# 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/Methanohalobium_evestigatum_Z_7303_uid49857/NC_014254.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/Methanohalobium_evestigatum_Z_7303_uid49857/NC_014254.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanohalobium_evestigatum_Z_7303_uid49857/NC_014254.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|298676128|ref|YP_003727877.1|  [L=400]
Description: orc1/cdc6 family replication initiation protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-18   65.7   0.1    5.9e-18   64.6   0.1    1.6  1  Cdc6_C           CDC6, C terminal winged helix domain
    3.5e-11   43.8   0.0    2.6e-10   41.0   0.0    2.3  2  AAA_16           AAA ATPase domain
    4.4e-10   40.0   0.0    8.7e-10   39.0   0.0    1.4  1  AAA_22           AAA domain
    6.2e-07   29.9   0.0    1.7e-06   28.5   0.0    1.8  1  AAA              ATPase family associated with various cellul
      1e-06   28.9   0.2    2.2e-06   27.8   0.2    1.6  1  ATPase_2         ATPase domain predominantly from Archaea
    8.2e-06   25.4   0.0    1.5e-05   24.5   0.0    1.4  1  TniB             Bacterial TniB protein
    1.2e-05   24.6   0.0    2.4e-05   23.6   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
    0.00026   21.0   0.0    0.00041   20.3   0.0    1.3  1  NACHT            NACHT domain
     0.0022   16.9   0.3       0.41    9.4   0.0    2.3  2  AAA_32           AAA domain
      0.003   17.1   0.0     0.0088   15.6   0.0    1.8  2  AAA_7            P-loop containing dynein motor region
     0.0043   17.4   0.2      0.019   15.3   0.2    2.2  1  RNA_helicase     RNA helicase
      0.006   15.6   0.0      0.036   13.0   0.0    2.1  2  Kinesin          Kinesin motor domain
     0.0061   16.9   0.0      0.017   15.5   0.0    1.7  1  AAA_assoc_2      AAA C-terminal domain
     0.0069   16.4   0.2      0.048   13.7   0.0    2.3  3  ResIII           Type III restriction enzyme, res subunit
     0.0077   15.9   0.0       0.02   14.6   0.0    1.7  1  Sigma54_activat  Sigma-54 interaction domain
     0.0088   15.3   0.0       0.02   14.1   0.0    1.7  2  PIF1             PIF1-like helicase
  ------ inclusion threshold ------
      0.013   15.5   0.1       0.67   10.0   0.0    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
      0.019   14.2   0.0      0.023   13.9   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.019   14.2   0.0      0.036   13.4   0.0    1.4  1  Zeta_toxin       Zeta toxin
      0.061   13.4   0.0       0.17   12.0   0.0    1.7  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.063   13.3   0.0       0.12   12.4   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.083   13.2   0.0       0.19   12.1   0.0    1.7  1  AAA_19           AAA domain
       0.09   12.5   0.0       0.17   11.6   0.0    1.5  1  AAA_24           AAA domain
      0.097   12.4   0.0       0.17   11.6   0.0    1.4  1  AAA_11           AAA domain


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.1   7.9e-21   5.9e-18       1      83 [.     304     384 ..     304     385 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 7.9e-21
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                       L+ +++l++ ++k+ +ttgev ++Y+++C+   vd+l++++vs+++ eL+mlg++++  + kG r grtr i++n +
  gi|298676128|ref|YP_003727877.1| 304 LLGIIELHK-DQKKNCTTGEVVQKYQQICNINSVDALSRTRVSKMIGELDMLGLINAPLKTKGIR-GRTRTITINKH 378
                                       667899999.******************************************************7.**********9 PP

                                       CHHHHH CS
                            Cdc6_C  78 pddvle 83 
                                        d +++
  gi|298676128|ref|YP_003727877.1| 379 IDVMEN 384
                                       998875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   3.5e-13   2.6e-10       1      60 [.      27      94 ..      27     173 .. 0.84
   2 ?   -2.0   0.0       5.5   4.1e+03      90     107 ..     203     238 ..     181     273 .. 0.49

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 3.5e-13
                            AAA_16  1 rlvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd.......ggif..lrgkc 60
                                      rl+ R+ ++eq+++++e+v sg+   + +++G  G+GK+++vr +l++l+k+       +  +  +  +c
  gi|298676128|ref|YP_003727877.1| 27 RLIARDSQIEQIAELVEPVLSGEKpDNAFIYGKTGTGKTAVVRYVLKELQKElstdnssH--VmpIFINC 94
                                      6899********************9*************************9966665431..22244444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.5
                            AAA_16  90 esaeleawrekleeala..................a 107
                                       + + +++++e+l++ l+                   
  gi|298676128|ref|YP_003727877.1| 203 NFSFPPYDAEQLTQILNdraeiafnedvldnmvipL 238
                                       444555555555555553333333333333333332 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   1.2e-12   8.7e-10       8     115 ..      54     164 ..      49     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.2e-12
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdllrellralglelka..erlsseelle 80 
                                        +++G +GtGKT ++r +l++l++e   ++++++v+  f+++++ ++ + +l+e+ + ++ + k   ++ s +e+++
  gi|298676128|ref|YP_003727877.1|  54 AFIYGKTGTGKTAVVRYVLKELQKE-LSTDNSSHVMpiFINCNEIGNTSHVLHEIIKTVDFNYKIpsSGISISEYYR 129
                                       689******************9654.444456666677********99999999999999655548889******** PP

                            AAA_22  81 aleqalraravielliiDEaqhlrs.eealeeLrsl 115
                                       +l+  l++     +++ DE++hl + +++l +L++ 
  gi|298676128|ref|YP_003727877.1| 130 HLWWVLNKNNYSIIVVFDEIEHL-KdDNVLYNLSRA 164
                                       ******99999899999******.659999988654 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   2.3e-09   1.7e-06       3     125 ..      56     201 ..      54     208 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.3e-09
                                       EESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS......................STTHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel..........gvefleisgsellsk......................yvgesekkir 47 
                                       +yG  GtGKT++++ v kel          +v  + i++ e+ +                        ++e  +++ 
  gi|298676128|ref|YP_003727877.1|  56 IYGKTGTGKTAVVRYVLKELqkelstdnssHVMPIFINCNEIGNTshvlheiiktvdfnykipssgiSISEYYRHLW 132
                                       8******************94444443322355789999999977899999*******9988877666666666666 PP

                                       HHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS.SSTEEEEEEESS...GGGSTHHHH CS
                               AAA  48 elfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk.eskvivigatnr...pdkldpall 120
                                        ++++   ++   i+++DEi+ l  ++          v+  L ++ + +k + + ++ +ig+tn+    d++dp ++
  gi|298676128|ref|YP_003727877.1| 133 WVLNK---NNYSIIVVFDEIEHLKDDN----------VLYNLSRAGEYMKVNpNVNIGIIGTTNDlmlKDQIDPRVM 196
                                       66654...33249**********5555..........7888888777777766667999******999999999999 PP

                                       STTSS CS
                               AAA 121 rgRfd 125
                                       ++ ++
  gi|298676128|ref|YP_003727877.1| 197 SSLAQ 201
                                       54444 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 !   27.8   0.2   2.9e-09   2.2e-06       6     172 ..      33     188 ..      28     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.9e-09
                          ATPase_2   6 kelkelee....ilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkkl 78 
                                         ++++ e    +l+ e+ +  fiYG  g GKta+++ ++++l++         +l+++++s++   + + +e  + 
  gi|298676128|ref|YP_003727877.1|  33 SQIEQIAElvepVLSGEKPDNAFIYGKTGTGKTAVVRYVLKELQK---------ELSTDNSSHVMPIFINCNEIGNT 100
                                       555555551111567899999*********************944.........57777777777666655666666 PP

                          ATPase_2  79 ekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltke 155
                                       + +l + ++++ ++  + +    + ++   l   ++k+   ii+++De+  l+    +   +++++L ++ e+   +
  gi|298676128|ref|YP_003727877.1| 101 SHVLHEIIKTVDFNYKIPSSGISISEYYRHLWWVLNKNNYSIIVVFDEIEHLK----D--DNVLYNLSRAGEYMKVN 171
                                       6777777777777655557777899****************************....4..77888998888888777 PP

                          ATPase_2 156 khlcvviclsSeglfie 172
                                        ++ + i+++ + l+++
  gi|298676128|ref|YP_003727877.1| 172 PNVNIGIIGTTNDLMLK 188
                                       77766666666655554 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0     2e-08   1.5e-05      21     132 ..      36     153 ..      26     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2e-08
                              TniB  21 erLeeLley.pkrkrmpnlllvGdsnnGKtmivekFarlhppekded.aekvpvlvvqappkpdekrlyaaiLealg 95 
                                       e+++eL+e   + +++ n+ ++G++ +GKt++v+   ++ ++e ++d +++v  + +++ +  ++++  ++i++++ 
  gi|298676128|ref|YP_003727877.1|  36 EQIAELVEPvLSGEKPDNAFIYGKTGTGKTAVVRYVLKELQKELSTDnSSHVMPIFINCNEIGNTSHVLHEIIKTVD 112
                                       455555554255778899****************99988887755541456666789******************99 PP

                              TniB  96 aplkara...rvskleqqvlrllrelkvrvL.iiDEihnll 132
                                        ++k      ++s+ +++   +l++ +  ++ ++DEi++l 
  gi|298676128|ref|YP_003727877.1| 113 FNYKIPSsgiSISEYYRHLWWVLNKNNYSIIvVFDEIEHLK 153
                                       99887664567899999999*****999987257****986 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   3.2e-08   2.4e-05      28      80 ..      26      78 ..      14     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.2e-08
                            DUF815 28 ddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaee 80
                                      ++L+  d+q e++ e +e  l+g++  n++++G+ GtGK ++v+ +l+e+++e
  gi|298676128|ref|YP_003727877.1| 26 ERLIARDSQIEQIAELVEPVLSGEKPDNAFIYGKTGTGKTAVVRYVLKELQKE 78
                                      679999*******************************************9987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   5.4e-07   0.00041       4      97 ..      55     156 ..      52     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.4e-07
                                       EEEC-TTTCHHHHHHHHHHHHCTS-SCCCC.-SEEEEEETTTTTTS-..........-HCHHHCCCCTS--SSS-CC CS
                             NACHT   4 ilqGeaGsGKTtLlqklalawaegklpqga.fklvFflslrelsrsgna.......rsladllfsqlpepaapvsev 72 
                                       ++ G+ G GKT+ ++ +  +++++    +  + +++f+++ e+   + +         + + + s +  +++  ++ 
  gi|298676128|ref|YP_003727877.1|  55 FIYGKTGTGKTAVVRYVLKELQKELSTDNSsHVMPIFINCNEIGNTSHVlheiiktVDFNYKIPSSGISISEYYRHL 131
                                       799******************99876665558999********999888766655555566666666666666666* PP

                                       HHHHCCSCCCEEEEEE-STT-SS-T CS
                             NACHT  73 wavllelperlLlilDglDelvtdl 97 
                                       w vl ++  ++  ++D ++ l++d+
  gi|298676128|ref|YP_003727877.1| 132 WWVLNKNNYSIIVVFDEIEHLKDDN 156
                                       *********************9976 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00055      0.41      32      60 ..      53      81 ..      48      87 .. 0.90
   2 ?    5.2   0.1      0.01       7.8     481     507 ..     254     280 ..     245     285 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00055
                            AAA_32 32 NifvlGesgtGrttlvkrlleeiakkept 60
                                      N f+ G++gtG+t +v+ +l+e +k+ +t
  gi|298676128|ref|YP_003727877.1| 53 NAFIYGKTGTGKTAVVRYVLKELQKELST 81
                                      89********************9998766 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.01
                            AAA_32 481 adllrEAdywakkegaevveaehVekA 507
                                        +ll+ A ++ak+e++ vv++ehV kA
  gi|298676128|ref|YP_003727877.1| 254 LKLLENAGTIAKHENSPVVTEEHVYKA 280
                                       589*********************999 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05    0.0088      35      61 ..      53      79 ..      33     112 .. 0.76
   2 ?   -2.7   0.0       4.7   3.5e+03     159     180 ..     186     206 ..     149     207 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                             AAA_7 35 pvllvGptGtGKtviikdllkkldkek 61
                                      + +++G+tGtGKt++++ +lk+l+ke 
  gi|298676128|ref|YP_003727877.1| 53 NAFIYGKTGTGKTAVVRYVLKELQKEL 79
                                      67899**************99999653 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.7
                             AAA_7 159 gggrneitpRllrhfnvlaite 180
                                          + +i+pR+++  +  ++++
  gi|298676128|ref|YP_003727877.1| 186 ML-KDQIDPRVMSSLAQHNFSF 206
                                       33.4789999998888777766 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   2.6e-05     0.019       2      34 ..      55      87 ..      54     176 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-05
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsv 34
                                      ++yG++g+GK+ +++++ k+l+k+l ++++++v
  gi|298676128|ref|YP_003727877.1| 55 FIYGKTGTGKTAVVRYVLKELQKELSTDNSSHV 87
                                      79**********************987776665 PP

>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   4.9e-05     0.036      55      89 ..      30      65 ..       5     116 .. 0.79
   2 ?   -0.6   0.0      0.64   4.8e+02     269     296 ..     194     220 ..     193     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.9e-05
                                      HHHHHHHHHHHHHHHHHTTSE.EEEEEEESTTSSHH CS
                           Kinesin 55 qeevyeetakplvesvleGyn.atifaYGqtgsGKT 89
                                       ++ + e +++lve vl+G +    f YG+tg+GKT
  gi|298676128|ref|YP_003727877.1| 30 ARDSQIEQIAELVEPVLSGEKpDNAFIYGKTGTGKT 65
                                      4455556679*********983579**********9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.64
                                       HHHHHHHHTCCTSTSCGGGSHHHHHTGG CS
                           Kinesin 269 rvisaLaekkkskhipYRdSkLTrlLqd 296
                                       rv+s+La++ + ++ pY   +LT++L+d
  gi|298676128|ref|YP_003727877.1| 194 RVMSSLAQH-NFSFPPYDAEQLTQILND 220
                                       689999999.89999***********87 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.2e-05     0.017      13      54 ..     240     280 ..     233     294 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXX CS
                       AAA_assoc_2  13 ealaeladGDaRkaLnlLElaaeaaeakegkieitledleea 54 
                                       +ala+  +GDaR aL+lLE a + a++ e++ ++t+e++ +a
  gi|298676128|ref|YP_003727877.1| 240 SALAAKEHGDARIALKLLENAGTIAKH-ENSPVVTEEHVYKA 280
                                       67888889***********99999986.88899999988765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   6.5e-05     0.048       4      53 ..      30      80 ..      27      92 .. 0.83
   2 ?   -0.9   0.0         2   1.5e+03     130     148 ..     138     156 ..     124     182 .. 0.71
   3 ?   -2.3   0.0       5.1   3.8e+03     132     146 ..     301     315 ..     239     339 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.5e-05
                                      E-HHHHHHHHHHT.......TTSEEEEEESTTSTHHHHHHHHHHHH-S... CS
                            ResIII  4 lreyQeeaienlleklks.krdkrglikmaTGtGKTlvaaklierllkkgk 53
                                       r+ Q+e i +l+e + s ++  +++i   TGtGKT v   + ++l+k+ +
  gi|298676128|ref|YP_003727877.1| 30 ARDSQIEQIAELVEPVLSgEKPDNAFIYGKTGTGKTAVVRYVLKELQKELS 80
                                      58999999999998776558888***************9999999888765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2
                                       TTT-SEEEEETGGGTTS.T CS
                            ResIII 130 rdrfdviiiDEaHrlgakk 148
                                       ++++ ++++DE  +l++++
  gi|298676128|ref|YP_003727877.1| 138 NNYSIIVVFDEIEHLKDDN 156
                                       5666799999999998864 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.1
                                       T-SEEEEETGGGTTS CS
                            ResIII 132 rfdviiiDEaHrlga 146
                                       ++ ++ i E H+ ++
  gi|298676128|ref|YP_003727877.1| 301 KIVLLGIIELHKDQK 315
                                       222222334444444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.7e-05      0.02       2      61 ..      29      97 ..      28     108 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                                      ---SHHHHHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHH.....HSTTTTS..-EEEEETTTS CS
                   Sigma54_activat  2 igesealkelleqikkvaktd..lsvlitGesGtGKellaraihe.....askrkek..pfvavncaai 61
                                      i+++++++++ e ++ v + +   + +i G++GtGK+ + r + +      s+ +++    + +nc +i
  gi|298676128|ref|YP_003727877.1| 29 IARDSQIEQIAELVEPVLSGEkpDNAFIYGKTGTGKTAVVRYVLKelqkeLSTDNSShvMPIFINCNEI 97
                                      6788899999999999986554489****************9988555542222222113356777766 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.6e-05      0.02       6      49 ..      34      78 ..      30     161 .. 0.78
   2 ?   -2.4   0.0       2.7     2e+03     226     280 ..     177     234 ..     147     247 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-05
                                      HHHHHHHH.......HCTS-EEEEESTTSSCHHHHHHHHHHCHCT CS
                              PIF1  6 Qkkvfdaiieavln.ekgklfFvtGsgGtgKtflwkallkklrse 49
                                      Q + + + +e vl+ ek+ + F++G  GtgKt + + +lk l++e
  gi|298676128|ref|YP_003727877.1| 34 QIEQIAELVEPVLSgEKPDNAFIYGKTGTGKTAVVRYVLKELQKE 78
                                      4444555557666659****************9999888888764 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.7
                                       ...................HHCHCCS---S.S--...........EEEESSCCHHHHH CS
                              PIF1 226 alieiPedlllkksedk..ieeivsevygd.llqeltdkeyleerailcptnedvdei 280
                                        +i   +dl+lk++ d+  +++++++ +     +  + ++ l++ra+++ +++  d++
  gi|298676128|ref|YP_003727877.1| 177 GIIGTTNDLMLKDQIDPrvMSSLAQHNFSFpPYDAEQLTQILNDRAEIAFNEDVLDNM 234
                                       4566667777777765522455555555544445555666677777776666655554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00089      0.67       3      28 ..      55      80 ..      53      89 .. 0.87
   2 ?    2.5   0.1      0.18   1.4e+02      68     124 ..     143     186 ..     125     199 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00089
                                      EEE--SSSSHHHHHHHGGGGBS--EE CS
                             AAA_5  3 lLvGppGtgKselaerlaaalnreve 28
                                      ++ G++GtgK+ +++++++ l++e+ 
  gi|298676128|ref|YP_003727877.1| 55 FIYGKTGTGKTAVVRYVLKELQKELS 80
                                      799***************99988765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.18
                                       EEEEESGGG--.HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                             AAA_5  68 ilvlDEverae.sevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                       i+v+DE+e+++ ++vl  L +            ge++k++++    ++ +i+t+n+l+
  gi|298676128|ref|YP_003727877.1| 143 IVVFDEIEHLKdDNVLYNLSR-----------AGEYMKVNPN---VNIGIIGTTNDLM 186
                                       455555555554444444433...........3344444443...2255666666655 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.1e-05     0.023       4     136 ..      54     185 ..      51     260 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.1e-05
                           DUF2075   4 vlVtGvaGtGKtvvllnllael.....eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnls 75 
                                        ++ G++GtGKt v   +l el     +d++++   +    N +++    + l +  +  +++ ++  +   i ++ 
  gi|298676128|ref|YP_003727877.1|  54 AFIYGKTGTGKTAVVRYVLKELqkelsTDNSSHVMPI--FINCNEIGNTSHVLHEIIKTVDFNYKIPSSGISISEYY 128
                                       79********************776433333444444..44555554444444443333334444444433333333 PP

                           DUF2075  76 efkka.eekkeepkedvvivDEAhrlltksdqaekqseenqlkelmkr.akvvvalvDegQel 136
                                         ++     ++++   +v++DE   l + +      ++     e mk   +v + +++    l
  gi|298676128|ref|YP_003727877.1| 129 --RHLwWVLNKNNYSIIVVFDEIEHLKDDNVL----YNLSRAGEYMKVnPNVNIGIIGTTNDL 185
                                       ..222044455555566778887777773333....333344444554334666666555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.8e-05     0.036      10      42 ..      45      77 ..      36      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.8e-05
                        Zeta_toxin 10 ypsqerPklillgGqpGAGKselaellkdeler 42
                                      + s+e+P+  ++ G +G GK+++ +++ +el++
  gi|298676128|ref|YP_003727877.1| 45 VLSGEKPDNAFIYGKTGTGKTAVVRYVLKELQK 77
                                      56789*************************983 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00022      0.17       7      82 ..      55     154 ..      50     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                                       EEE--TTSSHHHHHHHHHHHTT-..........-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS....... CS
                             AAA_2   7 lllgptgvGktelakalaellfv......kkekkliradaselleeeevehlvsrligappgyvgaeegG....... 70 
                                        + g+tg+Gkt + + + + l+       +++   i ++++e+      +h++ + i + +++ +   +G       
  gi|298676128|ref|YP_003727877.1|  55 FIYGKTGTGKTAVVRYVLKELQKelstdnSSHVMPIFINCNEIGN---TSHVLHEIIKTVDFNYKIPSSGisiseyy 128
                                       5789********666555555544444433444446678888877...99*************************** PP

                                       ..............EEEEETGGG--- CS
                             AAA_2  71 ..............ivllDEidKihp 82 
                                                     iv +DEi+  + 
  gi|298676128|ref|YP_003727877.1| 129 rhlwwvlnknnysiIVVFDEIEHLKD 154
                                       **********************8776 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016      0.12       6      46 ..      34      78 ..      29     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                                      HHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE  6 etealgkklakal....gdvilLeGdLGaGKTtlvrglakalgve 46
                                      ++e++++ +  +l     d  +++G+ G+GKT+ vr ++k+l+ e
  gi|298676128|ref|YP_003727877.1| 34 QIEQIAELVEPVLsgekPDNAFIYGKTGTGKTAVVRYVLKELQKE 78
                                      55566666655556544456999*****************99765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00025      0.19      11      42 ..      52      83 ..      45     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00025
                            AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelggvkp 42
                                      ++ ++ +  GtGKT v++ ++++l+++ + + 
  gi|298676128|ref|YP_003727877.1| 52 DNAFIYGKTGTGKTAVVRYVLKELQKELSTDN 83
                                      5778999******************9987754 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   0.00023      0.17       4      79 ..      53     154 ..      50     168 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                            AAA_24   4 kiliyGpsgiGKTtlakel.gpkplfidtekGlksldadkfpdie.......swedfldevvel............. 59 
                                       + +iyG+ g+GKT +++   ++    + t+++++ +    f +++        + +++++v+++             
  gi|298676128|ref|YP_003727877.1|  53 NAFIYGKTGTGKTAVVRYVlKELQKELSTDNSSHVMPI--FINCNeigntshVLHEIIKTVDFNykipssgisisey 127
                                       568**************998777778888888866532..2233334444443333333333337778888888888 PP

