l+   s   ++t+ t
  gi|344210292|ref|YP_004786468.1| 150 PTFVLADTTENATIVrGTNASIRANLTNVgayRGVQTVQIAVDADQnGqysdaetlnesvhsLAGGQSQMSTATVRT 226
                                       6777777899******************999************7775667788888888888777788888888888 PP

                                       -...SEEEEEEE CS
                             Big_7  59 taltagthtltV 70 
                                       ++l+ g ++ +V
  gi|344210292|ref|YP_004786468.1| 227 ADLEPGGYQYRV 238
                                       888888888776 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.0003
                                       EE--TT--EB.TSEEEEEEEEE-S...S-EEEEEEEETTEE........EEEE-SSSEEEEEE--...SEEEE CS
                             Big_7   6 tsPangatvs.ggtvtisasAsdd...ggvskVefyvdgtl.g......lgtdtsapysltwtttaltagtht 67 
                                       t+    a+v+ g+t ++sa +++    +g ++V+++ d    +      l+++ +++ s+ ++tt+l+ gth+
  gi|344210292|ref|YP_004786468.1| 263 TA---PANVTrGETANVSAVVENVgdvDGLDNVTLRSDSMNtTysrtvsLAANETTTVSIDVNTTNLSRGTHN 332
                                       34...46699999******99888556777*****9997775577899999999******************7 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.38
                                       EEEEEEEETTEE...........EEEE-SSSEEEEEE--...SEEEEE CS
                             Big_7  31 vskVefyvdgtl.g.........lgtdtsapysltwtttaltagthtl 68 
                                       +++V   v+++  +         l+   +a +s+ +t t  t+gt+++
  gi|344210292|ref|YP_004786468.1| 341 IDTVSMTVQDSHfEvsdlagpnvLYVGDTAVFSADVTNTGETTGTQSI 388
                                       666666666666556666667778888999999999999999999887 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 4
                                       --EBTSEEEEEEEEE-S....S-EEEEEEEETTEE CS
                             Big_7  12 atvsggtvtisasAsdd....ggvskVefyvdgtl 42 
                                       + v    ++++ +++d+    ++  + + yv+g+ 
  gi|344210292|ref|YP_004786468.1| 417 TRVR---FEVEYTVTDStdypVEPLSLQTYVYGVY 448
                                       4444...5555555555443455555666666665 PP

>> Dicty_REP  Dictyostelium (Slime Mold) REP protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   4.4    0.0027       4.4     192     359 ..     178     356 ..     162     361 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0027
                         Dicty_REP 192 isllslvhqikvdsqnrdEeklselYsLyPfvdlekeesdieqesiese..ntqrensqpskeknkttttttttttt 266
                                       +  +  v++++++ +  ++ + s+  +L+ +v     +  + q ++++   +t   +    + + +t +tttt t+ 
  gi|344210292|ref|YP_004786468.1| 178 VGAYRGVQTVQIAVDADQNGQYSDAETLNESVH----SLAGGQSQMSTAtvRTADLEPGGYQYRVATENTTTTGTLH 250
                                       556667777777777777788888888888887....3333333333330033334444445556666777777777 PP

                         Dicty_REP 267 tsqartrkrka.idddklsenqake.kkknskksdddp................qsdfskkssrksgslkdvrvdni 325
                                       ++q+ t + ++ + + ++++ ++ +     ++                      ++ +s++ s   ++ + v +d+ 
  gi|344210292|ref|YP_004786468.1| 251 VQQPATFRVQNtTAPANVTRGETANvSAVVEN-----VgdvdgldnvtlrsdsmNTTYSRTVSLAANETTTVSIDVN 322
                                       88888877664144555555332220222222.....123345889999999989999******************* PP

                         Dicty_REP 326 sdseldddvnesispeekiisvsnkikqcllEvl 359
                                       +++ +  + n+s+   + i  vs  +++   Ev+
  gi|344210292|ref|YP_004786468.1| 323 TTNLSRGTHNHSLGTADDIDTVSMTVQDSHFEVS 356
                                       *99*********************9999988886 PP

>> Ig_GlcNase  Exo-beta-D-glucosaminidase Ig-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       2.3   3.7e+03      82      99 ..      67      84 ..      58     113 .. 0.53
   2 ?   -2.0   0.0       2.5     4e+03      32      92 ..     168     230 ..     154     243 .. 0.50
   3 ?    1.1   0.6      0.27   4.4e+02      71      92 ..     306     327 ..     217     334 .. 0.79
   4 ?    7.8   0.0    0.0021       3.5      34      92 ..     371     429 ..     340     437 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.3
                        Ig_GlcNase 82 ltveypaaalkgkkpkve 99
                                      +++++++a +++++++v 
  gi|344210292|ref|YP_004786468.1| 67 VQLQITNAGSETTTQQVA 84
                                      333333333332222222 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.5
                        Ig_GlcNase  32 etkvtvtLenkssvpAffvrlnlvdaa..geevlPvlwsDNyvtLlPgEsltltveypaaalk 92 
                                       + +++ +L+n ++   + +   +vda+  g+     + ++   +L  g+s+  t+++++a+l+
  gi|344210292|ref|YP_004786468.1| 168 NASIRANLTNVGAYRGVQTVQIAVDADqnGQYSDAETLNESVHSLAGGQSQMSTATVRTADLE 230
                                       555555555555544333322222222234444444455555555566666666666555555 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.27
                        Ig_GlcNase  71 yvtLlPgEsltltveypaaalk 92 
                                        v+L  +E++t+++++++++l+
  gi|344210292|ref|YP_004786468.1| 306 TVSLAANETTTVSIDVNTTNLS 327
                                       4788888888888888777665 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0021
                        Ig_GlcNase  34 kvtvtLenkssvpAffvrlnlvdaageevlPvlwsDNyvtLlPgEsltltveypaaalk 92 
                                         +  ++n++++       + +d+++++   ++  D  vtL PgEs+++++e++ + ++
  gi|344210292|ref|YP_004786468.1| 371 VFSADVTNTGETTGTQSIQHRIDSDDDDRPEAYGVDRNVTLAPGESTRVRFEVEYTVTD 429
                                       5566788888888777777778888888778888899************9988766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (613 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); 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:                        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: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 3856.11
//
Query:       gi|344210293|ref|YP_004786469.1|  [L=52]
Description: hypothetical protein HAH_5352 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   20.4   0.0    0.00038   20.4   0.0    1.0  1  HTH_45        Winged helix-turn-helix
     0.0043   17.1   0.0     0.0043   17.1   0.0    1.0  1  Replic_Relax  Replication-relaxation
     0.0096   15.7   0.0       0.01   15.6   0.0    1.0  1  DUF4364       Domain of unknown function (DUF4364)
  ------ inclusion threshold ------
      0.025   15.1   0.1       0.03   14.8   0.1    1.1  1  HTH_27        Winged helix DNA-binding domain
       0.04   13.9   0.1      0.045   13.7   0.1    1.2  1  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.051   13.5   0.0      0.053   13.5   0.0    1.1  1  PadR          Transcriptional regulator PadR-like family