                            AAA_24  60 ......aaeladyktl.viDtidelee 79 
                                               ++++y+++ v+D i++l +
  gi|298676128|ref|YP_003727877.1| 128 yrhlwwVLNKNNYSIIvVFDEIEHLKD 154
                                       888888666666766515688888765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023      0.17      18      44 ..      50      78 ..      31     107 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                            AAA_11 18 e..itliqGPPGtgKTktivellsqllsr 44
                                      +   + i G+ GtgKT ++ ++l++l ++
  gi|298676128|ref|YP_003727877.1| 50 KpdNAFIYGKTGTGKTAVVRYVLKELQKE 78
                                      244789********************433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.59u 1.17s 00:00:01.75 Elapsed: 00:00:03.19
# Mc/sec: 380.64
//
Query:       gi|298676129|ref|YP_003727878.1|  [L=323]
Description: transposase IS4 family protein [Methanohalobium evestigatum Z-7303]
Scores for complete 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-21   74.9   0.1    8.1e-21   73.8   0.1    1.6  1  DUF772       Transposase domain (DUF772)
    2.1e-12   47.1   1.8    5.4e-12   45.8   1.8    1.7  1  DDE_Tnp_1    Transposase DDE domain
    0.00017   21.3   0.1    0.00047   19.9   0.1    1.7  1  DDE_Tnp_4    DDE superfamily endonuclease
     0.0011   19.0   0.2     0.0033   17.4   0.1    1.8  2  DDE_Tnp_1_3  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.1   1.8e-24   8.1e-21       1      70 [.      60     129 ..      60     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 1.8e-24
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlf 70 
                                       Grp +++ +mlk+l+lq+++glSd e+e+++ +++sfr fl +    + +pd +t + fRkr+++    ++++
  gi|298676129|ref|YP_003727878.1|  60 GRPEADVIVMLKMLILQQWHGLSDQEIEKQCIDRISFRHFLKFP---EYIPDSTTVWLFRKRIIDtnkEKEVW 129
                                       9*****************************************96...88**************9988766555 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   1.8   1.2e-15   5.4e-12       6     214 .]     146     311 ..     142     311 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.2e-15
                         DDE_Tnp_1   6 vlivDattvrvpgtk................edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglk 66 
                                       + i Dat++     +                +d+ w +k gk+++gyklh+++dt   li ++++t++ vhd+k+  
  gi|298676129|ref|YP_003727878.1| 146 GMIQDATFIHSDPGHagadkprgseaktrrnKDGTWAKKSGKSHFGYKLHTIIDTDYQLIRRFETTTATVHDNKVDL 222
                                       566688888765555788888888888888899*****************************************733 PP

                         DDE_Tnp_1  67 qlldelrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnk 143
                                             r  ++ +v++D+GY++ ++  + +                           ++ ++ r+++l  ++++rn 
  gi|298676129|ref|YP_003727878.1| 223 S-----R--ENEVVYRDKGYFGSKCCGYDA---------------------------TMQRAVRGRPLGIREILRNS 265
                                       3.....4..9***********777766666...........................79****************** PP

                         DDE_Tnp_1 144 skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                                +++ +R + Erv +  k +f+ + + + +  rv +++l++++ +nl
  gi|298676129|ref|YP_003727878.1| 266 -------------------------RISAIRVTGERVYAVTKGVFKSGTTLVTTVKRVNLKMLFTAFGFNL 311
                                       .........................********************************99999998877765 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   1.1e-07   0.00047      25     132 ..     187     286 ..     165     304 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-07
                         DDE_Tnp_4  25 kkkntlkvlivvdpngkiifvskgypGsvsDkeilensgllkalkeavkpgdvilaDkgFklsekllvpykk..... 96 
                                       k++ ++k+  ++d +++ i   +  ++ v+D+++    +l++       +++v+  Dkg+ +s+  ++ y+      
  gi|298676129|ref|YP_003727878.1| 187 KSHFGYKLHTIIDTDYQLIRRFETTTATVHDNKV----DLSR-------ENEVVYRDKGYFGSK--CCGYDAtmqra 250
                                       7777999999999999999999999999999887....4443.......4589999********..55554455556 PP

                         DDE_Tnp_4  97 kkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                        ++ +l  +e  +n++i+ +r++ Erv +  kg f+
  gi|298676129|ref|YP_003727878.1| 251 VRGRPLGIREILRNSRISAIRVTGERVYAVTKGVFK 286
                                       9********************************998 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   7.4e-07    0.0033      35      95 ..     181     239 ..     145     249 .. 0.78
   2 ?   -1.7   0.0      0.59   2.7e+03      96     116 ..     280     301 ..     271     308 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7.4e-07
                       DDE_Tnp_1_3  35 rGkssmGWfyGfkLhliindkGeila.vkltpgnvdDrepveelakellgklfaDkgyiskk 95 
                                       + k s    +G+kLh ii+   ++++ ++ t++ v+D++    l++e  + ++ Dkgy + k
  gi|298676129|ref|YP_003727878.1| 181 WAKKSGKSHFGYKLHTIIDTDYQLIRrFETTTATVHDNKVD--LSRE-NEVVYRDKGYFGSK 239
                                       4455555679*********9999985389999999998763..5655.789*******9876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.59
                       DDE_Tnp_1_3  96 laeelleegielitklrk.nmk 116
                                       +++ ++++g +l+t++++ n+k
  gi|298676129|ref|YP_003727878.1| 280 VTKGVFKSGTTLVTTVKRvNLK 301
                                       5667888999999998752444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.91s 00:00:01.51 Elapsed: 00:00:01.32
# Mc/sec: 742.18
//
Query:       gi|298676130|ref|YP_003727879.1|  [L=1084]
Description: CnaB domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete 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-257  836.8 109.3    2.2e-37  127.7   4.0    8.2  8  SdrD_B           SdrD B-like domain
    1.4e-72  239.9  44.7    1.8e-09   37.8   1.2    8.7  8  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
      1e-27   96.2   0.0     0.0034   17.4   0.0    8.3  8  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
    1.7e-25   88.8  40.0     0.0048   16.9   0.2    8.5  8  CarbopepD_reg_2  CarboxypepD_reg-like domain
      2e-16   60.1  69.5    1.6e-05   25.1   0.6   10.2  8  SpaA             Prealbumin-like fold domain
    1.4e-12   47.6   4.4      0.088   12.9   0.0    6.7  7  UDP-g_GGTase     UDP-glucose:Glycoprotein Glucosyltransferase
    1.4e-12   48.1  10.4        3.6    8.4   0.0    8.7  8  TTR-52           Transthyretin-like family
    2.7e-11   43.9   7.7        0.7   10.4   0.1    5.9  5  AdenylateSensor  Adenylate sensor of SNF1-like protein kinase
    3.5e-11   43.3  14.0        3.6    7.7   0.0    8.3  8  DUF2012          Protein of unknown function (DUF2012)
    3.6e-06   27.0  35.3       0.18   11.8   0.3    8.1  8  phage_tail_N     Prophage tail fibre N-terminal
    0.00028   20.8   3.4         14    5.8   0.0    5.5  5  DUF2025          Protein of unknown function (DUF2025)
    0.00062   19.3  17.5          1    8.7   0.0    7.1  8  Dioxygenase_C    Dioxygenase
     0.0025   18.0  40.8      0.098   12.9   0.1    9.3  9  MetallophosN     N terminal of Calcineurin-like phosphoestera
     0.0026   17.9   0.6    1.6e+02    2.6   0.0    5.8  6  HupF_HypC        HupF/HypC family
     0.0031   17.5  42.6       0.56   10.3   0.1   10.3 11  Big_1            Bacterial Ig-like domain (group 1)
  ------ inclusion threshold ------
       0.03   14.4  18.9        6.9    6.8   0.0    8.0  8  DUF3244          Domain of unknown function (DUF3244)
      0.033   14.1  10.6         50    3.9   0.0    6.4  6  PEGA             PEGA domain
      0.035   12.9  38.2       0.57    8.9   1.2    5.9  6  PLRV_ORF5        Potato leaf roll virus readthrough protein
       0.05   13.6   7.5         25    5.0   0.0    5.7  5  CooC_C           CS1-pili formation C-terminal
      0.084   12.6   0.4        5.6    6.8   0.1    3.1  2  Glyco_hydro_42C  Beta-galactosidase C-terminal domain
       0.66    9.9  28.2          7    6.6   0.1    7.2  8  EMP24_GP25L      emp24/gp25L/p24 family/GOLD


Domain annotation for each model (and alignments):
>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.7   4.0   2.6e-40   2.2e-37       1     112 []     162     273 ..     162     273 .. 0.98
   2 !  109.2   9.7   1.5e-34   1.3e-31       1     112 []     283     392 ..     283     392 .. 0.94
   3 !  101.7   7.8   3.1e-32   2.6e-29       2     112 .]     397     506 ..     396     506 .. 0.94
   4 !  104.8   6.4   3.4e-33   2.9e-30       1     112 []     510     618 ..     510     618 .. 0.94
   5 !  111.3   6.4   3.3e-35   2.8e-32       2     112 .]     623     731 ..     622     731 .. 0.93
   6 !  107.7   6.0   4.2e-34   3.6e-31       1     112 []     735     844 ..     735     844 .. 0.96
   7 !  113.4   8.6   7.3e-36   6.2e-33       1     112 []     848     957 ..     848     957 .. 0.93
   8 !  106.1   4.6   1.3e-33   1.1e-30       1     103 [.     961    1061 ..     961    1067 .. 0.91

  Alignments for each domain:
  == domain 1  score: 127.7 bits;  conditional E-value: 2.6e-40
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvtakk 76 
                                       as+Gd+Vw+D+nkn iqd++e g +gvtV+L++ +g+++ atttTd++G+Y+Ftnl+pG+Y+V+ft p ++++t ++
  gi|298676130|ref|YP_003727879.1| 162 ASLGDYVWNDMNKNDIQDDEEVGLTGVTVNLYNCSGDSLrATTTTDENGYYNFTNLEPGNYYVNFTIPPEFEFTLQD 238
                                       58*************************************99************************************ PP

                            SdrD_B  77 aGsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       aG d+ +dSd++++tg+t+++ lasge+n tidaGl
  gi|298676130|ref|YP_003727879.1| 239 AGPDN-IDSDVNSTTGNTSCIILASGENNDTIDAGL 273
                                       **887.7****************************7 PP

  == domain 2  score: 109.2 bits;  conditional E-value: 1.5e-34
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvtakk 76 
                                       a+iGd+VweD+n+nGiqd+ge gis++ VtL + +++++ ++ttTda+G+Y+Ft +tpG+Y+V+f+ ++gy++t+++
  gi|298676130|ref|YP_003727879.1| 283 ATIGDRVWEDSNGNGIQDDGELGISDIIVTLHNCSDDTIvSSTTTDADGYYNFT-VTPGSYYVNFS-SDGYVFTSAN 357
                                       58*****************************8877777769************9.9*********5.68******** PP

                            SdrD_B  77 aGsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       +G+dd +dSda++ +g+t++v+l+++e+n t+daGl
  gi|298676130|ref|YP_003727879.1| 358 QGTDDGVDSDANS-SGITDCVNLDNNETNYTVDAGL 392
                                       **********976.77******************97 PP

  == domain 3  score: 101.7 bits;  conditional E-value: 3.1e-32
                            SdrD_B   2 siGdfVweDanknGiqdagekgisgvtVtLkd.akgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakka 77 
                                       siGd+VweD n++Giq++g++gi +vt++L+d ++g+++a+ tTd +G Y+Ft+l+pG+Y+V+f+ap+gy++t   +
  gi|298676130|ref|YP_003727879.1| 397 SIGDYVWEDVNADGIQNDGNTGIGNVTINLYDcDTGNKIANNTTDVDGDYNFTGLSPGNYYVNFEAPHGYEFTILGQ 473
                                       8*****************************872567788************************************** PP

                            SdrD_B  78 GsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       G++ + d +a+   g+t+++tl sge+n tid+Gl
  gi|298676130|ref|YP_003727879.1| 474 GANYE-DNNANI-LGNTTCITLVSGENNDTIDVGL 506
                                       ***99.999875.66999***************96 PP

  == domain 4  score: 104.8 bits;  conditional E-value: 3.4e-33
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvtakk 76 
                                       a+iGdfVweD++k+G+qd ge+gisg tV+L++ +++++ ++t+T+asG+Y+F+ +tpG+Y+V+f+ ++gy++t+++
  gi|298676130|ref|YP_003727879.1| 510 ATIGDFVWEDSDKDGVQDPGETGISGLTVELYNCSTDELeSSTITNASGYYNFS-VTPGNYYVQFS-SDGYNFTQAN 584
                                       58*******************************99999989************8.9*********5.68*******9 PP

                            SdrD_B  77 aGsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       + s+d +dSdad+ +g+t+++t+ sge+netidaGl
  gi|298676130|ref|YP_003727879.1| 585 KESED-VDSDADS-SGNTTCITVVSGETNETIDAGL 618
                                       99887.6****86.67999****************7 PP

  == domain 5  score: 111.3 bits;  conditional E-value: 3.3e-35
                            SdrD_B   2 siGdfVweDanknGiqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvtakka 77 
                                        iGdfVweD++ +Giqd+ge+gi ++ V+L++ +++ + ++ttT++sG+Y+Ft ++pGeY+V+f+ ++gy++t +++
  gi|298676130|ref|YP_003727879.1| 623 MIGDFVWEDSDMDGIQDDGETGIPDIRVELYNCSTDNLvSNTTTNNSGYYNFT-VEPGEYYVNFS-SDGYEFTLQNQ 697
                                       69****************************8866555549************9.9*********5.68********* PP

                            SdrD_B  78 GsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       G +d++dSda++ +g+t+++tl+s+e+n tidaGl
  gi|298676130|ref|YP_003727879.1| 698 GGEDTVDSDANS-SGVTECITLESNETNDTIDAGL 731
                                       *********976.77*******************7 PP

  == domain 6  score: 107.7 bits;  conditional E-value: 4.2e-34
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakka 77 
                                       asiGd+VweD n++G+q++g++gi++vtV+L++ +g+ ++tt T++sG+Y+Ft+l+pG+Y+++f+ + gy++t   +
  gi|298676130|ref|YP_003727879.1| 735 ASIGDYVWEDVNGDGVQNDGDTGIDNVTVNLYNCNGDFLETTKTNESGYYNFTGLAPGDYYINFIDSPGYEFTILGQ 811
                                       68*************************************************************************** PP

                            SdrD_B  78 GsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       G+  + d +ad   g+t+++tl sge+n tidaGl
  gi|298676130|ref|YP_003727879.1| 812 GASYE-DNNADL-LGNTTCITLVSGENNDTIDAGL 844
                                       *9998.989875.56999****************7 PP

  == domain 7  score: 113.4 bits;  conditional E-value: 7.3e-36
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvtakk 76 
                                       a+iGdfVweD+nknG+qd ge+gisg tV+L++ +++ + ++ttT+asG+Y+F+ ++pGeY+V+f+ ++gy++t ++
  gi|298676130|ref|YP_003727879.1| 848 ATIGDFVWEDTNKNGKQDIGESGISGLTVELYNCSTDDLvSNTTTNASGYYNFS-VEPGEYYVNFS-SDGYEFTLAN 922
                                       58*****************************8877666659************8.9*********5.68******** PP

                            SdrD_B  77 aGsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       +G+d+++dSdad+ +g+t+++t++sge+n t+daGl
  gi|298676130|ref|YP_003727879.1| 923 QGVDNTVDSDADS-SGNTTCITVESGETNDTVDAGL 957
                                       ***********86.6799****************97 PP

  == domain 8  score: 106.1 bits;  conditional E-value: 1.3e-33
                            SdrD_B    1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvta 74  
                                        a+iGdfVweD+nknG+qd ge+gisg tV+L++ +++++ ++ttT+asG+Y+F+ +tpG+Y+V+f+ ++gy++t+
  gi|298676130|ref|YP_003727879.1|  961 ATIGDFVWEDTNKNGKQDIGESGISGLTVELYNCSTDELeSSTTTNASGYYNFS-VTPGSYYVQFS-SDGYEFTS 1033
                                        58*******************************99999989************8.9*********5.68****** PP

                            SdrD_B   75 kkaGsddaldSdadpatgltktvtlasge 103 
                                        +++G+dd++dSdad+ +g+t+++t++ ++
  gi|298676130|ref|YP_003727879.1| 1034 SNQGTDDSMDSDADS-SGNTTCITVEIRR 1061
                                        *************87.5688888887764 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.1   1.7e-11   1.5e-08       8      56 ..     179     228 ..     176     249 .. 0.87
   2 !   33.0   0.8   6.2e-11   5.3e-08      10      60 ..     302     352 ..     292     391 .. 0.85
   3 !   29.3   0.2   8.7e-10   7.4e-07      10      64 ..     415     470 ..     411     506 .. 0.79
   4 !   37.8   1.2   2.1e-12   1.8e-09       6      61 ..     525     580 ..     524     617 .. 0.84
   5 !   33.3   0.4   5.3e-11   4.5e-08       8      62 ..     639     693 ..     637     726 .. 0.88
   6 !   29.3   0.2   8.8e-10   7.5e-07       8      59 ..     752     804 ..     749     821 .. 0.90
   7 !   33.8   0.9   3.5e-11     3e-08      12      63 ..     869     920 ..     864     963 .. 0.79
   8 !   35.9   0.8   7.7e-12   6.6e-09      12      63 ..     982    1033 ..     977    1053 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.7e-11
                   CarboxypepD_reg   8 dasgapiagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsa 56 
                                       d    +++g+tV ++n ++++ +a+tttd++G++++++l+pg+y v ++ 
  gi|298676130|ref|YP_003727879.1| 179 DDEEVGLTGVTVNLYNcSGDSLRATTTTDENGYYNFTNLEPGNYYVNFTI 228
                                       6677899*********778899************************9875 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 6.2e-11
                   CarboxypepD_reg  10 sgapiagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsapGya 60 
                                          +i+   Vt+ n +d++ v+stttdadG+++++ ++pg+y v +s++Gy 
  gi|298676130|ref|YP_003727879.1| 302 GELGISDIIVTLHNcSDDTIVSSTTTDADGYYNFT-VTPGSYYVNFSSDGYV 352
                                       445789999****97788889*************9.**************96 PP

  == domain 3  score: 29.3 bits;  conditional E-value: 8.7e-10
                   CarboxypepD_reg  10 sgapiagatVtvtnadtg.tvastttdadGafrlrglppgtysvtvsapGyatatr 64 
                                        +++i ++t+ +++ dtg + a+ ttd dG+++++gl pg+y v ++ap   ++t+
  gi|298676130|ref|YP_003727879.1| 415 GNTGIGNVTINLYDCDTGnKIANNTTDVDGDYNFTGLSPGNYYVNFEAPHGYEFTI 470
                                       56799*********6665278***************************98887776 PP

  == domain 4  score: 37.8 bits;  conditional E-value: 2.1e-12
                   CarboxypepD_reg   6 VtdasgapiagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsapGyat 61 
                                       V d+  ++i+g tV+++n + ++ ++st t+a+G+++++ ++pg+y v++s++Gy  
  gi|298676130|ref|YP_003727879.1| 525 VQDPGETGISGLTVELYNcSTDELESSTITNASGYYNFS-VTPGNYYVQFSSDGYNF 580
                                       88999*************5566789*************7.***************73 PP

  == domain 5  score: 33.3 bits;  conditional E-value: 5.3e-11
                   CarboxypepD_reg   8 dasgapiagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsapGyata 62 
                                       d   ++i+  +V+++n + ++ v++ttt+++G+++++ ++pg+y v +s++Gy+ +
  gi|298676130|ref|YP_003727879.1| 639 DDGETGIPDIRVELYNcSTDNLVSNTTTNNSGYYNFT-VEPGEYYVNFSSDGYEFT 693
                                       667789**********777899**************9.***************754 PP

  == domain 6  score: 29.3 bits;  conditional E-value: 8.8e-10
                   CarboxypepD_reg   8 dasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtv.sapGy 59 
                                       +  +++i ++tV ++n ++++  +t+t+++G+++++gl+pg+y + +  +pGy
  gi|298676130|ref|YP_003727879.1| 752 NDGDTGIDNVTVNLYNCNGDFLETTKTNESGYYNFTGLAPGDYYINFiDSPGY 804
                                       556789**************************************998677777 PP

  == domain 7  score: 33.8 bits;  conditional E-value: 3.5e-11
                   CarboxypepD_reg  12 apiagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsapGyatat 63 
                                        +i+g tV+++n + ++ v++ttt+a+G+++++ ++pg+y v +s++Gy+ + 
  gi|298676130|ref|YP_003727879.1| 869 SGISGLTVELYNcSTDDLVSNTTTNASGYYNFS-VEPGEYYVNFSSDGYEFTL 920
                                       579*********667789**************7.***************8433 PP

  == domain 8  score: 35.9 bits;  conditional E-value: 7.7e-12
                   CarboxypepD_reg   12 apiagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsapGyatat 63  
                                         +i+g tV+++n + ++ ++sttt+a+G+++++ ++pg+y v++s++Gy+ ++
  gi|298676130|ref|YP_003727879.1|  982 SGISGLTVELYNcSTDELESSTTTNASGYYNFS-VTPGSYYVQFSSDGYEFTS 1033
                                        579*********5566789*************7.***************8554 PP

>> bMG3  Bacterial alpha-2-macroglobulin MG3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.4e-05     0.012      28      60 ..     185     218 ..     180     264 .. 0.86
   2 !    7.9   0.0    0.0036       3.1      28      61 ..     306     340 ..     301     370 .. 0.74
   3 !   10.2   0.0    0.0007       0.6      28      60 ..     419     452 ..     413     482 .. 0.84
   4 ?    6.3   0.0     0.012       9.8      28      59 ..     533     565 ..     530     590 .. 0.85
   5 !    9.5   0.0    0.0012         1      28      59 ..     645     677 ..     639     703 .. 0.81
   6 !   17.4   0.0     4e-06    0.0034      28      60 ..     758     790 ..     753     808 .. 0.91
   7 !    8.6   0.0    0.0021       1.8      28      59 ..     871     903 ..     868     935 .. 0.79
   8 !    8.2   0.0    0.0029       2.5      28      59 ..     984    1016 ..     981    1042 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                              bMG3  28 vagaeVrlldkkgevl.aegtTDaqGvarfaall 60 
                                       ++g++V+l++++g+ l a++tTD++G+++f++l+
  gi|298676130|ref|YP_003727879.1| 185 LTGVTVNLYNCSGDSLrATTTTDENGYYNFTNLE 218
                                       689*************668899********9884 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0036
                              bMG3  28 vagaeVrlldkkgevla.egtTDaqGvarfaalla 61 
                                       ++++ V+l +++++++  ++tTDa+G+++f+ +  
  gi|298676130|ref|YP_003727879.1| 306 ISDIIVTLHNCSDDTIVsSTTTDADGYYNFTVTPG 340
                                       578889****999887516789********98744 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0007
                              bMG3  28 vagaeVrlld.kkgevlaegtTDaqGvarfaall 60 
                                       + +++++l+d ++g+ +a+ tTD +G ++f++l+
  gi|298676130|ref|YP_003727879.1| 419 IGNVTINLYDcDTGNKIANNTTDVDGDYNFTGLS 452
                                       679*******5579****************9984 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.012
                              bMG3  28 vagaeVrlldkkgevlaegt.TDaqGvarfaal 59 
                                       ++g +V+l++++ ++l + t T+a+G+++f+ +
  gi|298676130|ref|YP_003727879.1| 533 ISGLTVELYNCSTDELESSTiTNASGYYNFSVT 565
                                       6899************97655********9876 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.0012
                              bMG3  28 vagaeVrlldkkge.vlaegtTDaqGvarfaal 59 
                                       +++++V+l++++ + ++ ++tT+++G+++f+ +
  gi|298676130|ref|YP_003727879.1| 645 IPDIRVELYNCSTDnLVSNTTTNNSGYYNFTVE 677
                                       799*******876515667899********976 PP

  == domain 6  score: 17.4 bits;  conditional E-value: 4e-06
                              bMG3  28 vagaeVrlldkkgevlaegtTDaqGvarfaall 60 
                                       + +++V+l++++g+ l +++T+++G+++f++l+
  gi|298676130|ref|YP_003727879.1| 758 IDNVTVNLYNCNGDFLETTKTNESGYYNFTGLA 790
                                       679**************************9874 PP

  == domain 7  score: 8.6 bits;  conditional E-value: 0.0021
                              bMG3  28 vagaeVrlldkkg.evlaegtTDaqGvarfaal 59 
                                       ++g +V+l++++  +++ ++tT+a+G+++f+ +
  gi|298676130|ref|YP_003727879.1| 871 ISGLTVELYNCSTdDLVSNTTTNASGYYNFSVE 903
                                       68999*****875156678899********977 PP

  == domain 8  score: 8.2 bits;  conditional E-value: 0.0029
                              bMG3   28 vagaeVrlldkkgevlae.gtTDaqGvarfaal 59  
                                        ++g +V+l++++ ++l + +tT+a+G+++f+ +
  gi|298676130|ref|YP_003727879.1|  984 ISGLTVELYNCSTDELESsTTTNASGYYNFSVT 1016
                                        6899************862678*******9876 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   6.6e-06    0.0056      13      50 ..     184     226 ..     177     229 .. 0.72
   2 !   14.7   0.6   2.6e-05     0.022      27      56 ..     324     352 ..     317     375 .. 0.87
   3 !    7.1   0.3    0.0062       5.3      25      52 ..     435     462 ..     412     471 .. 0.83
   4 !   16.9   0.2   5.6e-06    0.0048      20      58 ..     544     581 ..     527     602 .. 0.82
   5 !   15.9   0.4   1.1e-05    0.0095      22      57 ..     658     692 ..     647     711 .. 0.85
   6 !    8.7   0.3     0.002       1.7      13      50 ..     757     798 ..     745     806 .. 0.72
   7 !   16.3   0.4   8.4e-06    0.0072      23      57 ..     885     918 ..     871     940 .. 0.83
   8 !   16.8   0.3   5.8e-06    0.0049      20      58 ..     995    1032 ..     984    1050 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.6e-06
                   CarbopepD_reg_2  13 plpgatVyvkg.....tkkgtvTdenGnFelknlpagkytLvv 50 
                                        l g+tV + +      ++ t+TdenG+++++nl++g+y +++
  gi|298676130|ref|YP_003727879.1| 184 GLTGVTVNLYNcsgdsLRATTTTDENGYYNFTNLEPGNYYVNF 226
                                       566666655432222256899******************8877 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.6e-05
                   CarbopepD_reg_2  27 gtvTdenGnFelknlpagkytLvvsyvGyk 56 
                                        t+Td++G+++++ +++g y +++s+ Gy 
  gi|298676130|ref|YP_003727879.1| 324 STTTDADGYYNFT-VTPGSYYVNFSSDGYV 352
                                       69**********7.999***********96 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0062
                   CarbopepD_reg_2  25 kkgtvTdenGnFelknlpagkytLvvsy 52 
                                        ++ +Td +G ++++ l +g+y +++++
  gi|298676130|ref|YP_003727879.1| 435 IANNTTDVDGDYNFTGLSPGNYYVNFEA 462
                                       46789*****************999876 PP

  == domain 4  score: 16.9 bits;  conditional E-value: 5.6e-06
                   CarbopepD_reg_2  20 yvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktq 58 
                                       +  + +  t+T+++G+++++ +++g+y +++s+ Gy+  
  gi|298676130|ref|YP_003727879.1| 544 STDELESSTITNASGYYNFS-VTPGNYYVQFSSDGYNFT 581
                                       56677889***********6.999************864 PP

  == domain 5  score: 15.9 bits;  conditional E-value: 1.1e-05
                   CarbopepD_reg_2  22 kgtkkgtvTdenGnFelknlpagkytLvvsyvGykt 57 
                                        +   +t+T+ +G+++++ +++g+y +++s+ Gy+ 
  gi|298676130|ref|YP_003727879.1| 658 DNLVSNTTTNNSGYYNFT-VEPGEYYVNFSSDGYEF 692
                                       556679***********7.***************85 PP

  == domain 6  score: 8.7 bits;  conditional E-value: 0.002
                   CarbopepD_reg_2  13 plpgatVyvkgtk....kgtvTdenGnFelknlpagkytLvv 50 
                                        +  +tV + + +      t T+e+G+++++ l +g+y +++
  gi|298676130|ref|YP_003727879.1| 757 GIDNVTVNLYNCNgdflETTKTNESGYYNFTGLAPGDYYINF 798
                                       555555555443333336788*****************8875 PP

  == domain 7  score: 16.3 bits;  conditional E-value: 8.4e-06
                   CarbopepD_reg_2  23 gtkkgtvTdenGnFelknlpagkytLvvsyvGykt 57 
                                       +   +t+T+++G+++++ +++g+y +++s+ Gy+ 
  gi|298676130|ref|YP_003727879.1| 885 DLVSNTTTNASGYYNFS-VEPGEYYVNFSSDGYEF 918
                                       55678***********6.***************85 PP

  == domain 8  score: 16.8 bits;  conditional E-value: 5.8e-06
                   CarbopepD_reg_2   20 yvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktq 58  
                                        +  + +  t+T+++G+++++ +++g y +++s+ Gy+  
  gi|298676130|ref|YP_003727879.1|  995 STDELESSTTTNASGYYNFS-VTPGSYYVQFSSDGYEFT 1032
                                        56677889***********6.999************864 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   1.2   1.1e-07   9.4e-05       3      59 ..     182     225 ..     180     232 .. 0.84
   2 !    7.8   2.9    0.0046         4      28      58 ..     303     344 ..     230     356 .. 0.63
   3 !   25.1   0.6   1.9e-08   1.6e-05       2      68 ..     415     467 ..     402     471 .. 0.88
   4 ?    5.3   0.9     0.029        25       3      59 ..     530     572 ..     527     613 .. 0.88
   5 !    7.8   0.2    0.0049       4.2       2      58 ..     641     683 ..     630     684 .. 0.87
   6 !   14.2   5.8   4.8e-05     0.041       8      58 ..     689     796 ..     687     802 .. 0.55
   7 !    7.7   2.2    0.0051       4.3      20      58 ..     860     909 ..     800     910 .. 0.67
   8 ?    3.1   6.9      0.14   1.2e+02      18      59 ..     971    1023 ..     913    1033 .. 0.53

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.1e-07
                                       CCB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEEEE CS
                              SpaA   3 gkpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYllv 59 
                                       +  L G++  ly+++              ++  +t ttdenG+ +f++L++G+Y++ 
  gi|298676130|ref|YP_003727879.1| 182 EVGLTGVTVNLYNCS-------------GDSLRATTTTDENGYYNFTNLEPGNYYVN 225
                                       567899999999999.............35678999*******************96 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0046
                                       T.............TTCCEESEEE-BTTSEEEEEEEESEEEEE CS
                              SpaA  28 a............kktgtevttlttdenGkatfegLplGtYll 58 
                                       +              ++t v + ttd++G+ +f+ + +G+Y++
  gi|298676130|ref|YP_003727879.1| 303 ElgisdiivtlhnCSDDTIVSSTTTDADGYYNFT-VTPGSYYV 344
                                       03333344444443455666999***********.99****98 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 1.9e-08
                                       CCCB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-STTEE CS
                              SpaA   2 tgkpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYllvEtkaPegYv 68 
                                       +++ + +++  ly++d             tg+++++ ttd +G  +f+gL +G+Y++   +aP gY+
  gi|298676130|ref|YP_003727879.1| 415 GNTGIGNVTINLYDCD-------------TGNKIANNTTDVDGDYNFTGLSPGNYYVN-FEAPHGYE 467
                                       5677777888888888.............89*************************97.88999997 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.029
                                       CCB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEEEE CS
                              SpaA   3 gkpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYllv 59 
                                       ++ ++G + +ly+++             t++   +  t++ G+ +f+ + +G+Y+++
  gi|298676130|ref|YP_003727879.1| 530 ETGISGLTVELYNCS-------------TDELESSTITNASGYYNFS-VTPGNYYVQ 572
                                       577889999999999.............456667777**********.99*****96 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.0049
                                       CCCB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEEE CS
                              SpaA   2 tgkpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYll 58 
                                       +++ +++++ +ly+++             t++ v + tt++ G+ +f+ +++G+Y++
  gi|298676130|ref|YP_003727879.1| 641 GETGIPDIRVELYNCS-------------TDNLVSNTTTNNSGYYNFT-VEPGEYYV 683
                                       5667777777888888.............7899***************.******98 PP

  == domain 6  score: 14.2 bits;  conditional E-value: 4.8e-05
                                       S-EEEEEET............................TTSCCCHCHHTT.TTCCEE..................... CS
                              SpaA   8 GaeFtlykv............................dtttdgkdaleakktgtev..................... 35 
                                       G eFtl+++                            +                 +                     
  gi|298676130|ref|YP_003727879.1| 689 GYEFTLQNQggedtvdsdanssgvtecitlesnetndT-----------------Idaglyqpasigdyvwedvngd 748
                                       66788887733333333333333333333322222220.................2333334444444444444444 PP

                                       .........................SEEE-BTTSEEEEEEEESEEEEE CS
                              SpaA  36 .........................ttlttdenGkatfegLplGtYll 58 
                                                                +t +t+e G+ +f+gL++G+Y++
  gi|298676130|ref|YP_003727879.1| 749 gvqndgdtgidnvtvnlyncngdflETTKTNESGYYNFTGLAPGDYYI 796
                                       4444444445555555555555555*********************98 PP

  == domain 7  score: 7.7 bits;  conditional E-value: 0.0051
                                       CCCHCHHTT.............TTCCEESEEE-BTTSEEEEEEEESEEEEE CS
                              SpaA  20 tdgkdalea............kktgtevttlttdenGkatfegLplGtYll 58 
                                       ++gk+++++              t++ v + tt++ G+ +f+ +++G+Y++
  gi|298676130|ref|YP_003727879.1| 860 KNGKQDIGEsgisgltvelynCSTDDLVSNTTTNASGYYNFS-VEPGEYYV 909
                                       4444444445555566666554478999**************.******98 PP

  == domain 8  score: 3.1 bits;  conditional E-value: 0.14
                                        TSCCCHCHHTT.............TTCCEESEEE-BTTSEEEEEEEESEEEEEE CS
                              SpaA   18 tttdgkdalea............kktgtevttlttdenGkatfegLplGtYllv 59  
                                        t+++gk+++++              t++   + tt++ G+ +f+ + +G+Y+++
  gi|298676130|ref|YP_003727879.1|  971 TNKNGKQDIGEsgisgltvelynCSTDELESSTTTNASGYYNFS-VTPGSYYVQ 1023
                                        2333333333344444444444433455559999**********.9******96 PP

>> UDP-g_GGTase  UDP-glucose:Glycoprotein Glucosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.79   6.8e+02      14      52 ..     186     225 ..     176     259 .. 0.84
   2 ?    4.1   0.0     0.057        48      24      54 ..     317     347 ..     304     381 .. 0.69
   3 !   12.9   0.0    0.0001     0.088      13      89 ..     533     608 ..     525     613 .. 0.75
   4 !    7.8   0.0    0.0041       3.5      18      72 ..     650     702 ..     636     725 .. 0.66
   5 ?   -1.9   0.0       4.1   3.5e+03      29      59 ..     773     804 ..     755     833 .. 0.73
   6 !    6.8   0.0    0.0085       7.2      13      54 ..     871     912 ..     863     950 .. 0.68
   7 !    9.1   0.0    0.0016       1.3      13      69 ..     984    1036 ..     976    1064 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.79
                                       TT-EEEEE-SS-S-SEEEE--SGGGEEEEEE.-SEEEEEE CS
                      UDP-g_GGTase  14 rGlqleLgtekkksvaDTivmanlGYfQlka.nPGvwkle 52 
                                        G++++L + + +s+  T+     GY+ +   +PG + ++
  gi|298676130|ref|YP_003727879.1| 186 TGVTVNLYNCSGDSLRATTTTDENGYYNFTNlEPGNYYVN 225
                                       699999999999999999999999****975489999776 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.057
                                       S-S-SEEEE--SGGGEEEEEE-SEEEEEEE- CS
                      UDP-g_GGTase  24 kkksvaDTivmanlGYfQlkanPGvwklelr 54 
                                       ++++++ ++     GY+ +  +PG + ++ +
  gi|298676130|ref|YP_003727879.1| 317 SDDTIVSSTTTDADGYYNFTVTPGSYYVNFS 347
                                       33444444444556************98875 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.0001
                                       -TT-EEEEE-SS-S-SEEEE--SGGGEEEEEE-SEEEEEEE-TTHHHHHEEEEE--SS-S..--TT--.--EEEE-S CS
                      UDP-g_GGTase  13 prGlqleLgtekkksvaDTivmanlGYfQlkanPGvwklelregrssdiyeiesvgaegl..sspkde.gkevvlts 86 
                                        +Gl++eL + ++++++ +++ +  GY+ +  +PG + ++ +    sd y+++++++e+   +s  d+ g++  +t 
  gi|298676130|ref|YP_003727879.1| 533 ISGLTVELYNCSTDELESSTITNASGYYNFSVTPGNYYVQFS----SDGYNFTQANKESEdvDSDADSsGNTTCITV 605
                                       5799****9999999999999999**************9985....7888888886665421333333466666665 PP

                                       TT- CS
                      UDP-g_GGTase  87 feg 89 
                                       ++g
  gi|298676130|ref|YP_003727879.1| 606 VSG 608
                                       555 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0041
                                       EEEE-SS-S-SEEEE--SGGGEEEEEE-SEEEEEEE-TTHHHHHEEEEE--SS-S CS
                      UDP-g_GGTase  18 leLgtekkksvaDTivmanlGYfQlkanPGvwklelregrssdiyeiesvgaegl 72 
                                       +eL + ++++++  +  +n GY+ +  +PG + ++ ++      ++++++g e++
  gi|298676130|ref|YP_003727879.1| 650 VELYNCSTDNLVSNTTTNNSGYYNFTVEPGEYYVNFSSD--GYEFTLQNQGGEDT 702
                                       566554444545555679**************9998732..23355666655553 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 4.1
                                       EEEE--SGGGEEEEEE.-SEEEEEEE-TTHHH CS
                      UDP-g_GGTase  29 aDTivmanlGYfQlka.nPGvwklelregrss 59 
                                        +T+  +  GY+ +    PG + ++  ++ + 
  gi|298676130|ref|YP_003727879.1| 773 LETTKTNESGYYNFTGlAPGDYYINFIDSPGY 804
                                       56777778899999875899999988776655 PP

  == domain 6  score: 6.8 bits;  conditional E-value: 0.0085
                                       -TT-EEEEE-.SS-S-SEEEE--SGGGEEEEEE-SEEEEEEE- CS
                      UDP-g_GGTase  13 prGlqleLgt.ekkksvaDTivmanlGYfQlkanPGvwklelr 54 
                                        +Gl++eL + ++++ v++T+  +  GY+ +  +PG + ++ +
  gi|298676130|ref|YP_003727879.1| 871 ISGLTVELYNcSTDDLVSNTT-TNASGYYNFSVEPGEYYVNFS 912
                                       579999998834455556665.5667************99876 PP

  == domain 7  score: 9.1 bits;  conditional E-value: 0.0016
                                        -TT-EEEEE-SS-S-SEEEE--SGGGEEEEEE-SEEEEEEE-TTHHHHHEEEEE--S CS
                      UDP-g_GGTase   13 prGlqleLgtekkksvaDTivmanlGYfQlkanPGvwklelregrssdiyeiesvga 69  
                                         +Gl++eL + ++++++ ++  +  GY+ +  +PG + ++ +    sd ye++s ++
  gi|298676130|ref|YP_003727879.1|  984 ISGLTVELYNCSTDELESSTTTNASGYYNFSVTPGSYYVQFS----SDGYEFTSSNQ 1036
                                        579999**99888888888899999************99985....67777766633 PP

>> TTR-52  Transthyretin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.035        30      12      44 ..     186     215 ..     181     235 .. 0.81
   2 ?    4.2   0.1     0.082        70      19      46 ..     314     338 ..     302     361 .. 0.77
   3 ?    5.0   0.0     0.047        40      12      45 ..     420     450 ..     415     461 .. 0.86
   4 ?    3.8   0.0      0.11        95      11      46 ..     533     565 ..     529     584 .. 0.82
   5 ?    6.9   0.0     0.012        10      12      49 ..     646     680 ..     641     693 .. 0.82
   6 ?    6.6   0.0     0.015        13      11      45 ..     758     788 ..     754     798 .. 0.86
   7 !    8.4   0.0    0.0042       3.6      11      49 ..     871     906 ..     867     919 .. 0.83
   8 ?    4.6   0.0     0.062        53      11      46 ..     984    1016 ..     980    1033 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.035
                                       SS-EEEEEEHHHHTS--EEEEEE--TTSEEEEE CS
                            TTR-52  12 knvkVkLwekdtldpddlldetkTdedGnFels 44 
                                        +v+V+L++   +  d+l ++t+Tde+G+++ +
  gi|298676130|ref|YP_003727879.1| 186 TGVTVNLYN---CSGDSLRATTTTDENGYYNFT 215
                                       678999999...578**************9987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.082
                                       EEHHHHTS--EEEEEE--TTSEEEEEEE CS
                            TTR-52  19 wekdtldpddlldetkTdedGnFelsgs 46 
                                       ++   +  d+++++t+Td+dG+++ + +
  gi|298676130|ref|YP_003727879.1| 314 HN---CSDDTIVSSTTTDADGYYNFTVT 338
                                       33...477999**********9998865 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.047
                                       SS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEE CS
                            TTR-52  12 knvkVkLwekdtldpddlldetkTdedGnFelsg 45 
                                        nv+++L++ dt    +++++++Td dG ++ +g
  gi|298676130|ref|YP_003727879.1| 420 GNVTINLYDCDT---GNKIANNTTDVDGDYNFTG 450
                                       6899*****877...899************9987 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.11
                                       GSS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEEE CS
                            TTR-52  11 aknvkVkLwekdtldpddlldetkTdedGnFelsgs 46 
                                       +++ +V+L++     +d+l ++t T+++G+++ s +
  gi|298676130|ref|YP_003727879.1| 533 ISGLTVELYNCS---TDELESSTITNASGYYNFSVT 565
                                       577899999965...59999**********999865 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.012
                                       SS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEEEE-- CS
                            TTR-52  12 knvkVkLwekdtldpddlldetkTdedGnFelsgsene 49 
                                        +++V+L++     +d+l+++t+T+++G+++ + +  e
  gi|298676130|ref|YP_003727879.1| 646 PDIRVELYNCS---TDNLVSNTTTNNSGYYNFTVEPGE 680
                                       678999*9965...5**************998876555 PP

  == domain 6  score: 6.6 bits;  conditional E-value: 0.015
                                       GSS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEE CS
                            TTR-52  11 aknvkVkLwekdtldpddlldetkTdedGnFelsg 45 
                                       + nv+V+L++ +     d l++tkT+e+G+++ +g
  gi|298676130|ref|YP_003727879.1| 758 IDNVTVNLYNCN----GDFLETTKTNESGYYNFTG 788
                                       67999****975....59*************9987 PP

  == domain 7  score: 8.4 bits;  conditional E-value: 0.0042
                                       GSS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEEEE-- CS
                            TTR-52  11 aknvkVkLwekdtldpddlldetkTdedGnFelsgsene 49 
                                       +++ +V+L++     +ddl+++t+T+++G+++ s +  e
  gi|298676130|ref|YP_003727879.1| 871 ISGLTVELYNCS---TDDLVSNTTTNASGYYNFSVEPGE 906
                                       677899999965...5**************999976555 PP

  == domain 8  score: 4.6 bits;  conditional E-value: 0.062
                                        GSS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEEE CS
                            TTR-52   11 aknvkVkLwekdtldpddlldetkTdedGnFelsgs 46  
                                        +++ +V+L++     +d+l ++t+T+++G+++ s +
  gi|298676130|ref|YP_003727879.1|  984 ISGLTVELYNCS---TDELESSTTTNASGYYNFSVT 1016
                                        577899999965...599************999865 PP