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.3e-07   0.00038      32      72 ..       2      49 ..       1      52 [] 0.88

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.3e-07
                            HTH_45 32 sykllnkYLdmLvekgli.......kkskekYvlTekGlelleklkel 72
                                      s   +++ L+ L e +l+       +k++  Y +TekG ++ e++++ 
  gi|344210293|ref|YP_004786469.1|  2 SIAHVSRALQELRESELVdllvsedRKKGRVYDITEKGVDIWETIERK 49
                                      56678899*********9999999888999*************99975 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.5e-06    0.0043      27      71 ..       6      45 ..       2      52 .] 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
                      Replic_Relax 27 arrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarllaa 71
                                      ++r+L++Lre +l++ l  +++++++     vY++t+kG ++ ++
  gi|344210293|ref|YP_004786469.1|  6 VSRALQELRESELVDLLVSEDRKKGR-----VYDITEKGVDIWET 45
                                      78**************8888677777.....********998754 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.5e-06      0.01      35      75 ..       5      48 ..       1      49 [. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.5e-06
                           DUF4364 35 dlqqalseLvesglieee...ekenktlykiTekGketlelfen 75
                                      +++ al+eL es+l++     ++++  +y iTekG ++ e++e 
  gi|344210293|ref|YP_004786469.1|  5 HVSRALQELRESELVDLLvseDRKKGRVYDITEKGVDIWETIER 48
                                      67899*******998765311557889**********9998875 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 ?   14.8   0.1     1e-05      0.03      33      68 .]       4      39 ..       1      39 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1e-05
                            HTH_27 33 shisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +h+s +l +L e +Lv    +e  ++ + + +T+kG
  gi|344210293|ref|YP_004786469.1|  4 AHVSRALQELRESELVDLLVSEDRKKGRVYDITEKG 39
                                      79***********9996666654467799******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 ?   13.7   0.1   1.5e-05     0.045      33      53 ..       1      22 [.       1      37 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                                      SSHHHHHHHHHHHHHTTSEE.E CS
                         HTH_Crp_2 33 ltretvsrilseLkreglis.r 53
                                      ++  +vsr+l+eL++  l++  
  gi|344210293|ref|YP_004786469.1|  1 MSIAHVSRALQELRESELVDlL 22
                                      6889**************9852 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.8e-05     0.053      36      70 ..       8      40 ..       1      45 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCC CS
                              PadR 36 paLkrLekeglveseweesgegpprkyYrlTdaGr 70
                                      +aL++L++++lv+   +e  ++++ ++Y +T++G 
  gi|344210293|ref|YP_004786469.1|  8 RALQELRESELVDLLVSE--DRKKGRVYDITEKGV 40
                                      79***********99886..689999*******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); 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:                         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 0.32s 00:00:00.74 Elapsed: 00:00:00.51
# Mc/sec: 304.36
//
Query:       gi|344210294|ref|YP_004786470.1|  [L=211]
Description: hypothetical protein HAH_5353 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score 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   13.4   0.1       0.08   12.7   0.1    1.3  1  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr
      0.065   13.3   0.0       0.17   12.0   0.0    1.7  2  HTH_20        Helix-turn-helix domain
      0.087   11.8   0.0        0.1   11.6   0.0    1.2  1  TMEM232       Transmembrane protein family 232
      0.099   12.9   0.1       0.19   12.0   0.1    1.4  1  DUF3040       Protein of unknown function (DUF3040)
        3.6    7.7   7.7        6.3    6.9   7.7    1.3  1  DUF2892       Protein of unknown function (DUF2892)


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 ?   12.7   0.1   2.2e-05      0.08      35      83 ..     148     199 ..     133     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.2e-05
                      Trp_oprn_chp  35 alsGadwa...paltalAlvllAaavAvlavrglgrrvvgvllalagagaav 83 
                                       +++G++w    +a+t l+ ++lAa vA  + + +++ ++++++ +aga  ++
  gi|344210294|ref|YP_004786470.1| 148 EAEGRQWYqyyAAVTVLGAMVLAASVAFSLPGSIVLGLFSLVVGVAGACSVY 199
                                       6677777522267888888999999999999999999999999999998776 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.7e-05      0.17       3      34 ..      50      82 ..      48      94 .. 0.89
   2 ?   -2.2   0.0       1.3   4.5e+03       4      16 ..      91     103 ..      88     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.7e-05
                                      HHHHHS-HHHHHHHHHH.STCTTB-HHHHHHHH CS
                            HTH_20  3 iaeALahPvRrrilraL.araegltaselaerl 34
                                      i+e+L +  Rr++l  L  r+e ++++elae +
  gi|344210294|ref|YP_004786470.1| 50 IFEILKNSRRREVLHFLrERGEQVSLGELAEHV 82
                                      89***************99***********976 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                                       HHHHS-HHHHHHH CS
                            HTH_20   4 aeALahPvRrril 16 
                                       ++AL++  R r++
  gi|344210294|ref|YP_004786470.1|  91 TDALTSSERKRVY 103
                                       6899999999986 PP

>> TMEM232  Transmembrane protein family 232
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.9e-05       0.1     330     412 ..      85     168 ..      38     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.9e-05
                           TMEM232 330 ilaeicLyaatselrktaligfldcksskk.klelkdkseeekelkeaslldlleyfsskisdncdqviWiirYglv 405
                                       i +e +  a ts+ rk +++g+++c+ +k  ++ ++d ++++ + + ++  d  e +  ++  +++  +W  +Y++v
  gi|344210294|ref|YP_004786470.1|  85 IENETTTDALTSSERKRVYVGLYQCHLPKMdDIGVVDFNQDRGHITLTEKADDFEKYLNRTEGEAEGRQWYQYYAAV 161
                                       5567777899****************99852799999999999999999999999889999999************9 PP

                           TMEM232 406 ynlvkls 412
                                         l  ++
  gi|344210294|ref|YP_004786470.1| 162 TVLGAMV 168
                                       9887665 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   5.2e-05      0.19      38      82 ..     148     195 ..     131     197 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.2e-05
                           DUF3040  38 rrslrrlavlavllfvaGllllvlGvaaaa...vvlgvvGfvvmlagv 82 
                                       + + r+++   +++ v+G+++l + va +    +vlg++ +vv +ag+
  gi|344210294|ref|YP_004786470.1| 148 EAEGRQWYQYYAAVTVLGAMVLAASVAFSLpgsIVLGLFSLVVGVAGA 195
                                       33346667788889999*********9999777777777777777776 PP

>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   7.7    0.0018       6.3      15      56 ..     163     200 ..     158     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0018
                           DUF2892  15 vvGlvllllallglsggwgwllglvGavllltgltgfCplya 56 
                                       v+G+++l++++++     +  ++++G++ l+ g+ g C +y 
  gi|344210294|ref|YP_004786470.1| 163 VLGAMVLAASVAFS----LPGSIVLGLFSLVVGVAGACSVYH 200
                                       67888888888887....566789****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1197  (0.0667633); expected 358.6 (0.02)
Passed bias filter:                      876  (0.0488594); 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):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 1209.96
//
Query:       gi|344210295|ref|YP_004786471.1|  [L=381]
Description: phosphonate metabolism protein [Haloarcula hispanica ATCC 33960]
Scores for complete 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   39.6   0.7    0.00014   21.5   0.0    2.5  3  Amidohydro_3  Amidohydrolase family
    0.00012   21.5   0.6     0.0025   17.2   0.0    2.9  2  Amidohydro_1  Amidohydrolase family


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 !   16.1   0.1   6.6e-07    0.0059       3      23 ..      47      67 ..      47      89 .. 0.87
   2 ?   -2.9   0.0      0.38   3.4e+03     363     385 ..     225     247 ..     208     281 .. 0.71
   3 !   21.5   0.0   1.6e-08   0.00014     417     450 ..     332     364 ..     284     378 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.6e-07
                      Amidohydro_3  3 iDakGrlvlPGFvDsHtHlag 23
                                      iDa+G++vlPG+vD H   ++
  gi|344210295|ref|YP_004786471.1| 47 IDATGKYVLPGLVDLHGDDIE 67
                                      9***************87655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.38
                      Amidohydro_3 363 llnagvkvalgsDapvgpfdpwp 385
                                         n +++va ++D  v+++d++ 
  gi|344210295|ref|YP_004786471.1| 225 ASNRNIPVASHDDETVSSVDNAA 247
                                       34455556666665555555554 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 1.6e-08
                      Amidohydro_3 417 yTrgpAkalgledrkGtLevGadADlvvldadpl 450
                                       +++ pA+a gl dr G+Le Ga+ADl++ d dp+
  gi|344210295|ref|YP_004786471.1| 332 VSTAPAAAAGLYDR-GRLECGARADLIIVDPDPV 364
                                       7899*********9.***************9886 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1     0.045   4.1e+02       1      10 [.      53      62 ..      53      63 .. 0.94
   2 !   17.2   0.0   2.7e-07    0.0025     277     326 ..     321     368 ..     211     378 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.045
                                      EEEE-EEEEE CS
                      Amidohydro_1  1 ivlPGlIDaH 10
                                      +vlPGl+D+H
  gi|344210295|ref|YP_004786471.1| 53 YVLPGLVDLH 62
                                      69******** PP

  == domain 2  score: 17.2 bits;  conditional E-value: 2.7e-07
                                       HCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGT CS
                      Amidohydro_1 277 egglslkealrmaTingAkalglddkvGsievGkdADlvvvdldilaafv 326
                                       +g+    ++lr++ + +A a gl+ + G++e G +ADl++vd+d+ ++++
  gi|344210295|ref|YP_004786471.1| 321 NGDPLKDRVLRVS-TAPAAAAGLY-DRGRLECGARADLIIVDPDPVPSIA 368
                                       4444444556655.5699999**8.99**************998755554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 2246.15
//
Query:       gi|344210296|ref|YP_004786472.1|  [L=356]
Description: putative glucose-fructose oxidoreductase [Haloarcula hispanica ATCC 33960]
Scores for 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-21   75.0   0.0    1.8e-20   74.0   0.0    1.6  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.024   14.7   0.0    1.5  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 !   74.0   0.0     2e-24   1.8e-20       2     120 .]      22     143 ..      21     143 .. 0.93

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 2e-24
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE...EESSHHHHHTCTTESEEEE-S-GGGH CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve...aysdleelladpeidavivatpngth 75 
                                       r+a+ G+G+ + + + p  + ++l ev+ l+++++e+a+++a++ gv+   +y+++ +  a ++ da++++tpn +h
  gi|344210296|ref|YP_004786472.1|  22 RYALLGLGWWTIDLALPAIQDSDLGEVTTLVSSSSEKAKRLADENGVDhgiSYEEFHDGDAADRFDAIYIGTPNALH 98 
                                       899*******777777777777**************************999999999999999************** PP

                                       HHHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  76 eelakaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                        e+a+ a+e  k++l+EKP+ +tve a+++ve ++ + + ++++y
  gi|344210296|ref|YP_004786472.1|  99 LEYAETAAELDKAILCEKPMEATVERAQKMVEVCADAAVPLMIAY 143
                                       ***********************************9998888765 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 ?   14.7   0.0   2.7e-06     0.024       1      65 [.     155     222 ..     155     254 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-06
                                       HHHHHTTTTSSEEEEEE.EEECBEEECHHHHCCGGSH..HCSTSHHHHTCHHHHHHHHHHHTSEEEEE CS
                    GFO_IDH_MocA_C   1 KelIengklGevvsvdv.wtldtragaeakkrwkrrk..kksgGvlgdlgiHdiDllqwLfGqppsvv 65 
                                       KelIe+g +Ge+vsv + +     + ++++ +w+ ++   + g +++dlgi+ i+ +++L+  +p  v
  gi|344210296|ref|YP_004786472.1| 155 KELIEDGFIGEPVSVYGnNSQPLLEMNPDTDQWRLDPelSGYGTSVMDLGIYSINTTRFLLDREPLAV 222
                                       9**************9988888999999999***9999999999****************98877555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 2117.26
//
Query:       gi|344210297|ref|YP_004786473.1|  [L=409]
Description: putative sugar phosphatase of HAD superfamily [Haloarcula hispanica ATCC 33960]
Scores for complete 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   81.7   0.0    2.8e-22   78.7   0.0    2.4  3  Hydrolase_6     Haloacid dehalogenase-like hydrolase
      4e-16   59.3   0.1    6.8e-16   58.5   0.1    1.4  1  NUDIX           NUDIX domain
    1.5e-14   53.8   0.2    3.3e-14   52.7   0.2    1.6  1  Hydrolase_like  HAD-hyrolase-like
    2.5e-10   41.0   1.0    9.9e-10   39.0   0.9    2.0  1  Hydrolase       haloacid dehalogenase-like hydrolase
    0.00044   20.4   0.0     0.0026   17.9   0.0    2.1  2  HAD_2           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 !   78.7   0.0   7.7e-26   2.8e-22       1     101 []       9     108 ..       9     108 .. 0.98
   2 ?   -0.8   0.0      0.45   1.6e+03       6      29 ..     149     172 ..     147     181 .. 0.84
   3 ?   -3.6   0.0       3.4   1.2e+04      29      38 ..     346     355 ..     344     359 .. 0.87