>> AdenylateSensor  Adenylate sensor of SNF1-like protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.069        59      66      92 ..     335     361 ..     325     376 .. 0.76
   2 !   10.4   0.1   0.00082       0.7      65      98 ..     561     595 ..     537     605 .. 0.74
   3 !    9.8   0.0    0.0013       1.1      64      96 ..     672     706 ..     642     716 .. 0.71
   4 !    8.8   0.0    0.0026       2.2      66      98 ..     900     934 ..     878     942 .. 0.76
   5 !    9.7   0.0    0.0013       1.1      62      97 ..    1009    1044 ..     988    1055 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.069
                                       EEEETTEEEEEEEEEEEEESSSSSTTT CS
                   AdenylateSensor  66 fqlepnnylvdfkfdGwessssekeet 92 
                                       f + p +y v+f +dG+  +s ++ + 
  gi|298676130|ref|YP_003727879.1| 335 FTVTPGSYYVNFSSDGYVFTSANQGTD 361
                                       8899*************9776554332 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00082
                                       EEEEETTEEEEEEEEEEEEESSSSS.TTTTTSSTT CS
                   AdenylateSensor  65 lfqlepnnylvdfkfdGwessssek.eetaeeded 98 
                                        f + p ny v f +dG++ ++ +k +e +++d d
  gi|298676130|ref|YP_003727879.1| 561 NFSVTPGNYYVQFSSDGYNFTQANKeSEDVDSDAD 595
                                       5899***************8776652344444433 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0013
                                       EEEEEETTEEEEEEEEEEEEESSSSS..TTTTTSS CS
                   AdenylateSensor  64 qlfqlepnnylvdfkfdGwessssek..eetaeed 96 
                                         f +ep  y v+f +dG+e + +++  e+t+++d
  gi|298676130|ref|YP_003727879.1| 672 YNFTVEPGEYYVNFSSDGYEFTLQNQggEDTVDSD 706
                                       5699****************988877334444443 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0026
                                       EEEETTEEEEEEEEEEEEESSSSS..TTTTTSSTT CS
                   AdenylateSensor  66 fqlepnnylvdfkfdGwessssek..eetaeeded 98 
                                       f +ep  y v+f +dG+e +  ++  ++t+++d d
  gi|298676130|ref|YP_003727879.1| 900 FSVEPGEYYVNFSSDGYEFTLANQgvDNTVDSDAD 934
                                       99****************87665533555555554 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.0013
                                        EEEEEEEETTEEEEEEEEEEEEESSSSSTTTTTSST CS
                   AdenylateSensor   62 eiqlfqlepnnylvdfkfdGwessssekeetaeede 97  
                                            f + p +y v f +dG+e +ss++ +  + d+
  gi|298676130|ref|YP_003727879.1| 1009 GYYNFSVTPGSYYVQFSSDGYEFTSSNQGTDDSMDS 1044
                                        555699****************88777643333332 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0042       3.6      12      48 ..     190     228 ..     173     236 .. 0.71
   2 ?    5.8   0.0     0.017        15      22      54 ..     323     354 ..     303     385 .. 0.82
   3 !    6.8   0.0    0.0082         7      10      53 ..     422     468 ..     413     471 .. 0.75
   4 ?    5.2   0.0     0.026        22      21      55 ..     549     582 ..     480     615 .. 0.81
   5 ?    3.6   0.1     0.079        67       8      54 ..     646     693 ..     641     695 .. 0.74
   6 !    7.1   0.0    0.0066       5.6      22      54 ..     774     807 ..     753     810 .. 0.75
   7 ?    3.5   0.0     0.084        71      23      54 ..     889     919 ..     868     961 .. 0.80
   8 ?    4.7   0.1     0.037        31      21      54 ..    1000    1032 ..     981    1036 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0042
                           DUF2012  12 vlL...dsgqqrkfkalvrrDGsFifrdlpegsYlLeves 48 
                                       v L   + g +   ++ + ++G ++f++l++g Y+++   
  gi|298676130|ref|YP_003727879.1| 190 VNLyncS-GDSLRATTTTDENGYYNFTNLEPGNYYVNFTI 228
                                       3335533.333367889999**************998765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.017
                           DUF2012  22 fkalvrrDGsFifrdlpegsYlLevespeyvFe 54 
                                        ++ + +DG ++f+ + +gsY+++  s +yvF 
  gi|298676130|ref|YP_003727879.1| 323 SSTTTDADGYYNFT-VTPGSYYVNFSSDGYVFT 354
                                       4788999******6.999**************7 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0082
                           DUF2012  10 trvlL...dsgqqrkfkalvrrDGsFifrdlpegsYlLevesp.eyvF 53 
                                       +++ L   d+g +   +  + +DG ++f+ l++g Y+++ e+p +y+F
  gi|298676130|ref|YP_003727879.1| 422 VTINLydcDTGNK-IANNTTDVDGDYNFTGLSPGNYYVNFEAPhGYEF 468
                                       4555565555555.6678899*****************9998724555 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.026
                           DUF2012  21 kfkalvrrDGsFifrdlpegsYlLevespeyvFep 55 
                                       + ++ ++++G ++f+ + +g Y+++  s +y+F +
  gi|298676130|ref|YP_003727879.1| 549 ESSTITNASGYYNFS-VTPGNYYVQFSSDGYNFTQ 582
                                       568999********6.999**************98 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.079
                           DUF2012   8 antrvlL.....dsgqqrkfkalvrrDGsFifrdlpegsYlLevespeyvFe 54 
                                       +++rv L     d       ++ ++++G ++f+ +++g+Y+++  s +y+F 
  gi|298676130|ref|YP_003727879.1| 646 PDIRVELyncstD--NL-VSNTTTNNSGYYNFT-VEPGEYYVNFSSDGYEFT 693
                                       5666777433211..11.346889999****96.****************95 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.0066
                           DUF2012  22 fkalvrrDGsFifrdlpegsYlLe.vespeyvFe 54 
                                        +++++++G ++f+ l +g Y+++ ++sp+y+F 
  gi|298676130|ref|YP_003727879.1| 774 ETTKTNESGYYNFTGLAPGDYYINfIDSPGYEFT 807
                                       47899**************88885489*****96 PP

  == domain 7  score: 3.5 bits;  conditional E-value: 0.084
                           DUF2012  23 kalvrrDGsFifrdlpegsYlLevespeyvFe 54 
                                       ++ ++++G ++f+ +++g+Y+++  s +y+F 
  gi|298676130|ref|YP_003727879.1| 889 NTTTNASGYYNFS-VEPGEYYVNFSSDGYEFT 919
                                       5778899999995.*****************7 PP

  == domain 8  score: 4.7 bits;  conditional E-value: 0.037
                           DUF2012   21 kfkalvrrDGsFifrdlpegsYlLevespeyvFe 54  
                                        + ++ ++++G ++f+ + +gsY+++  s +y+F 
  gi|298676130|ref|YP_003727879.1| 1000 ESSTTTNASGYYNFS-VTPGSYYVQFSSDGYEFT 1032
                                        46789999******6.999*************96 PP

>> phage_tail_N  Prophage tail fibre N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.5   4.7e+03      40      61 ..     203     225 ..     200     231 .. 0.81
   2 !    9.9   0.3   0.00084      0.71      37      69 ..     321     353 ..     296     378 .. 0.81
   3 ?    4.6   0.9     0.035        29       7      86 ..     410     485 ..     405     501 .. 0.78
   4 !    7.4   0.1    0.0048       4.1      39      72 ..     550     583 ..     508     603 .. 0.84
   5 !   11.8   0.3   0.00021      0.18      36      80 ..     659     706 ..     633     722 .. 0.76
   6 !    8.2   0.2    0.0027       2.3      37      68 ..     886     917 ..     864     925 .. 0.80
   7 ?    0.9   0.1       0.5   4.2e+02      34      81 ..     925     971 ..     917     979 .. 0.80
   8 ?    5.2   0.1     0.022        19      40      69 ..    1002    1031 ..     984    1048 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.5
                      phage_tail_N  40 senpdeaGrysl.dvetGkysvi 61 
                                         ++de+G y + + e G+y v 
  gi|298676130|ref|YP_003727879.1| 203 TTTTDENGYYNFtNLEPGNYYVN 225
                                       6789******9845799999886 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00084
                      phage_tail_N  37 tvasenpdeaGrysldvetGkysvilkvdgfpe 69 
                                        v+s ++d +G y + v  G y v +  dg+  
  gi|298676130|ref|YP_003727879.1| 321 IVSSTTTDADGYYNFTVTPGSYYVNFSSDGYVF 353
                                       4788999**********************9864 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.035
                      phage_tail_N   7 GvlkdGtGkPvqnctiqlkarrtsttvvvntvasenpdeaGrysld.vetGkysvilkv.dgfpeshaGditvyeds 81 
                                       G+ +dG  + + n+ti l  + t        +a++++d +G+y +     G+y v ++   g++    G+ + yed 
  gi|298676130|ref|YP_003727879.1| 410 GIQNDGN-TGIGNVTINLYDCDTGN-----KIANNTTDVDGDYNFTgLSPGNYYVNFEApHGYEFTILGQGANYEDN 480
                                       6666764.56788899998888875.....5678889*******973678*****9986368888889999***998 PP

                      phage_tail_N  82 kPGtl 86 
                                       +   l
  gi|298676130|ref|YP_003727879.1| 481 NANIL 485
                                       87666 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0048
                      phage_tail_N  39 asenpdeaGrysldvetGkysvilkvdgfpesha 72 
                                       +s  ++ +G y + v  G+y v +  dg++  +a
  gi|298676130|ref|YP_003727879.1| 550 SSTITNASGYYNFSVTPGNYYVQFSSDGYNFTQA 583
                                       46678899*********************98776 PP

  == domain 5  score: 11.8 bits;  conditional E-value: 0.00021
                      phage_tail_N  36 ntvasenpdeaGrysldvetGkysvilkvdgfp...eshaGditvyed 80 
                                       n v++ +++++G y + ve G+y v +  dg++   + + G+ tv  d
  gi|298676130|ref|YP_003727879.1| 659 NLVSNTTTNNSGYYNFTVEPGEYYVNFSSDGYEftlQNQGGEDTVDSD 706
                                       56788899***********************97322344555566555 PP

  == domain 6  score: 8.2 bits;  conditional E-value: 0.0027
                      phage_tail_N  37 tvasenpdeaGrysldvetGkysvilkvdgfp 68 
                                        v++ +++ +G y + ve G+y v +  dg++
  gi|298676130|ref|YP_003727879.1| 886 LVSNTTTNASGYYNFSVEPGEYYVNFSSDGYE 917
                                       3667778999********************96 PP

  == domain 7  score: 0.9 bits;  conditional E-value: 0.5
                      phage_tail_N  34 vvntvasenpdeaGrysldvetGkysvilkvdgfpeshaGditvyeds 81 
                                       v ntv s+        ++ ve G+   ++    +++  +Gd  v+ed+
  gi|298676130|ref|YP_003727879.1| 925 VDNTVDSDADSSGNTTCITVESGETNDTVDAGLYQPATIGDF-VWEDT 971
                                       6689988877777789************************97.56665 PP

  == domain 8  score: 5.2 bits;  conditional E-value: 0.022
                      phage_tail_N   40 senpdeaGrysldvetGkysvilkvdgfpe 69  
                                        s +++ +G y + v  G y v +  dg++ 
  gi|298676130|ref|YP_003727879.1| 1002 STTTNASGYYNFSVTPGSYYVQFSSDGYEF 1031
                                        5678889********************863 PP

>> DUF2025  Protein of unknown function (DUF2025)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.28   2.4e+02      13      42 ..     327     356 ..     316     365 .. 0.80
   2 ?    2.6   0.0      0.16   1.4e+02      15      40 ..     556     581 ..     545     590 .. 0.83
   3 ?    3.2   0.0       0.1        87       8      41 ..     661     694 ..     655     705 .. 0.81
   4 ?    5.8   0.0     0.016        14       8      48 ..     887     927 ..     881     941 .. 0.84
   5 ?    2.1   0.0      0.23     2e+02      14      40 ..    1006    1032 ..     995    1044 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.28
                                       GS---EEEEETTTTEEEEES-GGG-SSSS- CS
                           DUF2025  13 dqlkGfvGfnrktGkyivrfsedsfGldva 42 
                                        +  G+  f    G y v fs d + +  a
  gi|298676130|ref|YP_003727879.1| 327 TDADGYYNFTVTPGSYYVNFSSDGYVFTSA 356
                                       45679999***************9876655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.16
                                       ---EEEEETTTTEEEEES-GGG-SSS CS
                           DUF2025  15 lkGfvGfnrktGkyivrfsedsfGld 40 
                                         G+  f    G+y v+fs d + + 
  gi|298676130|ref|YP_003727879.1| 556 ASGYYNFSVTPGNYYVQFSSDGYNFT 581
                                       479999***************98765 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.1
                                       GGGGGGS---EEEEETTTTEEEEES-GGG-SSSS CS
                           DUF2025   8 ickaadqlkGfvGfnrktGkyivrfsedsfGldv 41 
                                       + +++ +  G+  f    G+y v fs d + + +
  gi|298676130|ref|YP_003727879.1| 661 VSNTTTNNSGYYNFTVEPGEYYVNFSSDGYEFTL 694
                                       5666777899******************987655 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.016
                                       GGGGGGS---EEEEETTTTEEEEES-GGG-SSSS-GGG-EE CS
                           DUF2025   8 ickaadqlkGfvGfnrktGkyivrfsedsfGldvaddsitp 48 
                                       + +++ +  G+  f    G+y v fs d + + +a++ +  
  gi|298676130|ref|YP_003727879.1| 887 VSNTTTNASGYYNFSVEPGEYYVNFSSDGYEFTLANQGVDN 927
                                       566777889*********************99999887765 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.23
                                        S---EEEEETTTTEEEEES-GGG-SSS CS
                           DUF2025   14 qlkGfvGfnrktGkyivrfsedsfGld 40  
                                        +  G+  f    G y v+fs d + + 
  gi|298676130|ref|YP_003727879.1| 1006 NASGYYNFSVTPGSYYVQFSSDGYEFT 1032
                                        5679999***************98765 PP

>> Dioxygenase_C  Dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0012         1      73      98 ..     199     224 ..     182     233 .. 0.88
   2 ?    4.9   0.0     0.019        16      70      99 ..     317     345 ..     304     359 .. 0.81
   3 ?    5.6   0.1     0.011       9.8      78     106 ..     438     466 ..     422     477 .. 0.82
   4 ?    1.5   0.0       0.2   1.7e+02      73      99 ..     547     572 ..     532     587 .. 0.81
   5 ?    1.4   0.1      0.22   1.9e+02      69      99 ..     655     684 ..     641     701 .. 0.78
   6 ?    2.5   0.1       0.1        86      76      99 ..     774     797 ..     752     806 .. 0.84
   7 ?   -2.9   0.1       4.4   3.8e+03      77      98 ..     889     909 ..     879     919 .. 0.77
   8 ?   -1.3   0.0       1.4   1.2e+03      74      99 ..     999    1023 ..     988    1031 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                                       TTEEEEE--TTSEEEEEEE----EE- CS
                     Dioxygenase_C  73 nlrgriltdeeGryrirtikPapYpi 98 
                                        lr ++ tde+G+y+++ ++P+ Y +
  gi|298676130|ref|YP_003727879.1| 199 SLRATTTTDENGYYNFTNLEPGNYYV 224
                                       5788999*****************76 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.019
                                       STTTTEEEEE--TTSEEEEEEE----EE-- CS
                     Dioxygenase_C  70 pelnlrgriltdeeGryrirtikPapYpip 99 
                                       ++  +  ++ td++G+y++ t+ P++Y ++
  gi|298676130|ref|YP_003727879.1| 317 SDDTIVSSTTTDADGYYNF-TVTPGSYYVN 345
                                       5666778899*******98.89*****765 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.011
                                       EE--TTSEEEEEEE----EE--TTSHHHH CS
                     Dioxygenase_C  78 iltdeeGryrirtikPapYpipndGptgk 106
                                         td +G y+++ + P+ Y ++ + p g 
  gi|298676130|ref|YP_003727879.1| 438 NTTDVDGDYNFTGLSPGNYYVNFEAPHGY 466
                                       569****************9998888765 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.2
                                       TTEEEEE--TTSEEEEEEE----EE-- CS
                     Dioxygenase_C  73 nlrgriltdeeGryrirtikPapYpip 99 
                                        l+ +++t++ G+y++ ++ P+ Y ++
  gi|298676130|ref|YP_003727879.1| 547 ELESSTITNASGYYNF-SVTPGNYYVQ 572
                                       567899********98.699***9765 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.22
                                       SSTTTTEEEEE--TTSEEEEEEE----EE-- CS
                     Dioxygenase_C  69 apelnlrgriltdeeGryrirtikPapYpip 99 
                                        +  nl  ++ t++ G+y++ t++P+ Y ++
  gi|298676130|ref|YP_003727879.1| 655 CSTDNLVSNTTTNNSGYYNF-TVEPGEYYVN 684
                                       556688889999****9998.89****9765 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.1
                                       EEEE--TTSEEEEEEE----EE-- CS
                     Dioxygenase_C  76 griltdeeGryrirtikPapYpip 99 
                                        ++ t+e G+y+++ + P+ Y i+
  gi|298676130|ref|YP_003727879.1| 774 ETTKTNESGYYNFTGLAPGDYYIN 797
                                       566799***************875 PP

  == domain 7  score: -2.9 bits;  conditional E-value: 4.4
                                       EEE--TTSEEEEEEE----EE- CS
                     Dioxygenase_C  77 riltdeeGryrirtikPapYpi 98 
                                       ++ t++ G+y++ +++P+ Y +
  gi|298676130|ref|YP_003727879.1| 889 NTTTNASGYYNF-SVEPGEYYV 909
                                       566888898887.689998865 PP

  == domain 8  score: -1.3 bits;  conditional E-value: 1.4
                                        TEEEEE--TTSEEEEEEE----EE-- CS
                     Dioxygenase_C   74 lrgriltdeeGryrirtikPapYpip 99  
                                        l+ ++ t++ G+y++ ++ P++Y ++
  gi|298676130|ref|YP_003727879.1|  999 LESSTTTNASGYYNF-SVTPGSYYVQ 1023
                                        5678889999*9998.699*999764 PP

>> MetallophosN  N terminal of Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   0.00011     0.098      20      56 ..     202     239 ..     177     251 .. 0.82
   2 ?    6.4   0.3     0.013        11      20      49 ..     323     351 ..     305     362 .. 0.83
   3 ?    6.7   0.1      0.01       8.9      22      52 ..     438     469 ..     415     479 .. 0.89
   4 ?    1.5   0.4      0.43   3.7e+02      22      53 ..     552     582 ..     545     590 .. 0.72
   5 ?    1.7   1.1      0.38   3.2e+02      20      54 ..     662     695 ..     657     702 .. 0.79
   6 ?    0.1   0.1       1.2     1e+03      16      39 ..     687     710 ..     685     715 .. 0.85
   7 ?    3.9   0.2     0.073        63       6      35 ..     754     790 ..     749     813 .. 0.73
   8 ?    2.9   0.3      0.15   1.3e+02      19      52 ..     887     919 ..     877     930 .. 0.79
   9 ?    4.7   0.5     0.042        36      21      56 ..    1002    1036 ..     996    1048 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                      MetallophosN  20 nvtkTdakGrYeLk.sdkkakfVyistPagyevptedg 56 
                                        +t+Td++G Y+++  +  + +V +++P ++e+  +d+
  gi|298676130|ref|YP_003727879.1| 202 ATTTTDENGYYNFTnLEPGNYYVNFTIPPEFEFTLQDA 239
                                       4789**********889999************988875 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                      MetallophosN  20 nvtkTdakGrYeLksdkkakfVyistPagy 49 
                                       + t+Tda+G Y+++ +  + +V +s  +gy
  gi|298676130|ref|YP_003727879.1| 323 SSTTTDADGYYNFTVTPGSYYVNFSS-DGY 351
                                       679***********999999998875.455 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.01
                      MetallophosN  22 tkTdakGrYeLk.sdkkakfVyistPagyevp 52 
                                        +Td +G Y+++  +  + +V +  P gye+ 
  gi|298676130|ref|YP_003727879.1| 438 NTTDVDGDYNFTgLSPGNYYVNFEAPHGYEFT 469
                                       58**********9999*************986 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.43
                      MetallophosN  22 tkTdakGrYeLksdkkakfVyistPagyevpt 53 
                                       t T+a+G Y+++ +  + +V +s  +gy++ +
  gi|298676130|ref|YP_003727879.1| 552 TITNASGYYNFSVTPGNYYVQFSS-DGYNFTQ 582
                                       678888888888888888887775.5555554 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.38
                      MetallophosN  20 nvtkTdakGrYeLksdkkakfVyistPagyevpte 54 
                                       + t+T+++G Y+++ +    +V +s  +gye+  +
  gi|298676130|ref|YP_003727879.1| 662 SNTTTNNSGYYNFTVEPGEYYVNFSS-DGYEFTLQ 695
                                       5689*********9999988888875.66666555 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 1.2
                      MetallophosN  16 sDGvnvtkTdakGrYeLksdkkak 39 
                                       sDG+++t  ++ G+ + +sd +++
  gi|298676130|ref|YP_003727879.1| 687 SDGYEFTLQNQGGEDTVDSDANSS 710
                                       8**********9998888777765 PP

  == domain 7  score: 3.9 bits;  conditional E-value: 0.073
                      MetallophosN   6 kgkgvagVvVs......DGvnvtkTdakGrYeLk.sd 35 
                                        ++g+ +V+V+      D  ++tkT+++G Y+++  +
  gi|298676130|ref|YP_003727879.1| 754 GDTGIDNVTVNlyncngDFLETTKTNESGYYNFTgLA 790
                                       567888888876666556689**********998544 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.15
                      MetallophosN  19 vnvtkTdakGrYeLksdkkakfVyistPagyevp 52 
                                       v+ t+T+a+G Y+++ +    +V +s  +gye+ 
  gi|298676130|ref|YP_003727879.1| 887 VSNTTTNASGYYNFSVEPGEYYVNFSS-DGYEFT 919
                                       6789***********999998988875.666665 PP

  == domain 9  score: 4.7 bits;  conditional E-value: 0.042
                      MetallophosN   21 vtkTdakGrYeLksdkkakfVyistPagyevptedg 56  
                                         t+T+a+G Y+++ +  + +V +s  +gye+ ++++
  gi|298676130|ref|YP_003727879.1| 1002 STTTNASGYYNFSVTPGSYYVQFSS-DGYEFTSSNQ 1036
                                        699******************9997.8898888776 PP