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 7.7e-26
                                       EEEESTTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEHHHHHHHHHHHH CS
                       Hydrolase_6   1 flfDidGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvvtsataaaeylkkr 77 
                                       fl+D+dGv++ gd+a+p+a+e +n+l ++ k++ +lTN  + ++e++a++l+klg+d+++ +++ts+ a+a+yl++ 
  gi|344210297|ref|YP_004786473.1|   9 FLLDLDGVVYLGDEALPEAVESVNRLDERDKELRFLTNDPRFQRETIANRLRKLGIDAEKGEIITSGWATAHYLSQ- 84 
                                       79*************************************************************************9. PP

                                       SXXXEEEEESXHHHHHHHHHTTXE CS
                       Hydrolase_6  78 kadkkvlvigeeglreelkeagfk 101
                                       ++  +  v+g+ gl+ el+e g++
  gi|344210297|ref|YP_004786473.1|  85 QDMTTAAVVGSGGLEIELQEEGIE 108
                                       999******************986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.45
                                       TTTSEETTEE-TTHHHHHHHHHHT CS
                       Hydrolase_6   6 dGvLwrgdkaipgaaealnalraa 29 
                                       dG +   d ++pga  +++a++aa
  gi|344210297|ref|YP_004786473.1| 149 DGSFPTPDGPVPGAGAIVRAVEAA 172
                                       677777899*********999886 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.4
                                       TT-EEEEEE- CS
                       Hydrolase_6  29 agkpvvllTN 38 
                                       +gk v ++TN
  gi|344210297|ref|YP_004786473.1| 346 SGKAVHFVTN 355
                                       689999***9 PP

>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.1   1.9e-19   6.8e-16       3     119 ..     271     387 ..     269     399 .. 0.84

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 1.9e-19
                                       EEEEEEEEEETTSEEEEEEESSSSTTTEESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   3 rravgvvllnekgevLlvrrskkpfpgWelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpyg 79 
                                       r++v++v+ n+ +evLl++r+  ++  W+lP G+ve  E + +A+ RE+ EEtGl+    +l+g++ +  +  ++y+
  gi|344210297|ref|YP_004786473.1| 271 RPGVAAVVVNDADEVLLLKRA--DKEQWALPTGTVERCEPVGDAVTREVDEETGLQIAVERLIGVYSHPEQQVFSYP 345
                                       78999999999999*******..66669***********999************98888899996666666666666 PP

                                       E...EEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHHHHHH CS
                             NUDIX  80 d...eheilyvfleevegelepndenevsevrwvpleellkek 119
                                       +    h+++ +f+++ eg  +  de+e  ev ++++++l + +
  gi|344210297|ref|YP_004786473.1| 346 SgkaVHFVTNCFRCSIEGGTPEADEDEALEVGFFDMNDL-PSD 387
                                       688999999999999888888888***************.433 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.2   9.3e-18   3.3e-14       2      73 ..     180     249 ..     179     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 9.3e-18
                                       .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEE CS
                    Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddla 73 
                                       +gKPep m+++al  l  d  +  +iGD++atDi+gA++aG++++LV+  + +++ +++   +p+  + +la
  gi|344210297|ref|YP_004786473.1| 180 VGKPEPLMFEMALDGLADD-VQAAAIGDNPATDILGAHRAGLTGILVAEDKPTAASARDL-QQPDLTISSLA 249
                                       6***************555.699****************************999997755.69999888876 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.9   2.8e-13   9.9e-10       2     210 .]       7     219 ..       6     219 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 2.8e-13
                                       SEEEEESBTTTBCHHHHHHHHHHHH......CHHHHHHHHHH..HHCHHHHHH.HHHHHHHHHHH..HHHHHETTTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxx..xxxxxxxxx.xxxxxxxxxxx..xxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa......alalaaaletg..sehpigkal.vaaakarsgal..tgfatfigrg 67 
                                       +++++D+dG+++ g   + ++++s+      +++l+  ++     +  i+++l     +a++g++  +g+at     
  gi|344210297|ref|YP_004786473.1|   7 DAFLLDLDGVVYLGDEALPEAVESVnrlderDKELRFLTNDPrfQRETIANRLrKLGIDAEKGEIitSGWAT----- 78 
                                       799************8888888888666655555555555549999999999955555555555556*****..... PP

                                       HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 ayaigkpewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdn 144
                                       a    +++++ta       g    ++q++g +   +  +  a++  ad+++ ++++  a ++++ +g  +++ t+ +
  gi|344210297|ref|YP_004786473.1|  79 AHYLSQQDMTTAA--VVGSGGLEIELQEEGIEITDD--DPNAMVVGADEKTSYQDIQRAARHIQ-RGA-TFVGTNPD 149
                                       ************9..677777777778888888877..***********************999.899.*****777 PP

                                       HHHHH..HHHHHTT..GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                       xxxxx..xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase 145 petae..raanqlG..ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                        +++        +G   ++++a  +++ ++v+kp+p +++ a++ L ++  + a++GD++  D+ ++ +Ag
  gi|344210297|ref|YP_004786473.1| 150 GSFPTpdGPVPGAGaiVRAVEAAAGTEPTVVGKPEPLMFEMALDGL-ADDVQAAAIGDNPAtDILGAHRAG 219
                                       755551134444554333334444455555****************.66669***************9998 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       0.3   1.1e+03      81     128 ..      24      74 ..      10      80 .. 0.76
   2 !   17.9   0.0   7.2e-07    0.0026     126     177 ..     173     224 ..     165     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.3
                             HAD_2  81 ydgvkelLeeLkeagyklgivTsk...sreaveekleqlgiesyFdvivts 128
                                       ++++ e ++ L e++ +l   T+    +re++ + l++lgi+     i+ts
  gi|344210297|ref|YP_004786473.1|  24 LPEAVESVNRLDERDKELRFLTNDprfQRETIANRLRKLGIDAEKGEIITS 74 
                                       677888888888888888888887666778888888888887666666655 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 7.2e-07
                             HAD_2 126 vtsedvekkKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagikvia 177
                                        ++e +   KP+p ++e al+ l  +  ++  +GD+p tDi +a++ag++ i 
  gi|344210297|ref|YP_004786473.1| 173 AGTEPTVVGKPEPLMFEMALDGLA-DDVQAAAIGDNPaTDILGAHRAGLTGIL 224
                                       677788889************995.7778999****************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2669.60
//
Query:       gi|344210298|ref|YP_004786474.1|  [L=58]
Description: hypothetical protein HAH_5357 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); 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: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 381.48
//
Query:       gi|344210299|ref|YP_004786475.1|  [L=404]
Description: ferrichrome-binding protein [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.7e-10   39.2   0.0    1.1e-09   38.2   0.0    1.5  2  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
       0.15   12.1   0.0       0.35   11.0   0.0    1.5  1  TmoB          Toluene-4-monooxygenase system protein B (TmoB)


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 ?   -2.9   0.0      0.45     4e+03       4      21 ..      82      99 ..      79     106 .. 0.79
   2 !   38.2   0.0   1.3e-13   1.1e-09      90     233 ..     174     343 ..     133     348 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.45
                                      -SHHHHHHHHHTT-GGGE CS
                      Peripla_BP_2  4 lspsvteillalGatdkv 21
                                       ++ ++++l+al + d v
  gi|344210299|ref|YP_004786475.1| 82 MYNQYADMLVALNHGDAV 99
                                      678899999999877765 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 1.3e-13
                                       --TTS.....................HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEE CS
                      Peripla_BP_2  90 ssntg.....................eslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfgg 145
                                        ++++                     + l e +  +++++++ +++e+l a +++ ++ +++ ++ e ++p++v  +
  gi|344210299|ref|YP_004786475.1| 174 VGPFFgnfysgthgdpqepysenyhyYTLWELFGRVATVFQERKRYEQLRAVHQELIETIQTELPPEEDRPTAVRVT 250
                                       33333344444447777777777777788888999********************************6666666665 PP

                                       TTE...EEEE-TTSTTTHHHHT..S--EESTTT--.STT-EEE-HHHHHHH--SEEEEEEH..HHHT-S--HHHHT- CS
                      Peripla_BP_2 146 ade.ggyvvagsnsyigdllda..lgieniaaesk.kseyeeisaEqilasdpdvifvsgr..aeadnktgleflke 216
                                         + +++++  +   +  l+d+  l +++++ ++   + +++++ E++l +dpdvi+  +   +  d + + e l++
  gi|344210299|ref|YP_004786475.1| 251 LGDgQFWTYHLNR-PGFWLADTrpLAANDAFGDETwDGLWGSVGYETMLDADPDVILHLWGmtPRYDMDDVRERLAS 326
                                       5551666665544.4444444445999999999889*********************99998899999999****** PP

                                       SHHHHTSHHHHTT-EEE CS
                      Peripla_BP_2 217 npllaelpAvkngrVya 233
                                       + + +el Avk  rVya
  gi|344210299|ref|YP_004786475.1| 327 HSVGKELAAVKDDRVYA 343
                                       ****************7 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 ?   11.0   0.0   3.9e-05      0.35      11      55 ..     303     345 ..     300     362 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.9e-05
                              TmoB  11 DfvvqLvaVdtedtmdqVaekvahhavGrrvrpkpgaplrVrrqG 55 
                                       D  ++L   +    md V e++a+h+vG+ +++      rV+ +G
  gi|344210299|ref|YP_004786475.1| 303 DVILHLWGMTPRYDMDDVRERLASHSVGKELAAVK--DDRVYAHG 345
                                       67778888899999****************99543..34666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2337.97
//
Query:       gi|344210300|ref|YP_004786476.1|  [L=199]
Description: GntR family transcriptional regulator [Haloarcula hispanica ATCC 33960]
Scores for 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-08   32.2   0.1      2e-07   30.8   0.1    1.7  1  MarR_2           MarR family
    3.7e-07   30.0   0.0    7.1e-07   29.1   0.0    1.5  1  MarR             MarR family
    0.00011   21.9   0.0    0.00027   20.7   0.0    1.7  1  HTH_IclR         IclR helix-turn-helix domain
     0.0004   20.0   0.0    0.00087   18.9   0.0    1.5  1  GntR             Bacterial regulatory proteins, gntR family
    0.00044   19.7   0.0    0.00072   19.1   0.0    1.3  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0005   19.9   0.1    0.00087   19.1   0.1    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm
     0.0015   18.5   0.4     0.0027   17.6   0.3    1.6  1  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0034   16.8   0.0     0.0058   16.1   0.0    1.3  1  RepL             Firmicute plasmid replication protein (RepL)
     0.0077   16.2   0.1      0.014   15.4   0.1    1.4  1  HTH_11           HTH domain
     0.0085   16.0   0.0      0.015   15.3   0.0    1.4  1  TBPIP            TBPIP/Hop2 winged helix domain
     0.0093   15.7   0.1      0.018   14.8   0.1    1.4  1  HTH_DeoR         DeoR-like helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   15.8   0.0       0.14   12.2   0.0    2.2  2  HTH_29           Winged helix-turn helix
      0.011   16.2   0.0      0.026   15.0   0.0    1.6  1  HTH_27           Winged helix DNA-binding domain
      0.014   15.3   0.0      0.038   13.9   0.0    1.8  2  HTH_5            Bacterial regulatory protein, arsR family
      0.015   15.2   0.0      0.044   13.8   0.0    1.7  1  HTH_36           Helix-turn-helix domain
       0.02   14.7   0.6      0.028   14.2   0.6    1.3  1  7TM-7TMR_HD      7TM receptor with intracellular HD hydrolase
      0.026   14.6   0.2      0.097   12.8   0.0    1.9  2  HTH_20           Helix-turn-helix domain
      0.079   13.3   0.0       0.17   12.2   0.0    1.6  1  Penicillinase_R  Penicillinase repressor
      0.082   12.3   0.0       0.12   11.7   0.0    1.2  1  RNA_pol_Rpc34    RNA polymerase Rpc34 subunit
      0.084   13.0   0.1       0.23   11.6   0.1    1.7  2  Trp_repressor    Trp repressor protein