>> HupF_HypC  HupF/HypC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.41   3.5e+02      22      42 ..     382     402 ..     371     406 .. 0.84
   2 ?    0.5   0.0      0.81   6.9e+02      22      42 ..     496     516 ..     483     517 .. 0.81
   3 ?    1.4   0.0      0.43   3.6e+02      18      42 ..     604     628 ..     593     629 .. 0.82
   4 ?    1.9   0.0      0.28   2.4e+02      20      42 ..     719     741 ..     709     745 .. 0.87
   5 ?   -0.6   0.0       1.7   1.5e+03      22      42 ..     834     854 ..     823     855 .. 0.82
   6 ?    2.6   0.0      0.18   1.6e+02      18      42 ..     943     967 ..     931     968 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.41
                                       TTEEEEEEGTTCTTB-TT-EE CS
                         HupF_HypC  22 gGvrrevslalveevkvGdyV 42 
                                       +++  +v+ +l  +v++GdyV
  gi|298676130|ref|YP_003727879.1| 382 NETNYTVDAGLYRPVSIGDYV 402
                                       566778999***99******9 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.81
                                       TTEEEEEEGTTCTTB-TT-EE CS
                         HupF_HypC  22 gGvrrevslalveevkvGdyV 42 
                                       g++  +++++l +++ +Gd+V
  gi|298676130|ref|YP_003727879.1| 496 GENNDTIDVGLYQPATIGDFV 516
                                       345789*************99 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.43
                                       EEECTTEEEEEEGTTCTTB-TT-EE CS
                         HupF_HypC  18 lvdvgGvrrevslalveevkvGdyV 42 
                                       +v  g++ ++++ +l +++ +Gd+V
  gi|298676130|ref|YP_003727879.1| 604 TVVSGETNETIDAGLYQQAMIGDFV 628
                                       4555567899*************99 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.28
                                       ECTTEEEEEEGTTCTTB-TT-EE CS
                         HupF_HypC  20 dvgGvrrevslalveevkvGdyV 42 
                                       + +++  +++ +l +++++GdyV
  gi|298676130|ref|YP_003727879.1| 719 ESNETNDTIDAGLYQPASIGDYV 741
                                       55677899**************9 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 1.7
                                       TTEEEEEEGTTCTTB-TT-EE CS
                         HupF_HypC  22 gGvrrevslalveevkvGdyV 42 
                                       g++  +++ +l +++ +Gd+V
  gi|298676130|ref|YP_003727879.1| 834 GENNDTIDAGLYQPATIGDFV 854
                                       3457899************99 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.18
                                       EEECTTEEEEEEGTTCTTB-TT-EE CS
                         HupF_HypC  18 lvdvgGvrrevslalveevkvGdyV 42 
                                       +v+ g++  +v+ +l +++ +Gd+V
  gi|298676130|ref|YP_003727879.1| 943 TVESGETNDTVDAGLYQPATIGDFV 967
                                       7899999****************99 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1   0.00066      0.56      14      51 ..     178     215 ..     176     224 .. 0.91
   2 !    9.5   0.5    0.0011      0.96      20      53 ..     305     338 ..     291     346 .. 0.79
   3 ?   -2.1   0.0       4.8   4.1e+03      26      43 ..     344     362 ..     340     363 .. 0.72
   4 ?   -0.8   0.9       1.8   1.6e+03      18      51 ..     416     449 ..     411     452 .. 0.71
   5 !    7.7   0.0    0.0041       3.5      13      53 ..     525     565 ..     525     575 .. 0.90
   6 ?    3.4   0.1     0.092        78      15      52 ..     639     676 ..     637     679 .. 0.81
   7 ?    1.9   0.2      0.26   2.3e+02      15      51 ..     752     787 ..     750     789 .. 0.82
   8 ?    1.6   0.1      0.33   2.8e+02      20      52 ..     870     902 ..     864     904 .. 0.73
   9 ?   -1.1   1.3       2.3     2e+03      21      48 ..     920     949 ..     911     953 .. 0.80
  10 !    7.0   0.1     0.007         6      20      53 ..     983    1016 ..     977    1024 .. 0.82
  11 ?   -2.1   0.0       4.7     4e+03      26      44 ..    1022    1041 ..    1019    1042 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00066
                             Big_1  14 kDangnpvagatVtfsvsggalsassgtTdanGkatvt 51 
                                       +D +   + g+tV++   +g+ + +++tTd+nG + +t
  gi|298676130|ref|YP_003727879.1| 178 QDDEEVGLTGVTVNLYNCSGDSLRATTTTDENGYYNFT 215
                                       68888899********9999999**********99886 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                             Big_1  20 pvagatVtfsvsggalsassgtTdanGkatvtlt 53 
                                        ++++ Vt+   +++++ ss+tTda+G + +t+t
  gi|298676130|ref|YP_003727879.1| 305 GISDIIVTLHNCSDDTIVSSTTTDADGYYNFTVT 338
                                       5666666666666888899**************9 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.8
                             Big_1  26 Vtfsvsggals.assgtTd 43 
                                       V+fs++g + + a++gt d
  gi|298676130|ref|YP_003727879.1| 344 VNFSSDGYVFTsANQGTDD 362
                                       99****9666636666554 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.8
                             Big_1  18 gnpvagatVtfsvsggalsassgtTdanGkatvt 51 
                                       ++ + ++t+++   ++ +  ++ tTd +G + +t
  gi|298676130|ref|YP_003727879.1| 416 NTGIGNVTINLYDCDTGNKIANNTTDVDGDYNFT 449
                                       56677777777655544447899******98876 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0041
                             Big_1  13 vkDangnpvagatVtfsvsggalsassgtTdanGkatvtlt 53 
                                       v+D   + ++g tV +   +++ ++ss++T+a+G + +++t
  gi|298676130|ref|YP_003727879.1| 525 VQDPGETGISGLTVELYNCSTDELESSTITNASGYYNFSVT 565
                                       6788889999****9998888888**************998 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.092
                             Big_1  15 DangnpvagatVtfsvsggalsassgtTdanGkatvtl 52 
                                       D   + ++++ V +   +++++ s++tT+++G + +t+
  gi|298676130|ref|YP_003727879.1| 639 DDGETGIPDIRVELYNCSTDNLVSNTTTNNSGYYNFTV 676
                                       666778888888888777666789**********9997 PP

  == domain 7  score: 1.9 bits;  conditional E-value: 0.26
                             Big_1  15 DangnpvagatVtfsvsggalsassgtTdanGkatvt 51 
                                       +   + + ++tV++   +g+    +++T+++G + +t
  gi|298676130|ref|YP_003727879.1| 752 NDGDTGIDNVTVNLYNCNGDF-LETTKTNESGYYNFT 787
                                       556788999999999999998.5699******99887 PP

  == domain 8  score: 1.6 bits;  conditional E-value: 0.33
                             Big_1  20 pvagatVtfsvsggalsassgtTdanGkatvtl 52 
                                        ++g tV +   +++ + s++tT+a+G + +++
  gi|298676130|ref|YP_003727879.1| 870 GISGLTVELYNCSTDDLVSNTTTNASGYYNFSV 902
                                       56777777766664444789*******999876 PP

  == domain 9  score: -1.1 bits;  conditional E-value: 2.3
                             Big_1  21 vagatVtfsvsg.gals.assgtTdanGka 48 
                                       +a++ V  +v++ ++ s +++ +T ++G++
  gi|298676130|ref|YP_003727879.1| 920 LANQGVDNTVDSdADSSgNTTCITVESGET 949
                                       789999999999766668999999999985 PP

  == domain 10  score: 7.0 bits;  conditional E-value: 0.007
                             Big_1   20 pvagatVtfsvsggalsassgtTdanGkatvtlt 53  
                                         ++g tV +   +++ ++ss+tT+a+G + +++t
  gi|298676130|ref|YP_003727879.1|  983 GISGLTVELYNCSTDELESSTTTNASGYYNFSVT 1016
                                        678888888877777779*************998 PP

  == domain 11  score: -2.1 bits;  conditional E-value: 4.7
                             Big_1   26 Vtfsvsg.galsassgtTda 44  
                                        V fs++g + +s+++gt d+
  gi|298676130|ref|YP_003727879.1| 1022 VQFSSDGyEFTSSNQGTDDS 1041
                                        89999996666677777765 PP

>> DUF3244  Domain of unknown function (DUF3244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.49   4.2e+02      39      89 ..     182     228 ..     171     233 .. 0.76
   2 ?   -0.7   0.1       1.8   1.5e+03      43      93 ..     307     352 ..     301     354 .. 0.70
   3 ?    6.8   0.0    0.0081       6.9      41      93 ..     418     466 ..     406     470 .. 0.84
   4 ?    2.9   0.1      0.14   1.2e+02      42      92 ..     533     578 ..     530     581 .. 0.80
   5 ?    1.5   0.1      0.36   3.1e+02      43      92 ..     646     690 ..     640     693 .. 0.79
   6 ?    1.1   0.0       0.5   4.3e+02      42      91 ..     758     803 ..     745     807 .. 0.71
   7 ?    3.4   0.0     0.092        79      42      92 ..     871     916 ..     867     919 .. 0.78
   8 ?    2.1   0.1      0.24   2.1e+02      42      92 ..     984    1029 ..     980    1033 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.49
                                       SS--SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEEE CS
                           DUF3244  39 esplsdvtitikdeetgevvyestivnasgstisidlsgeesgeYklelts 89 
                                       e+ l+ vt+ +++   g  +   t++++ + +++   +++e+g+Y + +t 
  gi|298676130|ref|YP_003727879.1| 182 EVGLTGVTVNLYNC-SGDSLRATTTTDE-NGYYN--FTNLEPGNYYVNFTI 228
                                       55677888888888.6888888888877.45555..58**********994 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.8
                                       SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEEESS-E CS
                           DUF3244  43 sdvtitikdeetgevvyestivnasgstisidlsgeesgeYkleltskggy 93 
                                       sd+ +t+ +   + ++ +st+++a + ++++ ++   +g Y + ++s+g++
  gi|298676130|ref|YP_003727879.1| 307 SDIIVTLHNC-SDDTIVSSTTTDA-DGYYNFTVT---PGSYYVNFSSDGYV 352
                                       5667777777.4566666666666.588888764...78899988888765 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0081
                                       --SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEEESS-E CS
                           DUF3244  41 plsdvtitikdeetgevvyestivnasgstisidlsgeesgeYkleltskggy 93 
                                        +++vti ++d +tg+ + ++t+  +    +  + +g+++g+Y + ++ + gy
  gi|298676130|ref|YP_003727879.1| 418 GIGNVTINLYDCDTGNKIANNTTDVD--GDY--NFTGLSPGNYYVNFEAPHGY 466
                                       579****************9998866..444..568**********9977665 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.14
                                       -SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEEESS- CS
                           DUF3244  42 lsdvtitikdeetgevvyestivnasgstisidlsgeesgeYkleltskgg 92 
                                       +s +t+ +++ +t   +++sti+na + +++++++   +g+Y ++++s+g+
  gi|298676130|ref|YP_003727879.1| 533 ISGLTVELYNCST-DELESSTITNA-SGYYNFSVT---PGNYYVQFSSDGY 578
                                       5678999999955.55789999988.79****986...899***9999886 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.36
                                       SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEEESS- CS
                           DUF3244  43 sdvtitikdeetgevvyestivnasgstisidlsgeesgeYkleltskgg 92 
                                        d+ + +++ +t++ v + t+ n+   ++++ +   e+geY + ++s+g+
  gi|298676130|ref|YP_003727879.1| 646 PDIRVELYNCSTDNLVSNTTTNNS--GYYNFTV---EPGEYYVNFSSDGY 690
                                       678888899988888887777776..9999986...68999999998876 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.5
                                       -SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEE.ESS CS
                           DUF3244  42 lsdvtitikdeetgevvyestivnasgstisidlsgeesgeYklelt.skg 91 
                                       +++vt+ +++  +g  +++ t +n+ + ++  + +g+++g+Y + +  s+g
  gi|298676130|ref|YP_003727879.1| 758 IDNVTVNLYNC-NGDFLET-TKTNE-SGYY--NFTGLAPGDYYINFIdSPG 803
                                       67888888888.5666554.55555.2555..558*********9985655 PP

  == domain 7  score: 3.4 bits;  conditional E-value: 0.092
                                       -SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEEESS- CS
                           DUF3244  42 lsdvtitikdeetgevvyestivnasgstisidlsgeesgeYkleltskgg 92 
                                       +s +t+ +++ +t+  v +  ++na + ++++++   e+geY + ++s+g+
  gi|298676130|ref|YP_003727879.1| 871 ISGLTVELYNCSTDDLVSNT-TTNA-SGYYNFSV---EPGEYYVNFSSDGY 916
                                       67899999999888887655.5555.59****98...58*******99886 PP

  == domain 8  score: 2.1 bits;  conditional E-value: 0.24
                                        -SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEEEEEESS- CS
                           DUF3244   42 lsdvtitikdeetgevvyestivnasgstisidlsgeesgeYkleltskgg 92  
                                        +s +t+ +++ +t+  +++st++na + +++++++   +g Y ++++s+g+
  gi|298676130|ref|YP_003727879.1|  984 ISGLTVELYNCSTD-ELESSTTTNA-SGYYNFSVT---PGSYYVQFSSDGY 1029
                                        67889999999655.5677888877.69****986...8999999998876 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.76   6.5e+02      29      46 ..     335     352 ..     333     357 .. 0.86
   2 ?   -3.1   0.0       8.6   7.3e+03      31      43 ..     451     463 ..     447     467 .. 0.76
   3 ?    3.8   0.0     0.064        55      29      46 ..     562     579 ..     560     586 .. 0.86
   4 ?    3.1   0.1       0.1        86      29      46 ..     674     691 ..     672     696 .. 0.88
   5 ?    3.9   0.0     0.059        50      29      46 ..     900     917 ..     898     928 .. 0.88
   6 ?    3.0   0.0      0.11        97      29      46 ..    1013    1030 ..    1011    1035 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.76
                              PEGA  29 lsleaGnyslrvekeGYe 46 
                                        ++ +G+y +  + +GY 
  gi|298676130|ref|YP_003727879.1| 335 FTVTPGSYYVNFSSDGYV 352
                                       56899************5 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.6
                              PEGA  31 leaGnyslrveke 43 
                                       l +Gny +  e++
  gi|298676130|ref|YP_003727879.1| 451 LSPGNYYVNFEAP 463
                                       789*****99987 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.064
                              PEGA  29 lsleaGnyslrvekeGYe 46 
                                        s+ +Gny ++ + +GY 
  gi|298676130|ref|YP_003727879.1| 562 FSVTPGNYYVQFSSDGYN 579
                                       6799*************4 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.1
                              PEGA  29 lsleaGnyslrvekeGYe 46 
                                        ++e+G+y +  + +GYe
  gi|298676130|ref|YP_003727879.1| 674 FTVEPGEYYVNFSSDGYE 691
                                       579**************8 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.059
                              PEGA  29 lsleaGnyslrvekeGYe 46 
                                        s+e+G+y +  + +GYe
  gi|298676130|ref|YP_003727879.1| 900 FSVEPGEYYVNFSSDGYE 917
                                       689**************8 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.11
                              PEGA   29 lsleaGnyslrvekeGYe 46  
                                         s+ +G+y ++ + +GYe
  gi|298676130|ref|YP_003727879.1| 1013 FSVTPGSYYVQFSSDGYE 1030
                                        6799*************7 PP

>> PLRV_ORF5  Potato leaf roll virus readthrough protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.64   5.5e+02     209     285 ..     180     255 ..     158     297 .. 0.81
   2 ?    8.9   1.2   0.00066      0.57      70     111 ..     323     364 ..     314     396 .. 0.80
   3 ?    4.7   1.0     0.012        10      66     111 ..     550     591 ..     534     600 .. 0.78
   4 ?    4.9   1.2     0.011       9.2      65     109 ..     661     701 ..     646     751 .. 0.63
   5 ?    8.5   2.5   0.00085      0.73      69     152 ..     887     979 ..     876     984 .. 0.84
   6 ?    7.6   1.7    0.0016       1.3      68     110 ..     999    1041 ..     988    1056 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.64
                         PLRV_ORF5 209 dmelGlisvvldehlesdveaervrrpirekhilvaeryepegkivgnklrdktpiqeqerqtdstesddvsdagsv 285
                                       d e+Gl  v+++   + ++++ r +    e+  +   + ep    v+  +  +     q+  +d+ +sd+ s +g+ 
  gi|298676130|ref|YP_003727879.1| 180 DEEVGLTGVTVN-LYNCSGDSLRATTTTDENGYYNFTNLEPGNYYVNFTIPPEFEFTLQDAGPDNIDSDVNSTTGNT 255
                                       568999999998.77889999999999999999999999**999999999999999999*********999776653 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00066
                         PLRV_ORF5  70 sqssvsavaayvfnvpkGsysvdisceGyqsvdsisdnedGr 111
                                       s ++ +a   y f v  Gsy v+ s +Gy  ++   + +dG 
  gi|298676130|ref|YP_003727879.1| 323 SSTTTDADGYYNFTVTPGSYYVNFSSDGYVFTSANQGTDDGV 364
                                       5667789999*******************9999887777774 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.012
                         PLRV_ORF5  66 seyssqssvsavaayvfnvpkGsysvdisceGyqsvdsisdnedGr 111
                                       s     +  +a   y f+v  G+y v+ s +Gy+ ++   ++ed  
  gi|298676130|ref|YP_003727879.1| 550 S----STITNASGYYNFSVTPGNYYVQFSSDGYNFTQANKESEDVD 591
                                       3....34446788999******************999888877755 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.011
                         PLRV_ORF5  65 dseyssqssvsavaayvfnvpkGsysvdisceGyqsvdsisdned 109
                                            s+++ +    y f v  G+y v+ s +Gy  + +  + ed
  gi|298676130|ref|YP_003727879.1| 661 V----SNTTTNNSGYYNFTVEPGEYYVNFSSDGYEFTLQNQGGED 701
                                       3....444555567899*****************87644433332 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.00085
                         PLRV_ORF5  69 ssqssvsavaayvfnvpkGsysvdisceGy......qsvdsisdne...dGrsdGliaysnadsdywnvGeadGvki 136
                                        s+++ +a   y f+v  G+y v+ s +Gy      q vd++ d++    G    +   s    d  + G ++   i
  gi|298676130|ref|YP_003727879.1| 887 VSNTTTNASGYYNFSVEPGEYYVNFSSDGYeftlanQGVDNTVDSDadsSGNTTCITVESGETNDTVDAGLYQPATI 963
                                       6788899999*******************966666677888877542225777888888999999************ PP

                         PLRV_ORF5 137 kklradntyrqGhkel 152
                                        ++  ++t ++G++++
  gi|298676130|ref|YP_003727879.1| 964 GDFVWEDTNKNGKQDI 979
                                       ********99999986 PP

  == domain 6  score: 7.6 bits;  conditional E-value: 0.0016
                         PLRV_ORF5   68 yssqssvsavaayvfnvpkGsysvdisceGyqsvdsisdnedG 110 
                                          s ++ +a   y f+v  Gsy v+ s +Gy  ++s  + +d 
  gi|298676130|ref|YP_003727879.1|  999 LESSTTTNASGYYNFSVTPGSYYVQFSSDGYEFTSSNQGTDDS 1041
                                        445556678899*********************9998877764 PP

>> CooC_C  CS1-pili formation C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.28   2.4e+02      42      70 ..     324     352 ..     312     364 .. 0.79
   2 ?    5.0   0.0      0.03        25      42      92 ..     551     602 ..     539     603 .. 0.83
   3 ?    3.0   0.1      0.12   1.1e+02      33      83 ..     654     702 ..     651     709 .. 0.79
   4 ?    1.0   0.0      0.51   4.3e+02      42      80 ..     889     925 ..     876     941 .. 0.75
   5 ?    0.7   0.0      0.64   5.5e+02      42      72 ..    1002    1030 ..     991    1054 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.28
                            CooC_C  42 vavteedGvFtlevdakapsltvengdtl 70 
                                        + t++dG++ ++v+ ++ +  +++++ +
  gi|298676130|ref|YP_003727879.1| 324 STTTDADGYYNFTVTPGSYYVNFSSDGYV 352
                                       577899*********99999999988754 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.03
                            CooC_C  42 vavteedGvFtlevdakapsltvengdt.lyeveldlertrdevvlvGevtC 92 
                                        ++t++ G++ ++v+ ++ + ++++++  + +++ ++e++  ++   G++tC
  gi|298676130|ref|YP_003727879.1| 551 STITNASGYYNFSVTPGNYYVQFSSDGYnFTQANKESEDVDSDADSSGNTTC 602
                                       6899********************9998566666666777778888888888 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.12
                            CooC_C  33 nakilnhagvavteedGvFtlevdakapsltvengdtlyeveldlertrde 83 
                                       n +  n ++ + t++ G++ ++v+ ++ +  +++++  ye +l+ ++ +d+
  gi|298676130|ref|YP_003727879.1| 654 NCSTDNLVSNTTTNNSGYYNFTVEPGEYYVNFSSDG--YEFTLQNQGGEDT 702
                                       556677788888999999999999999999999998..7777777766655 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.51
                            CooC_C  42 vavteedGvFtlevdakapsltvengdtlyeveldlert 80 
                                        + t++ G++ ++v+ ++ +  +++++  ye +l  +++
  gi|298676130|ref|YP_003727879.1| 889 NTTTNASGYYNFSVEPGEYYVNFSSDG--YEFTLANQGV 925
                                       5778999********999999999998..5555544444 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.64
                            CooC_C   42 vavteedGvFtlevdakapsltvengdtlye 72  
                                         + t++ G++ ++v+ ++ + ++++++   e
  gi|298676130|ref|YP_003727879.1| 1002 STTTNASGYYNFSVTPGSYYVQFSSDGY--E 1030
                                        577889***************9999984..3 PP