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 !   30.8   0.1   2.3e-10     2e-07      16      55 ..     151     189 ..     142     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.3e-10
                                       CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  16 rrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                       +++g  l ++e+++r+  sk++vsr+l+ L+a+ L+er++
  gi|344210300|ref|YP_004786476.1| 151 DADGV-LPQSEIVDRTEFSKATVSRTLDTLEAKNLIERKR 189
                                       45554.89*****************************984 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   7.9e-10   7.1e-07      16      51 ..     154     189 ..     148     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 7.9e-10
                                       TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  16 gplsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                       g l +se+ ++ + sk+tv+r+ld+Le k+lieR++
  gi|344210300|ref|YP_004786476.1| 154 GVLPQSEIVDRTEFSKATVSRTLDTLEAKNLIERKR 189
                                       66899*****************************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 !   20.7   0.0     3e-07   0.00027      15      50 ..     152     187 ..     147     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3e-07
                                       TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  15 apqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       a++ l  se+ +rt  +k+tv+R L tL+   ++e+
  gi|344210300|ref|YP_004786476.1| 152 ADGVLPQSEIVDRTEFSKATVSRTLDTLEAKNLIER 187
                                       6677899***********************999997 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   9.7e-07   0.00087      22      60 ..     154     191 ..     146     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.7e-07
                                       SB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                              GntR  22 dkLPsereLaaefgVsrttvReALrrLeaeglverrqgr 60 
                                         L +++e++++ ++s+ tv + L++Lea++l+er++++
  gi|344210300|ref|YP_004786476.1| 154 GVL-PQSEIVDRTEFSKATVSRTLDTLEAKNLIERKRRG 191
                                       578.899****************************9874 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   8.1e-07   0.00072      12      48 .]     150     186 ..     141     186 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.1e-07
                            HTH_24  12 LqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       L +++ ++q+e+ +r+  S++tv+r l+ Le + lI+
  gi|344210300|ref|YP_004786476.1| 150 LDADGVLPQSEIVDRTEFSKATVSRTLDTLEAKNLIE 186
                                       667999*****************************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 !   19.1   0.1   9.7e-07   0.00087       8      56 ..     140     189 ..     137     194 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.7e-07
                                       HHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB   8 eyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56 
                                       ++E  vY  +l + g +  +ei  +++ ++++v ++L  Le k l+er++
  gi|344210300|ref|YP_004786476.1| 140 SNERIVYEIMLdADGVLPQSEIVDRTEFSKATVSRTLDTLEAKNLIERKR 189
                                       678889*****99**********************************987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3     3e-06    0.0027      22      60 ..     156     198 ..     123     199 .] 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3e-06
                                       HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE...EEES CS
                         HTH_Crp_2  22 ltqeelAsmlGltretvsrilseLkreglis.rgrr...iril 60 
                                       l q e+ ++   +  tvsr+l  L+ ++li+ ++r+   ++il
  gi|344210300|ref|YP_004786476.1| 156 LPQSEIVDRTEFSKATVSRTLDTLEAKNLIErKRRGvgnVIIL 198
                                       678899999999*******************534433356665 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.5e-06    0.0058      78     112 ..     158     192 ..     142     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.5e-06
                              RepL  78 nRelaeetgislktvsetlkileeanilkkkanGv 112
                                       + e+ ++t+ s +tvs+tl  le  n++ +k  Gv
  gi|344210300|ref|YP_004786476.1| 158 QSEIVDRTEFSKATVSRTLDTLEAKNLIERKRRGV 192
                                       67899**************************9998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.5e-05     0.014       7      51 ..     147     190 ..     142     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                            HTH_11   7 elLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepg 51 
                                       e+ l+a+g ++ +e+ ++++ S++tv r +++Le++   Ie +++
  gi|344210300|ref|YP_004786476.1| 147 EIMLDADGVLPQSEIVDRTEFSKATVSRTLDTLEAKN-LIERKRR 190
                                       666799999**************************98.6665554 PP

>> TBPIP  TBPIP/Hop2 winged helix 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     0.015      29      52 ..     166     189 ..     140     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                             TBPIP  29 klgKtavqkaLdeLvdegkiieKe 52 
                                       +++K++v ++Ld+L+++++i  K 
  gi|344210300|ref|YP_004786476.1| 166 EFSKATVSRTLDTLEAKNLIERKR 189
                                       89******************9996 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 !   14.8   0.1     2e-05     0.018       9      51 ..     150     192 ..     147     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                          HTH_DeoR   9 lkqqgklsveelvellgvSeaTiRRDLneLeeqglltRthGGa 51 
                                       l  +g l   e+v++ + S+aT+ R L++Le+++l++R + G+
  gi|344210300|ref|YP_004786476.1| 150 LDADGVLPQSEIVDRTEFSKATVSRTLDTLEAKNLIERKRRGV 192
                                       66667777789***************************87665 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.52   4.7e+02       4      30 ..      36      61 ..      35      62 .. 0.87
   2 ?   12.2   0.0   0.00016      0.14      11      53 ..     154     193 ..     147     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.52
                            HTH_29  4 allllaeGvstvsqiAkllglsrrtvy 30
                                      al+ll  G+  +  +++ + + ++tv+
  gi|344210300|ref|YP_004786476.1| 36 ALMLLLAGHL-ITPAVATVTIGETTVQ 61
                                      899******9.9999999999999986 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00016
                            HTH_29  11 GvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrp 53 
                                       Gv   s+i+ ++  s+ tv r+l+  e++    l++r+r+g +
  gi|344210300|ref|YP_004786476.1| 154 GVLPQSEIVDRTEFSKATVSRTLDTLEAKN---LIERKRRGVG 193
                                       444489************************...8998877755 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 ?   15.0   0.0   2.9e-05     0.026      21      52 ..     158     189 ..     146     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.9e-05
                            HTH_27  21 ladlcgrlnvedshisyslkkLtekGLvertg 52 
                                       ++++++r+ ++++++s  l+ L++k L+er++
  gi|344210300|ref|YP_004786476.1| 158 QSEIVDRTEFSKATVSRTLDTLEAKNLIERKR 189
                                       689*************************8876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.2   2.8e+03      11      22 ..     138     149 ..     137     153 .. 0.85
   2 ?   13.9   0.0   4.2e-05     0.038      19      46 ..     159     186 ..     143     187 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.2
                                       HTTSSEEHHHHH CS
                             HTH_5  11 Laegelcvcela 22 
                                       La++e+ v e++
  gi|344210300|ref|YP_004786476.1| 138 LASNERIVYEIM 149
                                       789999999998 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  19 celaeelglsqstvShHLkkLreaGLVe 46 
                                       +e+++ ++ s++tvS+ L  L+  +L+e
  gi|344210300|ref|YP_004786476.1| 159 SEIVDRTEFSKATVSRTLDTLEAKNLIE 186
                                       8************************997 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.9e-05     0.044       2      55 .]     137     185 ..     136     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.9e-05
                            HTH_36   2 rLspsaklllgslasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55 
                                       rL  ++++++ ++++      g    q+ +  r++ sk Tvsr ++ Le + +i
  gi|344210300|ref|YP_004786476.1| 137 RLASNERIVYEIMLDAD----G-VLPQSEIVDRTEFSKATVSRTLDTLEAKNLI 185
                                       56667777777777777....3.23589999******************99887 PP

>> 7TM-7TMR_HD  7TM receptor with intracellular HD hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.6   3.1e-05     0.028     116     154 ..      12      50 ..       9      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                       7TM-7TMR_HD 116 gallvrklrsRsdllragllvalvnvlvilalsliqssn 154
                                       +++++ +  +Rs+++ ag++v+ ++++++la +li+++ 
  gi|344210300|ref|YP_004786476.1|  12 VSTMIENTLQRSEVVAAGVFVISTALMLLLAGHLITPAV 50 
                                       567889999*************************99876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.1   1.9e+03      51      61 .]     121     131 ..     120     131 .. 0.89
   2 ?   12.8   0.0   0.00011     0.097      22      60 ..     153     191 ..     138     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.1
                                       CTTEEEECTEE CS
                            HTH_20  51 agLvevvregr 61 
                                       agL+e +r+++
  gi|344210300|ref|YP_004786476.1| 121 AGLLEARRQEW 131
                                       8******9986 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00011
                                       CTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20  22 aegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                       ++ l  se+ +r + sk+t+s+ L++Le   L+e+ r g
  gi|344210300|ref|YP_004786476.1| 153 DGVLPQSEIVDRTEFSKATVSRTLDTLEAKNLIERKRRG 191
                                       55566689999999********************99976 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019      0.17       5      57 ..     142     191 ..     138     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                       -SHHHHHHHHHS-.EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEET CS
                   Penicillinase_R   5 Eaevmeilwekge.atvkevveeleeekelaysTVktllrrLvkKgllsrekeg 57 
                                       E+ v+ei+ +++  +  +e+v++    +e +++TV  +l  L++K+l++r++ g
  gi|344210300|ref|YP_004786476.1| 142 ERIVYEIMLDADGvLPQSEIVDR----TEFSKATVSRTLDTLEAKNLIERKRRG 191
                                       55566665555554555555554....5677********************998 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.12      75     134 ..     129     187 ..     123     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                                       CCCHHHHHTSXHHHHHHHHHHHHHXSSXE.EHHHHHHTTGXXHHHHHHHHHHHHHTTXXEE CS
                     RNA_pol_Rpc34  75 reeAkkktslsedeslVysiIeesGneGI.wsrtiksklnLhksvvkkcLksLeskkyiks 134
                                       +e  ++ + l ++e +Vy+i  ++  +G+  + +i  ++   k+ v + L +Le+k++i  
  gi|344210300|ref|YP_004786476.1| 129 QEWEETASRLASNERIVYEIMLDA--DGVlPQSEIVDRTEFSKATVSRTLDTLEAKNLIER 187
                                       444566778999999*****9986..78725889************************965 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       6.4   5.8e+03      63      79 ..      50      66 ..      48      68 .. 0.84
   2 ?   11.6   0.1   0.00026      0.23      41      76 ..     145     182 ..     128     188 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6.4
                     Trp_repressor 63 iAtItRvsrsLktgsde 79
                                      +At+t ++ ++++gs++
  gi|344210300|ref|YP_004786476.1| 50 VATVTIGETTVQSGSPG 66
                                      89999999999998875 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00026
                     Trp_repressor  41 vvkeLLk..eelsqreIaeelgvSiAtItRvsrsLktg 76 
                                       v++ +L+  + l+q+eI + ++ S At++R   +L+ +
  gi|344210300|ref|YP_004786476.1| 145 VYEIMLDadGVLPQSEIVDRTEFSKATVSRTLDTLEAK 182
                                       344455421568******************99999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); 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: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1394.90
//
Query:       gi|344210301|ref|YP_004786477.1|  [L=218]
Description: hypothetical protein HAH_5360 [Haloarcula hispanica ATCC 33960]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       500  (0.0278878); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1525.07
//
Query:       gi|344210302|ref|YP_004786478.1|  [L=321]
Description: hypothetical protein HAH_5361 [Haloarcula hispanica ATCC 33960]
Scores for complete 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   18.2   0.0     0.0087   16.5   0.0    1.8  2  DUF4367   Domain of unknown function (DUF4367)
  ------ inclusion threshold ------
        2.3    9.2   4.1         10    7.1   1.8    2.5  2  Pap_E4    E4 protein


Domain annotation for each model (and alignments):
>> DUF4367  Domain of unknown function (DUF4367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   9.7e-07    0.0087      18      86 ..      54     131 ..      45     136 .. 0.91
   2 ?   -2.4   0.0      0.69   6.2e+03      19      47 ..     251     280 ..     241     311 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.7e-07
                           DUF4367  18 isedsesalleYkdengelisfsiskqskeesqklsidtedaevekieingikatyyekedge..........yvlv 84 
                                       ++++s+ + ++  ++++++++f+    ++  + ++ idt + + ++i++ g + t++e + ge          ++lv
  gi|344210302|ref|YP_004786478.1|  54 TVTNSTAFEVTTVSNDSGTVTFD--QGDRTCGGGFRIDTPNRTRTDIQVRGVTVTLVEQHSGEpfdeigreqfASLV 128
                                       789********************..7888888******************************999999999999999 PP

                           DUF4367  85 w.e 86 
                                       w e
  gi|344210302|ref|YP_004786478.1| 129 WkE 131
                                       944 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.69
                           DUF4367  19 sedsesalleYkdengelisfs.iskqske 47 
                                        +d++ + le +   g+ ++++ i+ +s+ 
  gi|344210302|ref|YP_004786478.1| 251 ATDDSQVKLELTRPGGGRTVVVrIDLESET 280
                                       566666666666666666666655554443 PP

>> Pap_E4  E4 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.8    0.0012        10      51      91 ..      34      74 ..      26      76 .. 0.81
   2 ?    1.5   0.0     0.067     6e+02      49      95 ..     226     275 ..     208     276 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0012
                            Pap_E4 51 sstspsspttkks.eeespwtvtttgssvtltaqtkdGttVt 91
                                      + +s+ssp++++s e+++++tvt +++  ++t+ ++d  tVt
  gi|344210302|ref|YP_004786478.1| 34 NAPSESSPSETESnETTGSITVTNSTAF-EVTTVSNDSGTVT 74
                                      567788888888889*******988877.9999999988887 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.067
                            Pap_E4  49 sssstspsspttkks.eeespwtvt.ttgssvtltaqtkd.GttVtvtlh 95 
                                       s+++ts   +t+    ++ +   v+ t  s+v+l+ + +  G tV+v++ 
  gi|344210302|ref|YP_004786478.1| 226 SNERTSYAIQTEFDDpDTLDATVVEaTDDSQVKLELTRPGgGRTVVVRID 275
                                       45555555555555544444444441556788888777652689999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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 0.28s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2273.72
//
Query:       gi|344210303|ref|YP_004786479.1|  [L=196]
Description: NADH dehydrogenase/oxidoreductase [Haloarcula hispanica ATCC 33960]
Scores for 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-22   77.5   0.1    1.1e-21   77.1   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 !   77.1   0.1   5.9e-26   1.1e-21      32     131 .]      58     143 ..      31     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 5.9e-26
                                       S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-TEE-HHHHHHHC.S CS
                       Oxidored_q6  32 adskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGtCAafGGipaaannpsvgeevgellevv 108
                                       a         + ++ad+++v G++++k ++++++++++++++k+v+++G+C ++GG ++ +   +v   ++++++v+
  gi|344210303|ref|YP_004786479.1|  58 A---------SPRQADLIIVPGTIVSKFAPRMKRVYDQMPEPKFVVSMGSCTISGGPFQEGY--NV---IKGAEQVI 120
                                       2.........2349********************************************5555..33...46899*** PP