>> Glyco_hydro_42C  Beta-galactosidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0065       5.6      17      46 ..     682     712 ..     680     723 .. 0.85
   2 ?    2.5   0.0      0.14   1.2e+02      17      42 ..     908     934 ..     906     946 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0065
                                       EEE-SSS-EE---.-TT-EEEES-......S CS
                   Glyco_hydro_42C  17 vlNfsneevtvtl.pasagdlltgelaeggv 46 
                                       ++Nfs++ +++tl +++++d+++ ++ + gv
  gi|298676130|ref|YP_003727879.1| 682 YVNFSSDGYEFTLqNQGGEDTVDSDANSSGV 712
                                       69********************998777764 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.14
                                       EEE-SSS-EE---.-TT-EEEES-... CS
                   Glyco_hydro_42C  17 vlNfsneevtvtl.pasagdlltgela 42 
                                       ++Nfs++ +++tl +++  ++++ ++ 
  gi|298676130|ref|YP_003727879.1| 908 YVNFSSDGYEFTLaNQGVDNTVDSDAD 934
                                       69***********99988888887655 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.013        11      39      82 ..     188     229 ..     171     260 .. 0.79
   2 ?    2.7   0.1      0.12   1.1e+02      38      83 ..     308     350 ..     291     372 .. 0.83
   3 ?    6.6   0.1    0.0082         7      39      83 ..     422     464 ..     411     471 .. 0.80
   4 ?   -1.4   0.1       2.2   1.9e+03      54      88 ..     549     582 ..     493     613 .. 0.77
   5 ?    5.3   1.1      0.02        17      37     118 ..     646     718 ..     596     729 .. 0.70
   6 ?    2.7   0.3      0.13   1.1e+02      10      79 ..     712     798 ..     708     808 .. 0.65
   7 ?    2.0   0.4      0.21   1.8e+02      52      88 ..     885     920 ..     854     987 .. 0.72
   8 ?   -1.4   0.2       2.2   1.9e+03      56      86 ..    1002    1031 ..     935    1061 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.013
                       EMP24_GP25L  39 vdlsvkdpdgngerlvkkkdresegdfsftakesgeykvCfdns 82 
                                       v ++++  + +g  l  +  +++ g + ft++e+g+y+v f+ +
  gi|298676130|ref|YP_003727879.1| 188 VTVNLY--NCSGDSLRATTTTDENGYYNFTNLEPGNYYVNFTIP 229
                                       666677..44446666666677778**************99864 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.12
                       EMP24_GP25L  38 dvdlsvkdpdgngerlvkkkdresegdfsftakesgeykvCfdnsf 83 
                                       d+ +++++   ++ ++v++  ++++g + ft+ ++g y+v f++  
  gi|298676130|ref|YP_003727879.1| 308 DIIVTLHN--CSDDTIVSSTTTDADGYYNFTV-TPGSYYVNFSSDG 350
                                       55566674..4448999999************.8******999865 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0082
                       EMP24_GP25L  39 vdlsvkdpdgngerlvkkkdresegdfsftakesgeykvCfdnsf 83 
                                       v ++++d d  g+ + ++  ++ +gd+ ft +++g+y+v f+ ++
  gi|298676130|ref|YP_003727879.1| 422 VTINLYDCDT-GNKIANN-TTDVDGDYNFTGLSPGNYYVNFEAPH 464
                                       6677777666.7788888.666678**************999875 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.2
                       EMP24_GP25L  54 vkkkdresegdfsftakesgeykvCfdnsfstkss 88 
                                        ++ ++ ++g + f++ ++g+y+v f++  +++++
  gi|298676130|ref|YP_003727879.1| 549 ESSTITNASGYYNFSV-TPGNYYVQFSSDGYNFTQ 582
                                       4444555566788888.789999999888777655 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.02
                       EMP24_GP25L  37 ldvdlsvkdpdgngerlvkkkdresegdfsftakesgeykvCfdnsfstksskkvsfdievgseasdykdsakkekl 113
                                        d+++++++ +    +lv++  + ++g + ft+ e+gey+v f++  +      ++++ + g++  d +d++ +   
  gi|298676130|ref|YP_003727879.1| 646 PDIRVELYNCST--DNLVSNTTTNNSGYYNFTV-EPGEYYVNFSSDGYE-----FTLQNQGGEDTVD-SDANSSGVT 713
                                       578888884444..5555555666677******.*********997654.....4555555554433.334444444 PP

                       EMP24_GP25L 114 etles 118
                                       e+++ 
  gi|298676130|ref|YP_003727879.1| 714 ECITL 718
                                       44555 PP

  == domain 6  score: 2.7 bits;  conditional E-value: 0.13
                       EMP24_GP25L  10 eekCfyeelkk.gtllt.gsyqvtdgg..................aaldvdlsvkdpdgngerlvkkkdresegdfs 66 
                                        ++C++ e ++ ++++  g yq  + g                     +v ++++  + ng  l ++k +es+  + 
  gi|298676130|ref|YP_003727879.1| 712 VTECITLESNEtNDTIDaGLYQPASIGdyvwedvngdgvqndgdtGIDNVTVNLY--NCNGDFLETTKTNESG-YYN 785
                                       5666666655555555424455554444555555555666665553356777788..6666777888778777.*** PP

                       EMP24_GP25L  67 ftakesgeykvCf 79 
                                       ft + +g+y++ f
  gi|298676130|ref|YP_003727879.1| 786 FTGLAPGDYYINF 798
                                       **********977 PP

  == domain 7  score: 2.0 bits;  conditional E-value: 0.21
                       EMP24_GP25L  52 rlvkkkdresegdfsftakesgeykvCfdnsfstkss 88 
                                        lv++  + ++g + f++ e+gey+v f++  + ++ 
  gi|298676130|ref|YP_003727879.1| 885 DLVSNTTTNASGYYNFSV-EPGEYYVNFSSDGYEFTL 920
                                       444444555566999999.9********998776654 PP

  == domain 8  score: -1.4 bits;  conditional E-value: 2.2
                       EMP24_GP25L   56 kkdresegdfsftakesgeykvCfdnsfstk 86  
                                        +  + ++g + f++ ++g y+v f++  + +
  gi|298676130|ref|YP_003727879.1| 1002 STTTNASGYYNFSV-TPGSYYVQFSSDGYEF 1031
                                        22222333444444.4555555555444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1084 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); 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):              21  [number of targets reported over threshold]
# CPU time: 0.76u 0.43s 00:00:01.19 Elapsed: 00:00:01.32
# Mc/sec: 2491.23
//
Query:       gi|298676131|ref|YP_003727880.1|  [L=602]
Description: hypothetical protein Metev_2265 [Methanohalobium evestigatum Z-7303]
Scores for 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-131  428.8  48.6    5.9e-34  116.7   8.7    4.8  5  SdrD_B           SdrD B-like domain
    1.4e-33  115.0  20.7    1.5e-09   38.0   0.9    5.8  6  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    4.1e-13   49.3   0.0      0.062   13.3   0.0    4.5  4  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
    2.4e-12   46.7   9.2     0.0015   18.5   0.4    4.7  4  CarbopepD_reg_2  CarboxypepD_reg-like domain
    2.6e-06   28.0   0.5         24    5.7   0.0    5.1  5  TTR-52           Transthyretin-like family
    4.7e-06   26.7   0.3       0.55   10.4   0.0    4.1  4  UDP-g_GGTase     UDP-glucose:Glycoprotein Glucosyltransferase
      2e-05   24.4   0.3       0.15   11.9   0.0    3.8  4  DUF1416          Protein of unknown function (DUF1416)
    4.3e-05   24.0   0.1       0.18   12.3   0.0    2.7  2  AdenylateSensor  Adenylate sensor of SNF1-like protein kinase
    0.00084   19.6   5.7        3.7    7.9   2.0    4.4  3  CARDB            CARDB
     0.0025   17.8  18.2        1.8    8.7   0.1    6.8  7  Big_1            Bacterial Ig-like domain (group 1)
  ------ inclusion threshold ------
      0.012   15.6   7.5        7.1    6.6   0.3    4.4  5  phage_tail_N     Prophage tail fibre N-terminal
      0.026   14.8   8.9       0.59   10.5   8.9    3.1  1  DUF11            Domain of unknown function DUF11
       0.03   13.1  13.8       0.41    9.3   0.8    3.3  3  PLRV_ORF5        Potato leaf roll virus readthrough protein
      0.079   13.3  38.8       0.54   10.6   6.6    6.7  4  SpaA             Prealbumin-like fold domain
      0.094   13.0   3.0         46    4.3   0.1    4.2  3  Tgi2PP           Effector immunity protein Tgi2PP
       0.16   11.4   0.9        3.5    7.0   0.0    3.1  3  Dioxygenase_C    Dioxygenase


Domain annotation for each model (and alignments):
>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   8.7   5.3e-37   5.9e-34       1     112 []       5     114 ..       5     114 .. 0.95
   2 !  114.6   8.4   2.2e-36   2.5e-33       1     112 []     118     227 ..     118     227 .. 0.95
   3 !  113.9   2.9   3.8e-36   4.2e-33       1     112 []     235     347 ..     235     347 .. 0.92
   4 !  105.2   0.4   1.8e-33   2.1e-30       2     112 .]     352     460 ..     351     460 .. 0.97
   5 ?   -0.9   0.4       1.6   1.8e+03      21      61 ..     516     556 ..     499     571 .. 0.63

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 5.3e-37
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvtakk 76 
                                       a+iGdfVweD+nknG+qd ge+gisg tV+L++ +++++ ++ttT+asG+Y+F+ +tpG+Y+V+f+ ++gy++t+++
  gi|298676131|ref|YP_003727880.1|   5 ATIGDFVWEDTNKNGKQDIGESGISGLTVELYNCSTDELeSSTTTNASGYYNFS-VTPGNYYVQFS-SDGYEFTSAN 79 
                                       58*******************************99999989************8.9*********5.68******** PP

                            SdrD_B  77 aGsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       +G+dd++dSdad+ +g+t+++t++sge+n t+daGl
  gi|298676131|ref|YP_003727880.1|  80 QGTDDSMDSDADS-SGNTTCITVESGETNDTVDAGL 114
                                       ***********86.6799*****************7 PP

  == domain 2  score: 114.6 bits;  conditional E-value: 2.2e-36
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvtakk 76 
                                       a+iGdfVweD+nknG+qd ge+gisg tV+L++ +++++ ++ttT+asG+Y+F+ +tpG+Y+V+f+ ++gy++t ++
  gi|298676131|ref|YP_003727880.1| 118 ATIGDFVWEDTNKNGKQDIGETGISGLTVELYNCSTDELeSSTTTNASGYYNFS-VTPGSYYVNFS-SDGYEFTLAN 192
                                       58*******************************99999989************8.9*********5.68******** PP

                            SdrD_B  77 aGsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       +G+dd +dSdad+ +g+t+++t++sg++n tidaGl
  gi|298676131|ref|YP_003727880.1| 193 QGTDDGVDSDADS-SGNTTCITVESGKTNDTIDAGL 227
                                       ***********86.6799*****************7 PP

  == domain 3  score: 113.9 bits;  conditional E-value: 3.8e-36
                            SdrD_B   1 asiGdfVweDanknGiqdagekgisgvtVtLkda.kgevvatttTdasGkYkFtnltpGeYkVefta..pagytvta 74 
                                       as+GdfVweD +++G+qd ge+gi +vtV L+d  +g+++att Td++G+Y Ft+ltpG Y+V+f+a   +gy++t+
  gi|298676131|ref|YP_003727880.1| 235 ASMGDFVWEDLDGDGTQDIGEPGIFNVTVYLYDCvTGNLIATTNTDEDGEYLFTGLTPGVYNVSFAAppESGYVFTP 311
                                       589****************************886266777*************************99644799**** PP

                            SdrD_B  75 kkaGsddaldSdadpatgltktvtlasgesnetidaGl 112
                                       k++Gsd++ dSda++ tg+t++++l sge+n tidaG+
  gi|298676131|ref|YP_003727880.1| 312 KDQGSDEK-DSDANS-TGNTTCINLVSGETNDTIDAGM 347
                                       ******98.***975.889*****************96 PP

  == domain 4  score: 105.2 bits;  conditional E-value: 1.8e-33
                            SdrD_B   2 siGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakkaG 78 
                                       s+ dfVw+D+n nGiqd gekg+++v+V+L++ +g+ +++ +T+asG YkF  + pG+Y+++f+ p+g +++++  G
  gi|298676131|ref|YP_003727880.1| 352 SVSDFVWNDTNCNGIQDPGEKGVANVEVRLYNIDGDYITSEITNASGFYKFL-VPPGHYYLNFVLPEGHEFSPQFMG 427
                                       799************************************************7.9*********************** PP

                            SdrD_B  79 sddaldSdadpatgltktvtlasgesnetidaGl 112
                                        d ++dSd+d+ tg+t+++ l+sge+n tidaG+
  gi|298676131|ref|YP_003727880.1| 428 GDINKDSDVDN-TGNTSIIMLTSGENNVTIDAGI 460
                                       *********87.779******************7 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 1.6
                            SdrD_B  21 ekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYk 61 
                                          ++  + tL  ++  v +   T + G+Y+  +    eY+
  gi|298676131|ref|YP_003727880.1| 516 GVEVNCLNTTLEPDESMVCNAIGTAKLGQYSNYGNVTAEYN 556
                                       33344444555444555557888888899976666666664 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.9   1.4e-12   1.5e-09      12      74 ..      26     106 ..      21     115 .. 0.75
   2 !   35.6   0.8   7.5e-12   8.4e-09      12      61 ..     139     188 ..     134     227 .. 0.81
   3 !   26.3   0.2     6e-09   6.7e-06      14      57 ..     258     302 ..     250     310 .. 0.89
   4 ?   -0.9   0.0       1.8   2.1e+03      29      68 ..     318     357 ..     305     362 .. 0.80
   5 !   25.6   0.0   9.8e-09   1.1e-05       7      63 ..     367     422 ..     365     459 .. 0.86
   6 ?   -2.9   0.2       7.7   8.6e+03      65      67 ..     507     509 ..     485     526 .. 0.51

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.4e-12
                   CarboxypepD_reg  12 apiagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsapGyatatr..................eevtl 69 
                                        +i+g tV+++n + ++ ++sttt+a+G+++++ ++pg+y v++s++Gy+ ++                   + +t+
  gi|298676131|ref|YP_003727880.1|  26 SGISGLTVELYNcSTDELESSTTTNASGYYNFS-VTPGNYYVQFSSDGYEFTSAnqgtddsmdsdadssgntTCITV 101
                                       579*********5566789*************7.***************8555544666655555555555555555 PP

                   CarboxypepD_reg  70 tagqt 74 
                                       + g+t
  gi|298676131|ref|YP_003727880.1| 102 ESGET 106
                                       55555 PP

  == domain 2  score: 35.6 bits;  conditional E-value: 7.5e-12
                   CarboxypepD_reg  12 apiagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsapGyat 61 
                                       ++i+g tV+++n + ++ ++sttt+a+G+++++ ++pg+y v +s++Gy+ 
  gi|298676131|ref|YP_003727880.1| 139 TGISGLTVELYNcSTDELESSTTTNASGYYNFS-VTPGSYYVNFSSDGYEF 188
                                       689*********5566789*************7.***************74 PP

  == domain 3  score: 26.3 bits;  conditional E-value: 6e-09
                   CarboxypepD_reg  14 iagatVtvtn.adtgtvastttdadGafrlrglppgtysvtvsap 57 
                                       i ++tV +++   ++  a+t td+dG++ ++gl+pg y+v + ap
  gi|298676131|ref|YP_003727880.1| 258 IFNVTVYLYDcVTGNLIATTNTDEDGEYLFTGLTPGVYNVSFAAP 302
                                       5689999999667889*************************9886 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1.8
                   CarboxypepD_reg  29 vastttdadGafrlrglppgtysvtvsapGyatatreevt 68 
                                       ++    +++G+ ++ +l  g+ + t+ a  y++a++++++
  gi|298676131|ref|YP_003727880.1| 318 EKDSDANSTGNTTCINLVSGETNDTIDAGMYQPASVSDFV 357
                                       5556678999999999999999999999999999988775 PP

  == domain 5  score: 25.6 bits;  conditional E-value: 9.8e-09
                   CarboxypepD_reg   7 tdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatat 63 
                                        d+  +++a+++V+++n d++  +s  t+a+G +++  +ppg y + +  p  ++++
  gi|298676131|ref|YP_003727880.1| 367 QDPGEKGVANVEVRLYNIDGDYITSEITNASGFYKFL-VPPGHYYLNFVLPEGHEFS 422
                                       689999******************************7.********99777666554 PP

  == domain 6  score: -2.9 bits;  conditional E-value: 7.7
                   CarboxypepD_reg  65 eev 67 
                                       +++
  gi|298676131|ref|YP_003727880.1| 507 TNI 509
                                       223 PP

>> bMG3  Bacterial alpha-2-macroglobulin MG3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00068      0.76      28      60 ..      28      61 ..      25      94 .. 0.76
   2 !    9.3   0.0   0.00097       1.1      28      59 ..     141     173 ..     138     203 .. 0.82
   3 !   10.6   0.0   0.00039      0.44      30      60 ..     260     291 ..     254     322 .. 0.84
   4 !   13.3   0.0   5.6e-05     0.062      26      59 ..     372     405 ..     370     426 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00068
                              bMG3 28 vagaeVrlldkkgevlae.gtTDaqGvarfaall 60
                                      ++g +V+l++++ ++l + +tT+a+G+++f+ + 
  gi|298676131|ref|YP_003727880.1| 28 ISGLTVELYNCSTDELESsTTTNASGYYNFSVTP 61
                                      6899************862678********9874 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00097
                              bMG3  28 vagaeVrlldkkgevlae.gtTDaqGvarfaal 59 
                                       ++g +V+l++++ ++l + +tT+a+G+++f+ +
  gi|298676131|ref|YP_003727880.1| 141 ISGLTVELYNCSTDELESsTTTNASGYYNFSVT 173
                                       6899************862678*******9876 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00039
                              bMG3  30 gaeVrlld.kkgevlaegtTDaqGvarfaall 60 
                                       +++V l+d  +g+++a+++TD++G + f++l 
  gi|298676131|ref|YP_003727880.1| 260 NVTVYLYDcVTGNLIATTNTDEDGEYLFTGLT 291
                                       899*****559*****************9874 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 5.6e-05
                              bMG3  26 kPvagaeVrlldkkgevlaegtTDaqGvarfaal 59 
                                       k va++eVrl++ +g+ + +  T+a+G ++f  +
  gi|298676131|ref|YP_003727880.1| 372 KGVANVEVRLYNIDGDYITSEITNASGFYKFLVP 405
                                       679**************************99765 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.4   1.3e-06    0.0015      20      58 ..      39      76 ..      27      96 .. 0.84
   2 !   16.4   0.4     6e-06    0.0068      20      56 ..     152     187 ..     140     202 .. 0.87
   3 !    9.2   0.0    0.0011       1.2      25      50 ..     274     299 ..     251     306 .. 0.80
   4 ?    4.4   0.0     0.032        36      26      50 ..     390     413 ..     366     416 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                   CarbopepD_reg_2 20 yvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktq 58
                                      +  + +  t+T+++G+++++ +++g+y +++s+ Gy+  
  gi|298676131|ref|YP_003727880.1| 39 STDELESSTTTNASGYYNFS-VTPGNYYVQFSSDGYEFT 76
                                      56677889***********6.999************965 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 6e-06
                   CarbopepD_reg_2  20 yvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyk 56 
                                       +  + +  t+T+++G+++++ +++g y +++s+ Gy+
  gi|298676131|ref|YP_003727880.1| 152 STDELESSTTTNASGYYNFS-VTPGSYYVNFSSDGYE 187
                                       56677889***********6.999************8 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0011
                   CarbopepD_reg_2  25 kkgtvTdenGnFelknlpagkytLvv 50 
                                        + t Tde+G++ ++ l++g y + +
  gi|298676131|ref|YP_003727880.1| 274 IATTNTDEDGEYLFTGLTPGVYNVSF 299
                                       46688****************98766 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.032
                   CarbopepD_reg_2  26 kgtvTdenGnFelknlpagkytLvv 50 
                                       +  +T+++G +++  +p+g y L++
  gi|298676131|ref|YP_003727880.1| 390 TSEITNASGFYKF-LVPPGHYYLNF 413
                                       5568*********.5******9986 PP

>> TTR-52  Transthyretin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.022        24      11      46 ..      28      60 ..      24      79 .. 0.82
   2 ?    5.5   0.0     0.025        28      11      46 ..     141     173 ..     137     188 .. 0.82
   3 ?    5.5   0.0     0.026        29      13      47 ..     260     291 ..     254     301 .. 0.82
   4 ?    4.4   0.0     0.054        61       8      42 ..     371     401 ..     369     408 .. 0.88
   5 ?   -1.5   0.0       3.9   4.4e+03      14      64 ..     517     574 ..     510     582 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.022
                                      GSS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEEE CS
                            TTR-52 11 aknvkVkLwekdtldpddlldetkTdedGnFelsgs 46
                                      +++ +V+L++     +d+l ++t+T+++G+++ s +
  gi|298676131|ref|YP_003727880.1| 28 ISGLTVELYNCS---TDELESSTTTNASGYYNFSVT 60
                                      677899999965...599************999865 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.025
                                       GSS-EEEEEEHHHHTS--EEEEEE--TTSEEEEEEE CS
                            TTR-52  11 aknvkVkLwekdtldpddlldetkTdedGnFelsgs 46 
                                       +++ +V+L++     +d+l ++t+T+++G+++ s +
  gi|298676131|ref|YP_003727880.1| 141 ISGLTVELYNCS---TDELESSTTTNASGYYNFSVT 173
                                       577899999965...599************999865 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.026
                                       S-EEEEEEHHHHTS--EEEEEE--TTSEEEEEEEE CS
                            TTR-52  13 nvkVkLwekdtldpddlldetkTdedGnFelsgse 47 
                                       nv+V L++     + +l+++t+TdedG++  +g +
  gi|298676131|ref|YP_003727880.1| 260 NVTVYLYDC---VTGNLIATTNTDEDGEYLFTGLT 291
                                       788888884...5689************9988865 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.054
                                       T-GGSS-EEEEEEHHHHTS--EEEEEE--TTSEEE CS
                            TTR-52   8 gkpaknvkVkLwekdtldpddlldetkTdedGnFe 42 
                                       +k ++nv+V+L++ d     d ++++ T+++G ++
  gi|298676131|ref|YP_003727880.1| 371 EKGVANVEVRLYNIDG----DYITSEITNASGFYK 401
                                       67899********775....99**********987 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 3.9
                                       -EEEEEEHHHHTS--EEEEEE..--TTSEEEEEEEE-.--......S--EEEEEE---- CS
                            TTR-52  14 vkVkLwekdtldpddlldetk..TdedGnFelsgsen.el.....tsidPylkiyhkCn 64 
                                       v+V+  +  tl+pd+ +  +   T + G+++  g+ + e+     ++ dP  ++ h+ +
  gi|298676131|ref|YP_003727880.1| 517 VEVNCLNT-TLEPDESMVCNAigTAKLGQYSNYGNVTaEYngvqvNDSDPSHYFGHDHW 574
                                       55555554.33555555544445888888877766543442222246666666666655 PP

>> UDP-g_GGTase  UDP-glucose:Glycoprotein Glucosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00049      0.55      13      71 ..      28      82 ..      20     108 .. 0.74
   2 !    9.0   0.0    0.0013       1.5      13      55 ..     141     183 ..     133     221 .. 0.72
   3 ?   -0.1   0.0      0.89     1e+03      45      88 ..     291     336 ..     284     341 .. 0.70
   4 ?    1.0   0.0      0.41   4.6e+02      33      54 ..     393     414 ..     368     454 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00049
                                      -TT-EEEEE-SS-S-SEEEE--SGGGEEEEEE-SEEEEEEE-TTHHHHHEEEEE--SS- CS
                      UDP-g_GGTase 13 prGlqleLgtekkksvaDTivmanlGYfQlkanPGvwklelregrssdiyeiesvgaeg 71
                                       +Gl++eL + ++++++ ++  +  GY+ +  +PG + ++ +    sd ye++s+++ +
  gi|298676131|ref|YP_003727880.1| 28 ISGLTVELYNCSTDELESSTTTNASGYYNFSVTPGNYYVQFS----SDGYEFTSANQGT 82
                                      579999**99888888888999999*************9985....7778887774333 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0013
                                       -TT-EEEEE-SS-S-SEEEE--SGGGEEEEEE-SEEEEEEE-T CS
                      UDP-g_GGTase  13 prGlqleLgtekkksvaDTivmanlGYfQlkanPGvwklelre 55 
                                        +Gl++eL + ++++++ ++  +  GY+ +  +PG + ++ ++
  gi|298676131|ref|YP_003727880.1| 141 ISGLTVELYNCSTDELESSTTTNASGYYNFSVTPGSYYVNFSS 183
                                       5799999*99888888888899999************999863 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.89
                                       -SEEEEEEE-.TTHHHHHEEEEE--SS-S--TT--.--EEEE-STT CS
                      UDP-g_GGTase  45 nPGvwklelr.egrssdiyeiesvgaeglsspkde.gkevvltsfe 88 
                                       +PGv++++   + +s  +++ +++g+++ +s  ++ g++  ++ ++
  gi|298676131|ref|YP_003727880.1| 291 TPGVYNVSFAaPPESGYVFTPKDQGSDEKDSDANStGNTTCINLVS 336
                                       7******998456799999999998888544443335665555555 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.41
                                       --SGGGEEEEEE-SEEEEEEE- CS
                      UDP-g_GGTase  33 vmanlGYfQlkanPGvwklelr 54 
                                       + +  G++ +   PG + l+  
  gi|298676131|ref|YP_003727880.1| 393 ITNASGFYKFLVPPGHYYLNFV 414
                                       566789***********99864 PP