                                       -E.EEE-SSS--HHHHHHHHHHH CS
                       Oxidored_q6 109 pvdinipGCPphpeailetllal 131
                                       pvdi++pGCPp+pea+++++++l
  gi|344210303|ref|YP_004786479.1| 121 PVDIHVPGCPPRPEALIYGVAKL 143
                                       ******************99875 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:                      383  (0.021362); 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 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1310.42
//
Query:       gi|344210304|ref|YP_004786480.1|  [L=230]
Description: HTH DNA binding domain-containing protein [Haloarcula hispanica ATCC 33960]
Scores for 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-17   61.3   0.0    8.7e-17   60.7   0.0    1.3  1  HTH_10          HTH DNA binding domain
     0.0028   17.6   0.0     0.0052   16.7   0.0    1.5  1  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.003   17.4   0.1     0.0072   16.2   0.1    1.7  1  MarR_2          MarR family
      0.003   17.6   0.0      0.024   14.7   0.0    2.1  2  HTH_20          Helix-turn-helix domain
     0.0041   16.8   0.0      0.014   15.1   0.0    1.8  2  Sigma70_r4_2    Sigma-70, region 4
     0.0056   16.2   0.0       0.02   14.5   0.0    1.8  2  GerE            Bacterial regulatory proteins, luxR family
     0.0058   16.4   0.0      0.021   14.6   0.0    1.9  1  HTH_38          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.026   14.4   0.0    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
      0.024   14.4   0.0      0.049   13.4   0.0    1.4  1  HTH_23          Homeodomain-like domain
      0.055   13.7   0.0       0.11   12.7   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
       0.09   12.6   0.0       0.16   11.8   0.0    1.3  1  HTH_30          PucR C-terminal 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 !   60.7   0.0   5.3e-20   8.7e-17       1      53 []     174     226 ..     174     226 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 5.3e-20
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LT +q+e+l++  e GY+d+PR+ ++k++A+elG ++st+s+hLrka+ +l+e
  gi|344210304|ref|YP_004786480.1| 174 LTSRQREALAAGREVGYYDVPRNGSVKDVAEELGCAPSTASNHLRKAQARLVE 226
                                       9************************************************9985 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 !   16.7   0.0   3.2e-06    0.0052      11      46 ..     194     229 ..     191     230 .] 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.2e-06
                                       HHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SE CS
                             HTH_1  11 aeegsftrAAeeLglsqpavsrqikrLEeelgvpLf 46 
                                        ++gs+   AeeLg +++++s ++++  ++l ++ f
  gi|344210304|ref|YP_004786480.1| 194 PRNGSVKDVAEELGCAPSTASNHLRKAQARLVERVF 229
                                       589***********************9999877766 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   4.4e-06    0.0072      22      48 ..     193     223 ..     172     228 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.4e-06
                                       E....EHHHHHHHHTSSHHHHHHHHHHHHHT CS
                            MarR_2  22 l....tvgelarrlglsksavsrilkrLvaa 48 
                                       +    +v+++a++lg  +s++s++l++++a+
  gi|344210304|ref|YP_004786480.1| 193 VprngSVKDVAEELGCAPSTASNHLRKAQAR 223
                                       334449**********************985 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.62     1e+03      22      37 ..     137     154 ..     130     157 .. 0.78
   2 !   14.7   0.0   1.5e-05     0.024      26      57 ..     198     228 ..     193     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.62
                                       CTTB-HHHHHHHH..TS- CS
                            HTH_20  22 aegltaselaerl..dls 37 
                                       +e++t++++ ++l  +++
  gi|344210304|ref|YP_004786480.1| 137 GEPATLEQVRDALpdGIT 154
                                       899******999975565 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.5e-05
                                       -HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  26 taselaerldlskntlsyHLrvLeeagLvevv 57 
                                       +++++ae+l+++++t+s+HLr+  +a Lve+v
  gi|344210304|ref|YP_004786480.1| 198 SVKDVAEELGCAPSTASNHLRKA-QARLVERV 228
                                       7899*****************95.77777765 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 ?   -1.6   0.0       1.4   2.3e+03      11      19 ..     174     182 ..     173     189 .. 0.86
   2 !   15.1   0.0   8.6e-06     0.014      28      53 ..     198     223 ..     196     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.4
                                       S-HHHHHHH CS
                      Sigma70_r4_2  11 Lperqreif 19 
                                       L+ rqre++
  gi|344210304|ref|YP_004786480.1| 174 LTSRQREAL 182
                                       8899**998 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 8.6e-06
                                       -HHHHHHHHT--HHHHHHHHHHHHHH CS
                      Sigma70_r4_2  28 sykEIAellgisegtVksrlsRArkk 53 
                                       s k++Ae+lg+ ++t  ++l++A ++
  gi|344210304|ref|YP_004786480.1| 198 SVKDVAEELGCAPSTASNHLRKAQAR 223
                                       89********************9665 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         2   3.3e+03       3      11 ..     174     182 ..     173     184 .. 0.84
   2 !   14.5   0.0   1.2e-05      0.02      19      45 ..     198     224 ..     196     225 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2
                                       S-HHHHHHH CS
                              GerE   3 LskRErevL 11 
                                       L++R+re L
  gi|344210304|ref|YP_004786480.1| 174 LTSRQREAL 182
                                       999*99987 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.2e-05
                                       -HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE  19 snkeIAeelniSekTVkvhksnimkKL 45 
                                       s+k++Aeel++++ T ++h++ ++ +L
  gi|344210304|ref|YP_004786480.1| 198 SVKDVAEELGCAPSTASNHLRKAQARL 224
                                       78********************99987 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.3e-05     0.021      22      43 ..     198     219 ..     173     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                            HTH_38  22 slreIArrLgrspsTIsRElkR 43 
                                       s++++A +Lg++psT s++l++
  gi|344210304|ref|YP_004786480.1| 198 SVKDVAEELGCAPSTASNHLRK 219
                                       899****************996 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 ?   14.4   0.0   1.6e-05     0.026      17      38 ..     198     219 ..     195     226 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                                       EHHHHHHHHTS-HHHHHHHHHH CS
                             HTH_5  17 cvcelaeelglsqstvShHLkk 38 
                                       +v + aeelg  +st S HL+k
  gi|344210304|ref|YP_004786480.1| 198 SVKDVAEELGCAPSTASNHLRK 219
                                       699*****************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     3e-05     0.049      19      40 ..     198     219 ..     190     225 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                            HTH_23  19 svreIAreLgvsrrTvyrwlkr 40 
                                       sv+++A+eLg+ ++T ++ l++
  gi|344210304|ref|YP_004786480.1| 198 SVKDVAEELGCAPSTASNHLRK 219
                                       99***************88776 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 ?   12.7   0.0   6.7e-05      0.11      24      45 ..     198     219 ..     196     223 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.7e-05
                                       -HHHHHHHHTS-HHHHHHHHHH CS
                    Fe_dep_repress  24 ktkdlaerLnvspssVsemlkk 45 
                                       ++kd+ae+L+ +ps++s  l+k
  gi|344210304|ref|YP_004786480.1| 198 SVKDVAEELGCAPSTASNHLRK 219
                                       689**************99998 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 ?   11.8   0.0    0.0001      0.16      12      38 ..     196     222 ..     194     225 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                                       TT-HHHHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_30  12 ggnisatAkaLhvHrnTlryRLrriee 38 
                                       +g+++++A++L++ + T ++ Lr+++ 
  gi|344210304|ref|YP_004786480.1| 196 NGSVKDVAEELGCAPSTASNHLRKAQA 222
                                       89**********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1489.21
//
[ok]