>> DUF1416  Protein of unknown function (DUF1416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.044        49      31      71 ..      26      67 ..      12      85 .. 0.81
   2 ?    3.6   0.0     0.054        60      30      71 ..     138     180 ..     124     199 .. 0.82
   3 ?   -2.8   0.0       5.3   5.9e+03      44      68 ..     270     295 ..     258     302 .. 0.74
   4 !   11.9   0.0   0.00014      0.15      27      77 ..     368     418 ..     349     426 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.044
                           DUF1416 31 epvggayvRLLd.ssgeFtaevvtsaeGefrFfaapGeWtvR 71
                                      + ++g  v L + s++e  +  +t+a+G + F  +pG++ v 
  gi|298676131|ref|YP_003727880.1| 26 SGISGLTVELYNcSTDELESSTTTNASGYYNFSVTPGNYYVQ 67
                                      55666677777746899999******************9986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.054
                           DUF1416  30 gepvggayvRLLd.ssgeFtaevvtsaeGefrFfaapGeWtvR 71 
                                       ++ ++g  v L + s++e  +  +t+a+G + F  +pG++ v 
  gi|298676131|ref|YP_003727880.1| 138 ETGISGLTVELYNcSTDELESSTTTNASGYYNFSVTPGSYYVN 180
                                       556677777777746899999******************9885 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.3
                           DUF1416  44 sgeFtaevvtsaeGefrFfa.apGeW 68 
                                       +g+  a   t ++Ge+ F   +pG +
  gi|298676131|ref|YP_003727880.1| 270 TGNLIATTNTDEDGEYLFTGlTPGVY 295
                                       78888999999999998864245655 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.00014
                           DUF1416  27 trdgepvggayvRLLdssgeFtaevvtsaeGefrFfaapGeWtvRalarkg 77 
                                         +++ v++  vRL + +g++ +   t+a+G ++F   pG++ +  + ++g
  gi|298676131|ref|YP_003727880.1| 368 DPGEKGVANVEVRLYNIDGDYITSEITNASGFYKFLVPPGHYYLNFVLPEG 418
                                       44678899999**********99999***************9998877766 PP

>> AdenylateSensor  Adenylate sensor of SNF1-like protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00016      0.18      61      96 ..      52      89 ..      32      99 .. 0.67
   2 !    8.7   0.0    0.0021       2.4      61      91 ..     165     195 ..     145     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                      EEEEEEEEETTEEEEEEEEEEEEESSSSS..TTTTTSS CS
                   AdenylateSensor 61 leiqlfqlepnnylvdfkfdGwessssek..eetaeed 96
                                           f + p ny v f +dG+e +s ++  ++++++d
  gi|298676131|ref|YP_003727880.1| 52 SGYYNFSVTPGNYYVQFSSDGYEFTSANQgtDDSMDSD 89
                                      5556699****************877665223333333 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0021
                                       EEEEEEEEETTEEEEEEEEEEEEESSSSSTT CS
                   AdenylateSensor  61 leiqlfqlepnnylvdfkfdGwessssekee 91 
                                            f + p +y v+f +dG+e +  ++ +
  gi|298676131|ref|YP_003727880.1| 165 SGYYNFSVTPGSYYVNFSSDGYEFTLANQGT 195
                                       5556699****************87665532 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.023        25      54      87 ..      35      73 ..       3      84 .. 0.79
   2 ?    4.4   0.0     0.039        44      54      87 ..     146     186 ..     115     197 .. 0.78
   3 !    7.9   2.0    0.0033       3.7      15      41 ..     486     512 ..     480     562 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.023
                                      E.....SEE-CTEEEEEEEEEE-S-S-CEEEEEEEESTT CS
                             CARDB 54 v.....psLaagesttvsftwtteategevtltvvvDpd 87
                                      +      +L+++++t+ s  +  + t+g+++++++ D +
  gi|298676131|ref|YP_003727880.1| 35 LyncstDELESSTTTNASGYYNFSVTPGNYYVQFSSDGY 73
                                      155555899**********99999**********99986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.039
                                       E.......SEE-CTEEEEEEEEEE-S-S-CEEEEEEEESTT CS
                             CARDB  54 v.......psLaagesttvsftwtteategevtltvvvDpd 87 
                                       v        +L+++++t+ s  +  + t+g+++++++ D +
  gi|298676131|ref|YP_003727880.1| 146 VelyncstDELESSTTTNASGYYNFSVTPGSYYVNFSSDGY 186
                                       14455555899*********999999**********99976 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0033
                                       EETTSEEEEEEEEEE-SSS-EEEEEEE CS
                             CARDB  15 afvgeentitvtvkNqGtaasgatkva 41 
                                       + vg+++t t++v+N+G+ + ++++v+
  gi|298676131|ref|YP_003727880.1| 486 VQVGTQVTWTYNVTNTGNVNLTNINVT 512
                                       6789*****************999986 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0036       4.1      20      53 ..      27      60 ..      21      63 .. 0.83
   2 ?   -0.6   0.1       1.2   1.3e+03      26      44 ..      66      85 ..      62      98 .. 0.79
   3 !    8.7   0.1    0.0016       1.8      17      53 ..     137     173 ..     134     181 .. 0.84
   4 ?   -1.8   0.0       2.8   3.2e+03      26      43 ..     179     197 ..     175     198 .. 0.79
   5 ?    2.2   0.0      0.17   1.9e+02      37      51 ..     274     288 ..     258     299 .. 0.74
   6 ?    0.5   0.0      0.54     6e+02      16      50 ..     369     402 ..     366     404 .. 0.73
   7 ?    3.6   2.4     0.061        69      23      47 ..     489     517 ..     486     527 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0036
                             Big_1 20 pvagatVtfsvsggalsassgtTdanGkatvtlt 53
                                       ++g tV +   +++ ++ss+tT+a+G + +++t
  gi|298676131|ref|YP_003727880.1| 27 GISGLTVELYNCSTDELESSTTTNASGYYNFSVT 60
                                      688888888877777779*************998 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                             Big_1 26 Vtfsvsg.galsassgtTda 44
                                      V fs++g + +sa++gt d+
  gi|298676131|ref|YP_003727880.1| 66 VQFSSDGyEFTSANQGTDDS 85
                                      88999996666677777775 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0016
                             Big_1  17 ngnpvagatVtfsvsggalsassgtTdanGkatvtlt 53 
                                         + ++g tV +   +++ ++ss+tT+a+G + +++t
  gi|298676131|ref|YP_003727880.1| 137 GETGISGLTVELYNCSTDELESSTTTNASGYYNFSVT 173
                                       56789999999998887777**************998 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 2.8
                             Big_1  26 Vtfsvsg.galsassgtTd 43 
                                       V+fs++g + ++a++gt d
  gi|298676131|ref|YP_003727880.1| 179 VNFSSDGyEFTLANQGTDD 197
                                       99****9666668888876 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.17
                             Big_1  37 assgtTdanGkatvt 51 
                                        +++ Td++G++ +t
  gi|298676131|ref|YP_003727880.1| 274 IATTNTDEDGEYLFT 288
                                       5799*******9875 PP

  == domain 6  score: 0.5 bits;  conditional E-value: 0.54
                             Big_1  16 angnpvagatVtfsvsggalsassgtTdanGkatv 50 
                                          + va+++V +   +g+   +s +T+a+G + +
  gi|298676131|ref|YP_003727880.1| 369 PGEKGVANVEVRLYNIDGDY-ITSEITNASGFYKF 402
                                       55677888888887666666.57999***998876 PP

  == domain 7  score: 3.6 bits;  conditional E-value: 0.061
                             Big_1  23 gatVtfsvsg...gals.assgtTdanGk 47 
                                       g++Vt++ +    g+++ ++  +Td++G+
  gi|298676131|ref|YP_003727880.1| 489 GTQVTWTYNVtntGNVNlTNINVTDSKGV 517
                                       789999866643555559**********8 PP

>> phage_tail_N  Prophage tail fibre N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3    0.0063       7.1      40      71 ..      46      77 ..      28      88 .. 0.85
   2 ?   -1.3   0.0       1.8     2e+03      45      81 ..      92     128 ..      82     137 .. 0.67
   3 ?    5.5   0.2     0.014        16      39      68 ..     158     187 ..     134     203 .. 0.85
   4 ?    4.2   0.0     0.034        39      34      61 ..     270     298 ..     247     306 .. 0.77
   5 ?   -3.4   0.0       7.8   8.8e+03      38      60 ..     389     411 ..     387     431 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0063
                      phage_tail_N 40 senpdeaGrysldvetGkysvilkvdgfpesh 71
                                      s +++ +G y + v  G+y v +  dg++   
  gi|298676131|ref|YP_003727880.1| 46 STTTNASGYYNFSVTPGNYYVQFSSDGYEFTS 77
                                      5678889********************97654 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.8
                      phage_tail_N  45 eaGr.ysldvetGkysvilkvdgfpeshaGditvyeds 81 
                                        +G+  ++ ve G+   ++    +++  +Gd  v+ed+
  gi|298676131|ref|YP_003727880.1|  92 SSGNtTCITVESGETNDTVDAGLYQPATIGDF-VWEDT 128
                                       44432578888888888888888888888886.45554 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.014
                      phage_tail_N  39 asenpdeaGrysldvetGkysvilkvdgfp 68 
                                       +s +++ +G y + v  G y v +  dg++
  gi|298676131|ref|YP_003727880.1| 158 SSTTTNASGYYNFSVTPGSYYVNFSSDGYE 187
                                       46678889********************97 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.034
                      phage_tail_N  34 vvntvasenpdeaGrysld.vetGkysvi 61 
                                         n +a  n+de+G+y +     G y v 
  gi|298676131|ref|YP_003727880.1| 270 TGNLIATTNTDEDGEYLFTgLTPGVYNVS 298
                                       4478999*********9972455777775 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 7.8
                      phage_tail_N  38 vasenpdeaGrysldvetGkysv 60 
                                       ++se ++ +G y + v  G+y +
  gi|298676131|ref|YP_003727880.1| 389 ITSEITNASGFYKFLVPPGHYYL 411
                                       67899999999*99999999965 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   8.9   0.00053      0.59       9      46 ..     485     520 ..     473     583 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00053
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtlPaglayv 46 
                                        v+ G +vt t  vtNtg+++++++ vtD    g++  
  gi|298676131|ref|YP_003727880.1| 485 VVQVGTQVTWTYNVTNTGNVNLTNINVTD--SKGVEVN 520
                                       799**************************..5555544 PP

>> PLRV_ORF5  Potato leaf roll virus readthrough protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.4   0.00048      0.54      68     152 ..      43     136 ..      27     143 .. 0.70
   2 ?    9.3   0.8   0.00037      0.41      68     111 ..     156     199 ..     144     221 .. 0.80
   3 ?    1.0   0.0      0.12   1.3e+02      61      93 ..     381     413 ..     371     435 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00048
                         PLRV_ORF5  68 yssqssvsavaayvfnvpkGsysvdisceGyqsvdsisdned.........GrsdGliaysnadsdywnvGeadGvk 135
                                         s ++ +a   y f+v  G+y v+ s +Gy  ++   + +d         G    +   s    d  + G ++   
  gi|298676131|ref|YP_003727880.1|  43 LESSTTTNASGYYNFSVTPGNYYVQFSSDGYEFTSANQGTDDsmdsdadssGNTTCITVESGETNDTVDAGLYQPAT 119
                                       345556678899*******************8777654443311111111255555666777778888888888888 PP

                         PLRV_ORF5 136 ikklradntyrqGhkel 152
                                       i ++  ++t ++G++++
  gi|298676131|ref|YP_003727880.1| 120 IGDFVWEDTNKNGKQDI 136
                                       88888888888888775 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00037
                         PLRV_ORF5  68 yssqssvsavaayvfnvpkGsysvdisceGyqsvdsisdnedGr 111
                                         s ++ +a   y f+v  Gsy v+ s +Gy  +    + +dG 
  gi|298676131|ref|YP_003727880.1| 156 LESSTTTNASGYYNFSVTPGSYYVNFSSDGYEFTLANQGTDDGV 199
                                       345556678899*******************9998888877775 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.12
                         PLRV_ORF5  61 tkkidseyssqssvsavaayvfnvpkGsysvdi 93 
                                          id  y + +  +a   y f vp G+y ++ 
  gi|298676131|ref|YP_003727880.1| 381 LYNIDGDYITSEITNASGFYKFLVPPGHYYLNF 413
                                       5679999**********************9985 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5  13.3         6   6.7e+03      36      59 ..      45      67 ..       9     180 .. 0.52
   2 ?   10.6   6.6   0.00048      0.54      35      59 ..     223     298 ..     183     314 .. 0.50
   3 ?    5.1   0.0     0.026        29       3      58 ..     371     411 ..     368     423 .. 0.89
   4 ?   -1.4   1.1       2.7   3.1e+03      34      52 ..     492     510 ..     429     545 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6
                                      SEEE-BTTSEEEEEEEESEEEEEE CS
                              SpaA 36 ttlttdenGkatfegLplGtYllv 59
                                       + tt++ G+ +f+ + +G+Y+++
  gi|298676131|ref|YP_003727880.1| 45 SSTTTNASGYYNFS-VTPGNYYVQ 67
                                      44455555555555.555555543 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00048
                                       E...................................................SEEE-BTTSEEEEEEEESEEEEEE CS
                              SpaA  35 v...................................................ttlttdenGkatfegLplGtYllv 59 
                                       +                                                   +t  tde+G+  f+gL +G Y + 
  gi|298676131|ref|YP_003727880.1| 223 IdaglyqpenpkasmgdfvwedldgdgtqdigepgifnvtvylydcvtgnliATTNTDEDGEYLFTGLTPGVYNVS 298
                                       13333333333333333334444444444444444444444444444444449999*****************886 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.026
                                       CCB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEEE CS
                              SpaA   3 gkpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYll 58 
                                       +k +a++e  ly++d              g+ +t+  t++ G  +f  +p+G Y+l
  gi|298676131|ref|YP_003727880.1| 371 EKGVANVEVRLYNID--------------GDYITSEITNASGFYKFL-VPPGHYYL 411
                                       678999999999999..............88899999*********9.9*****98 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.7
                                       EESEEE-BTTSEEEEEEEE CS
                              SpaA  34 evttlttdenGkatfegLp 52 
                                       +++t+   ++G+++ ++++
  gi|298676131|ref|YP_003727880.1| 492 VTWTYNVTNTGNVNLTNIN 510
                                       3333333334554444443 PP

>> Tgi2PP  Effector immunity protein Tgi2PP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.051        57      25      32 ..      53      60 ..      50      62 .. 0.90
   2 ?    4.3   0.1     0.041        46      25      32 ..     166     173 ..     163     176 .. 0.88
   3 ?    1.4   0.0      0.33   3.7e+02      10      31 ..     383     404 ..     379     405 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.051
                                      TEEEEEEE CS
                            Tgi2PP 25 GYadFlvl 32
                                      GY++F+v+
  gi|298676131|ref|YP_003727880.1| 53 GYYNFSVT 60
                                      *******8 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.041
                                       TEEEEEEE CS
                            Tgi2PP  25 GYadFlvl 32 
                                       GY++F+v+
  gi|298676131|ref|YP_003727880.1| 166 GYYNFSVT 173
                                       *******8 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.33
                                       EEE--B--TSS-SSTTEEEEEE CS
                            Tgi2PP  10 fIevDlqDaGkpylpGYadFlv 31 
                                       +I++D     +    G++ Flv
  gi|298676131|ref|YP_003727880.1| 383 NIDGDYITSEITNASGFYKFLV 404
                                       899999888899999*****98 PP

>> Dioxygenase_C  Dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.64   7.2e+02      74      99 ..      43      67 ..      30      80 .. 0.80
   2 ?   -0.1   0.0      0.48   5.4e+02      74      99 ..     156     180 ..     143     196 .. 0.79
   3 ?    7.0   0.0    0.0031       3.5      73      99 ..     272     298 ..     255     305 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.64
                                      TEEEEE--TTSEEEEEEE----EE-- CS
                     Dioxygenase_C 74 lrgriltdeeGryrirtikPapYpip 99
                                      l+ ++ t++ G+y++ ++ P+ Y ++
  gi|298676131|ref|YP_003727880.1| 43 LESSTTTNASGYYNF-SVTPGNYYVQ 67
                                      567888999999998.6999999765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.48
                                       TEEEEE--TTSEEEEEEE----EE-- CS
                     Dioxygenase_C  74 lrgriltdeeGryrirtikPapYpip 99 
                                       l+ ++ t++ G+y++ ++ P++Y ++
  gi|298676131|ref|YP_003727880.1| 156 LESSTTTNASGYYNF-SVTPGSYYVN 180
                                       5678889999*9998.699*999765 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0031
                                       TTEEEEE--TTSEEEEEEE----EE-- CS
                     Dioxygenase_C  73 nlrgriltdeeGryrirtikPapYpip 99 
                                       nl  ++ tde+G+y ++ + P+ Y++ 
  gi|298676131|ref|YP_003727880.1| 272 NLIATTNTDEDGEYLFTGLTPGVYNVS 298
                                       7777888*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.65u 0.48s 00:00:01.12 Elapsed: 00:00:00.59
# Mc/sec: 3068.23
//
Query:       gi|298676132|ref|YP_003727881.1|  [L=995]
Description: multi-sensor signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for 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-37  125.7   0.0      2e-12   47.1   0.0    5.0  4  PAS            PAS fold
    1.6e-36  124.7   0.2    5.6e-10   39.4   0.0    5.1  4  PAS_9          PAS domain
    1.3e-34  119.1   0.2    4.3e-34  117.4   0.1    2.0  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    2.7e-33  114.5   0.0    2.5e-11   43.8   0.0    4.9  5  PAS_4          PAS fold
    2.3e-28   97.7   0.6    2.6e-06   27.3   0.0    4.7  4  PAS_8          PAS domain
    3.2e-24   84.7   0.7    2.2e-22   78.9   0.2    2.9  2  HisKA          His Kinase A (phospho-acceptor) domain
    3.3e-17   62.5   0.1    4.5e-05   23.7   0.0    5.3  4  PAS_3          PAS fold
    0.00029   20.5   0.0        1.1    8.8   0.0    4.0  4  PAS_12         UPF0242 C-terminal PAS-like domain
    0.00044   20.4   0.1      0.071   13.3   0.0    4.0  5  PAS_7          PAS fold
    0.00056   20.2   0.0     0.0018   18.6   0.0    1.9  1  GAF_2          GAF domain
     0.0017   18.2   0.0     0.0049   16.7   0.0    1.8  1  HATPase_c_5    GHKL domain
      0.006   16.4   0.0      0.013   15.3   0.0    1.6  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li
     0.0087   16.6   0.1       0.92   10.1   0.0    3.7  3  PAS_10         PAS domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.033   14.2   0.0    1.8  2  HATPase_c_2    Histidine kinase-like ATPase domain
        3.4    7.5   5.6        3.3    7.5   0.1    2.8  2  Synaptobrevin  Synaptobrevin


Domain annotation for each model (and alignments):
>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.7e-07    0.0002       6      53 ..     251     298 ..     246     348 .. 0.82
   2 !   14.1   0.0     3e-05     0.035       6      46 ..     384     424 ..     379     495 .. 0.86
   3 !   36.9   0.0   2.5e-12     3e-09       2      99 ..     513     608 ..     512     617 .. 0.80
   4 !   47.1   0.0   1.6e-15     2e-12       2     113 .]     633     741 ..     632     741 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.7e-07
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTT CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldlihee 53 
                                       +l+s+ ++if++D    ++++N+ +e+ +G++re+++gk    l+  +
  gi|298676132|ref|YP_003727881.1| 251 VLDSSKVGIFILDSCFHVVWINEPMEDYFGIDREDIIGKDKRQLVEDK 298
                                       799************************************988777443 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3e-05
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBG CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgksl 46 
                                       + +++p  i  vD++g i+y+N+aae  lGls + +  +++
  gi|298676132|ref|YP_003727881.1| 384 VADTSPICITKVDRNGYIVYANHAAEMVLGLSKSKIQERTY 424
                                       5566777777799*******************988777765 PP

  == domain 3  score: 36.9 bits;  conditional E-value: 2.5e-12
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHH..HTT-ECCCC CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlle..qgeesrage 76 
                                       ++r+ ++++p +ifv ++dg  + vN+aa +++G++r+e+l+ +l+dl + +    + e++ q+++  + + ++++e
  gi|298676132|ref|YP_003727881.1| 513 KFRNYIDHSPIGIFVANKDGYYVDVNPAASSITGYTRDELLSMNLIDLHPQD----VLEQIYQAYNylVENGKTSVE 585
                                       578899****************************************998887....999998876511555555555 PP

                                       EEEECTTSSEEEEEEEEEEEEET CS
                               PAS  77 isfklrdgrpihlevraspvrda 99 
                                         f +++ + +++ + a+++ d 
  gi|298676132|ref|YP_003727881.1| 586 LPFITKKSELRYFILDAVKLSDD 608
                                       55555888888888888777776 PP

  == domain 4  score: 47.1 bits;  conditional E-value: 1.6e-15
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++r+++e+++d+i++ D dg+ilyvN+ +++ lG++ +e+l+ +l d  ++ d +e +++++  l+  ++  ++ ++
  gi|298676132|ref|YP_003727881.1| 633 RFRTVIEQAADAIIAHDFDGNILYVNDLTCDNLGYTKDELLSMNLADIDPNIDTYEPRKRYWDKLSYHSSYLIETVN 709
                                       799*******************************************999999999********************** PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +++ dg+++++ev ++ +   g+    +lg++rdi
  gi|298676132|ref|YP_003727881.1| 710 RRK-DGSEFPVEVKMTLMNLSGKP--VILGFVRDI 741
                                       ***.**********9988777666..9*******8 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   9.8e-10   1.2e-06       2      77 ..     257     324 ..     256     360 .. 0.75
   2 !   23.1   0.0   5.6e-08   6.7e-05       4     104 .]     390     499 ..     387     499 .. 0.86
   3 !   27.2   0.0     3e-09   3.6e-06       2     104 .]     523     619 ..     522     619 .. 0.77
   4 !   39.4   0.0   4.7e-13   5.6e-10       4     103 ..     645     742 ..     642     743 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 9.8e-10
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       +gi+i ++ ++++++Ne +++ +G ++e+++gk+ ++l+      +++l++++e+ +  e++  +  ++++++++ 
  gi|298676132|ref|YP_003727881.1| 257 VGIFILDSCFHVVWINEPMEDYFGIDREDIIGKDKRQLV------EDKLKHIFEDSD--EFANRLLATYDDNSYIE 324
                                       699*998888*****************************......666777777666..66666655555554444 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 5.6e-08
                             PAS_9   4 ili..dnpdgrilyaNeaalrllGyspeevlgksitdlf....vtdpeanerlraaleqgrk...kerevevvlirk 71 
                                       i+i  ++ +g i+yaN aa+ +lG s+  +  + ++d+     ++d +    ++  +e  +k   ++++v   ++ +
  gi|298676132|ref|YP_003727881.1| 390 ICItkVDRNGYIVYANHAAEMVLGLSKSKIQERTYDDVKwkitDFDGNYYPQEELPFELVQKylePVYDVRHAIQWP 466
                                       5555689***************************9999966665555555555555566666999************ PP

                             PAS_9  72 ngetfwvlltaspvkdddgelvgiivilrDite 104
                                       +g++ +  ++a+p++dd +++ g+++ +++i+e
  gi|298676132|ref|YP_003727881.1| 467 DGQRKLLSINAAPIFDDYNRFDGLVAAIENISE 499
                                       *******************************98 PP

  == domain 3  score: 27.2 bits;  conditional E-value: 3e-09
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                        gi++ n+dg  +++N+aa  ++Gy+++e+l  ++ dl   +  ++  +  + ++e+      +ve+ +i+k+ e  
  gi|298676132|ref|YP_003727881.1| 523 IGIFVANKDGYYVDVNPAASSITGYTRDELLSMNLIDLHpqDVLEQIYQAYNYLVEN---GKTSVELPFITKKSELR 596
                                       699**99*************************9999999333333333333444444...56999999999999999 PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       ++ l a+ + dd+     ++++ +Dite
  gi|298676132|ref|YP_003727881.1| 597 YFILDAVKLSDDK-----YLGFTTDITE 619
                                       9888888885554.....4479999997 PP

  == domain 4  score: 39.4 bits;  conditional E-value: 4.7e-13
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwvl 79 
                                       i+  + dg+ily+N+  ++ lGy+++e+l  ++ d+  ++ ++ e  +++++ ++  + +  e+v++rk+g++f+v+
  gi|298676132|ref|YP_003727881.1| 645 IIAHDFDGNILYVNDLTCDNLGYTKDELLSMNLADID-PNIDTYEPRKRYWDKLSYhSSYLIETVNRRKDGSEFPVE 720
                                       55555799****************************9.77777777777777777788******************* PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDit 103
                                       ++++ +  +++ +++  +++rDit
  gi|298676132|ref|YP_003727881.1| 721 VKMTLMNLSGKPVIL--GFVRDIT 742
                                       ******877888888..******9 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4   0.1   3.6e-37   4.3e-34       2     111 ..     879     988 ..     878     989 .. 0.97

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 3.6e-37
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHH CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlG 77 
                                       de++Lrqi+ nl+ Na+kf t++g+++v++++++d +++sv D+GiGip+++++++fe+f q d +++r++ gtGlG
  gi|298676132|ref|YP_003727881.1| 879 DEIKLRQILYNLIYNAIKF-TNKGSVTVTVRQKNDAYQFSVIDTGIGIPEDKQDEIFESFRQlDTGASRRYAGTGLG 954
                                       899****************.***********7779****************************************** PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftftlple 111
                                       l++vk+lve +gG+iwvese+ +Gttftft+p +
  gi|298676132|ref|YP_003727881.1| 955 LALVKRLVEIHGGQIWVESEESKGTTFTFTIPST 988
                                       *******************************976 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         6   7.2e+03       7      23 ..     113     129 ..     111     141 .. 0.78
   2 !   27.9   0.0   1.9e-09   2.2e-06       1     109 [.     252     368 ..     252     369 .. 0.93
   3 !   15.2   0.0   1.5e-05     0.018       2     108 ..     386     500 ..     385     502 .. 0.88
   4 !   43.8   0.0   2.1e-14   2.5e-11       2     109 ..     519     621 ..     518     622 .. 0.98
   5 !   21.5   0.0   1.8e-07   0.00021       2     110 .]     639     746 ..     638     746 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6
                             PAS_4   7 alavldpdgrvlyaNaa 23 
                                       +++ +d+dg++++ +++
  gi|298676132|ref|YP_003727881.1| 113 WIILFDEDGNITASSES 129
                                       67888****99986655 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 1.9e-09
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee......daarleralrrvlegeepieflee 71 
                                       lds+ +++++ld+ ++v+++N+ ++++fg+++e+++Gk  ++l+ +       d +++++ l +  + +  ie  e+
  gi|298676132|ref|YP_003727881.1| 252 LDSSKVGIFILDSCFHVVWINEPMEDYFGIDREDIIGKDKRQLVEDKlkhifeDSDEFANRLLATYDDNSYIENFEC 328
                                       79***************************************999999999999999999999999999********* PP

                             PAS_4  72 lll...pgeerhyelrllPlrdesGe.vigvlvisrDiTerr 109
                                       ++l   ++eer++e    P+   sG  + g +++ +DiT r+
  gi|298676132|ref|YP_003727881.1| 329 HVLpdsNREERWLEHWSQPI--KSGLyAGGRIEHYYDITYRK 368
                                       *999***********99999..56777999999999999775 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 1.5e-05
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee......daarleralrrvlegeepiefleel 72 
                                       d +p +++ +d++g ++yaN aa+ ++g++   +  +t+ ++  +         ++ e + + v +  ep++++ + 
  gi|298676132|ref|YP_003727881.1| 386 DTSPICITKVDRNGYIVYANHAAEMVLGLSKSKIQERTYDDVKWKItdfdgnYYPQEELPFELVQKYLEPVYDVRHA 462
                                       6799999***************999***************9644447778889999999999999999999999988 PP

                             PAS_4  73 ll..pgeerhyelrllPlrdesGevigvlvisrDiTer 108
                                           +g+++ +++++ P++d+  + +g+++ +  i+e 
  gi|298676132|ref|YP_003727881.1| 463 IQwpDGQRKLLSINAAPIFDDYNRFDGLVAAIENISEK 500
                                       88999999999999999999999999999999888875 PP

  == domain 4  score: 43.8 bits;  conditional E-value: 2.1e-14
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgee 78 
                                       d++p +++v ++dg ++++N+aa ++ g++++ell + l +l+p+++ +++ +a++ ++e +++  +l + +   e 
  gi|298676132|ref|YP_003727881.1| 519 DHSPIGIFVANKDGYYVDVNPAASSITGYTRDELLSMNLIDLHPQDVLEQIYQAYNYLVENGKTSVELPFITKKSEL 595
                                       89*************************************************************************** PP

                             PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTerr 109
                                       r++ l ++ l d     + +l++++DiTer+
  gi|298676132|ref|YP_003727881.1| 596 RYFILDAVKLSD-----DKYLGFTTDITERK 621
                                       ***********9.....9************8 PP

  == domain 5  score: 21.5 bits;  conditional E-value: 1.8e-07
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee.daarleralrrvlegeepiefleelllpge 77 
                                       ++  da+++ d dg++ly+N   ++ +g++ +ell + la++ p     ++  r+++++      ++++  ++ +g+
  gi|298676132|ref|YP_003727881.1| 639 EQAADAIIAHDFDGNILYVNDLTCDNLGYTKDELLSMNLADIDPNIdTYEPRKRYWDKLSYHSSYLIETVNRRKDGS 715
                                       678899***********************************9999999***********999877777777777*** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       e ++e+ ++ + + sG+   +l+++rDiT r++
  gi|298676132|ref|YP_003727881.1| 716 EFPVEVKMTLM-NLSGK-PVILGFVRDITVRKQ 746
                                       *********99.89***.889********9985 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.2e-08   1.5e-05       1      53 [.     242     299 ..     242     315 .. 0.77
   2 !   14.3   0.0   2.7e-05     0.032       9      54 ..     387     436 ..     379     450 .. 0.65
   3 !   27.3   0.0   2.2e-09   2.6e-06       2      46 ..     513     558 ..     512     572 .. 0.84
   4 !   25.6   0.0   7.4e-09   8.9e-06       2      54 ..     633     686 ..     632     697 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.2e-08
                             PAS_8   1 erlral....fesspdgiavvdlgd..rivdvNqaalellGys.adlkgellgqllpvlr 53 
                                       er+r++    ++ss +gi+++d     ++v++N+ +++ +G + +d++g++ +ql+++  
  gi|298676132|ref|YP_003727881.1| 242 ERHRTIvddvLDSSKVGIFILD--ScfHVVWINEPMEDYFGIDrEDIIGKDKRQLVEDKL 299
                                       688885444488*********9..666**************9999999999987766544 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.7e-05
                             PAS_8   9 sspdgiavvd.lgdrivdvNqaalellGys....adlkgellgqllpvlrp 54 
                                       +sp  i  vd +g  iv++N aa++ lG+s    ++   +++ + ++++++
  gi|298676132|ref|YP_003727881.1| 387 TSPICITKVDrNGY-IVYANHAAEMVLGLSkskiQERTYDDVKWKITDFDG 436
                                       55555554786888.*************77744444444444455555555 PP

  == domain 3  score: 27.3 bits;  conditional E-value: 2.2e-09
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellg 46 
                                       ++r+ +++sp gi+v++ +g   vdvN+aa  ++Gy+ ++l+ + l 
  gi|298676132|ref|YP_003727881.1| 513 KFRNYIDHSPIGIFVANkDGY-YVDVNPAASSITGYTrDELLSMNLI 558
                                       79999***********97777.***************8888877664 PP

  == domain 4  score: 25.6 bits;  conditional E-value: 7.4e-09
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrp 54 
                                       r+r+++e+++d+i+  d +g+ i++vN+ +++ lGy+ ++l+ + l ++ p ++ 
  gi|298676132|ref|YP_003727881.1| 633 RFRTVIEQAADAIIAHDfDGN-ILYVNDLTCDNLGYTkDELLSMNLADIDPNIDT 686
                                       9*************9999999.***************888888777655554444 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.076        91      43      64 ..     236     257 ..     210     258 .. 0.86
   2 !   78.9   0.2   1.8e-25   2.2e-22       1      67 []     764     832 ..     764     832 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.076
                                       HHHHHHHHHHHHHHHHHHHCCH CS
                             HisKA  43 tiesearrldhlvedlLdlsri 64 
                                       ++++ ++r + +v+d+Ld s+ 
  gi|298676132|ref|YP_003727881.1| 236 KLIEKEERHRTIVDDVLDSSKV 257
                                       5677888***********9985 PP

  == domain 2  score: 78.9 bits;  conditional E-value: 1.8e-25
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH.HHC...T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                             HisKA   1 slgrflagvaHELrtPLsailgnaea.Lkre.gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                       +++++la+v+HELrtPL++i+g++++ Lkr+ g+l++++ +yl++i++++++l++l++d+Ldl++ie+g
  gi|298676132|ref|YP_003727881.1| 764 AKSELLANVSHELRTPLTSIIGFSDViLKRKvGDLNDNQTRYLDKIHKSGQHLLDLINDILDLAKIESG 832
                                       589***********************55888************************************97 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.032        38       2      30 ..     269     295 ..     268     350 .. 0.80
   2 ?    5.2   0.0     0.022        26       2      86 ..     402     491 ..     401     494 .. 0.77
   3 !   23.7   0.0   3.7e-08   4.5e-05       2      71 ..     535     601 ..     534     609 .. 0.86
   4 !   22.1   0.0   1.1e-07   0.00013       2      87 ..     655     736 ..     654     738 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.032
                             PAS_3   2 iyvserveeilGyspeellgkveswldlv 30 
                                       + ++e +e+++G+++e+++gk  + ++lv
  gi|298676132|ref|YP_003727881.1| 269 VWINEPMEDYFGIDREDIIGK--DKRQLV 295
                                       67899****************..544444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.022
                             PAS_3   2 iyvserveeilGyspeellgk.veswldlvhpeDrervrea...lqealkkge.pyegeyRirrkdGeyrwvearar 73 
                                       +y++ + e +lG+s++ ++++ +++++  +   D +++ ++   ++ + k  e +y++ + i+++dG+   ++  a 
  gi|298676132|ref|YP_003727881.1| 402 VYANHAAEMVLGLSKSKIQERtYDDVKWKITDFDGNYYPQEelpFELVQKYLEpVYDVRHAIQWPDGQRKLLSINAA 478
                                       79999999999999999999988888888888885555444111445557777788999999999999999999999 PP

                             PAS_3  74 virdengkpvrvi 86 
                                       +i+d+ ++ + ++
  gi|298676132|ref|YP_003727881.1| 479 PIFDDYNRFDGLV 491
                                       9999888877665 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 3.7e-08
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkgepyegeyRirrkdGeyrwvear 71 
                                       + v+++ + i+Gy+++ell+   +++dl hp+D +e++++a++ ++++g+  ++e  +++k  e r++   
  gi|298676132|ref|YP_003727881.1| 535 VDVNPAASSITGYTRDELLSM--NLIDL-HPQDvLEQIYQAYNYLVENGK-TSVELPFITKKSELRYFILD 601
                                       689******************..99996.77777*********9999999.7999999*999999988655 PP

  == domain 4  score: 22.1 bits;  conditional E-value: 1.1e-07
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +yv++  ++ lGy+++ell+   +++d+    D  + r+ +++ l+  ++y +e   rrkdG+ + ve +++ + + 
  gi|298676132|ref|YP_003727881.1| 655 LYVNDLTCDNLGYTKDELLSM--NLADIDPNIDTYEPRKRYWDKLSYHSSYLIETVNRRKDGSEFPVEVKMTLM-NL 728
                                       89*******************..***************************************************.99 PP

                             PAS_3  79 ngkpvrvig 87 
                                       +gkpv ++g
  gi|298676132|ref|YP_003727881.1| 729 SGKPV-ILG 736
                                       99999.555 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.22   2.6e+02      67      99 ..     266     299 ..     233     308 .. 0.71
   2 ?    4.6   0.0     0.019        22      68      93 ..     400     425 ..     374     434 .. 0.86
   3 ?   -2.0   0.0       2.1   2.5e+03      63      89 ..     528     554 ..     520     592 .. 0.80
   4 !    8.8   0.0   0.00096       1.1      54     137 ..     639     725 ..     635     730 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.22
                            PAS_12  67 nkllfaNaqirallGwssdkfl.qdfseivqegl 99 
                                        +++++N+ +++  G   ++++ +d  ++v++ l
  gi|298676132|ref|YP_003727881.1| 266 FHVVWINEPMEDYFGIDREDIIgKDKRQLVEDKL 299
                                       3699**************9998345667777655 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.019
                            PAS_12  68 kllfaNaqirallGwssdkflqdfse 93 
                                        +++aN+  +++lG+s+ k+ ++  +
  gi|298676132|ref|YP_003727881.1| 400 YIVYANHAAEMVLGLSKSKIQERTYD 425
                                       599****************9887655 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.1
                            PAS_12  63 sqkenkllfaNaqirallGwssdkflq 89 
                                       ++k+   + +N    +++G+  d++l+
  gi|298676132|ref|YP_003727881.1| 528 ANKDGYYVDVNPAASSITGYTRDELLS 554
                                       666666677899999******999986 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.00096
                            PAS_12  54 EnlgailvysqkenkllfaNaqirallGwssdkflqdfseivqegleeW...kralaklsskteskirlvlKtKagq 127
                                       E+++  ++   ++  +l++N+ + + lG+ +d++l+     +++ ++++   kr  +kls +    i+ v + K g 
  gi|298676132|ref|YP_003727881.1| 639 EQAADAIIAHDFDGNILYVNDLTCDNLGYTKDELLSMNLADIDPNIDTYeprKRYWDKLSYHSSYLIETVNRRKDGS 715
                                       55666677778999********************9987777777666552225667788888888888888888888 PP

                            PAS_12 128 evllncllgi 137
                                       e ++++++ +
  gi|298676132|ref|YP_003727881.1| 716 EFPVEVKMTL 725
                                       7777776655 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0     6e-05     0.071       2     114 ..     253     371 ..     252     372 .. 0.79
   2 ?    1.5   0.0      0.27   3.3e+02       8     114 ..     392     504 ..     388     505 .. 0.73
   3 ?   -0.7   0.1       1.3   1.6e+03     103     114 ..     613     624 ..     518     625 .. 0.65
   4 ?   -3.1   0.0       6.9   8.3e+03       2      33 ..     639     670 ..     638     680 .. 0.79
   5 ?   -3.1   0.0         7   8.4e+03     105     115 .]     739     749 ..     726     749 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6e-05
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrl......aaara 72 
                                       ++ + Gi ++D+   +v +N+ + + +++ +e + +g+  ++l++   ++  f+  d++++++r l      + +++
  gi|298676132|ref|YP_003727881.1| 253 DSSKVGIFILDSCFHVVWINEPMEDYFGIDREDI-IGKDKRQLVEDKLKH-IFE--DSDEFANRLLatyddnSYIEN 325
                                       66678***************************99.999999998877543.333..555555555522233235667 PP

                             PAS_7  73 gkphsfererpdgrvievrgnpl....pdgGfVttytDiTerrrae 114
                                       ++ h +  + +++r++e  ++p+      gG +  y DiT r+  e
  gi|298676132|ref|YP_003727881.1| 326 FECHVLPDSNREERWLEHWSQPIksglYAGGRIEHYYDITYRKIIE 371
                                       9999******************94444569***********98766 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.27
                             PAS_7   8 isvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagd..veaeverrlaaaragkphsferer 82 
                                       i+ +D+++ +v  N+    +l+l+++ +q  +  +   +++   g++ +++  + + v++ l+ +  + +h+++   
  gi|298676132|ref|YP_003727881.1| 392 ITKVDRNGYIVYANHAAEMVLGLSKSKIQERTYDDVKWKITDFDGNYYPQEelPFELVQKYLEPVY-DVRHAIQWPD 467
                                       556899999999999999999999999977766555566666677777444236667888886554.4778888888 PP

                             PAS_7  83 pdgrvievrgnpl.....pdgGfVttytDiTerrrae 114
                                        + + +++++ p+        G+V+  + i+e++++e
  gi|298676132|ref|YP_003727881.1| 468 GQRKLLSINAAPIfddynRFDGLVAAIENISEKIEKE 504
                                       8888999999998544433478888888888888876 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.3
                             PAS_7 103 tytDiTerrrae 114
                                         tDiTer++ e
  gi|298676132|ref|YP_003727881.1| 613 FTTDITERKKVE 624
                                       457777777765 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 6.9
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpee 33 
                                       e+  ++i+  D d++++ +N+  ++ l+++++
  gi|298676132|ref|YP_003727881.1| 639 EQAADAIIAHDFDGNILYVNDLTCDNLGYTKD 670
                                       67778899999999999999999888888776 PP

  == domain 5  score: -3.1 bits;  conditional E-value: 7
                             PAS_7 105 tDiTerrraee 115
                                        DiT r++aee
  gi|298676132|ref|YP_003727881.1| 739 RDITVRKQAEE 749
                                       7*******996 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.5e-06    0.0018       2     137 ..      90     228 ..      89     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B--....-TTHHHHHHHHTS-EEES- CS
                             GAF_2   2 adleelldlvldelvel.gaalgyillvdddgglrlaawgeaeeefgaaldrpl....geglvgealrtgrpvilnd 73 
                                       +++e+ll++++d l++  +++  +i l d+dg+++ ++ ++ +++f++ l r      +++l    +++   +++++
  gi|298676132|ref|YP_003727881.1|  90 KNVEQLLQRTCDILTNSrTFESTWIILFDEDGNITASSESGVGPSFNDFLKRYErgemSRCLQDLFYQSDNLLVIEN 166
                                       689*************856**************99999999999*99999663332224444333444456777999 PP

                                       GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  74 leedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                        +++ + ++l + + g++  l+  l ++++++G+l++ +  ++  +e+  +l+ e+ ++i+ a+
  gi|298676132|ref|YP_003727881.1| 167 KKSNCSDCPLILKETGYN-ALVSRLEHGNKLYGILAV-SGSDDIISERGKQLFHEVTSDISYAL 228
                                       999999999996666654.5666777789*******8.7777789**************99987 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.1e-06    0.0049       3      92 ..     880     976 ..     878     985 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.1e-06
                       HATPase_c_5   3 dldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.......ek....kkless.kskkeeh 67 
                                       ++ l  il nl+ NAi   +k +     +++tvr+k++++ +s+  +  g       e+    ++l +  +++    
  gi|298676132|ref|YP_003727881.1| 880 EIKLRQILYNLIYNAIKFTNKGS-----VTVTVRQKNDAYQFSVIDTGIGipedkqdEIfesfRQLDTGaSRRYAGT 951
                                       5678899*********8877766.....9****************99666666655422433455554435667788 PP

                       HATPase_c_5  68 GiGlksireivkkykgnlsieaedg 92 
                                       G+Gl  ++++v+ ++g++++e e+ 
  gi|298676132|ref|YP_003727881.1| 952 GLGLALVKRLVEIHGGQIWVESEES 976
                                       999****************998875 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.1e-05     0.013       4      76 ..     884     954 ..     881     989 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                       HATPase_c_3   4 ekAlaelvdNsld.AdaenvkievnknrgktgeivieDdGkGmseeelknalr.latsskeakrkstslGkkGiG 76 
                                       ++ l  l+ N++   +  +v+++v ++ +++ ++++ D G G++e++ ++ ++ + + ++     s+ +   G+G
  gi|298676132|ref|YP_003727881.1| 884 RQILYNLIYNAIKfTNKGSVTVTVRQK-NDAYQFSVIDTGIGIPEDKQDEIFEsFRQLDTG---ASRRYAGTGLG 954
                                       566889******9889999******97.589***************999988624444444...34444444555 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.37   4.5e+02       4      39 ..     251     286 ..     248     348 .. 0.86
   2 !   10.1   0.0   0.00077      0.92       6     105 ..     386     497 ..     381     498 .. 0.74
   3 ?   -1.0   0.0       2.2   2.6e+03      42      83 ..     556     598 ..     515     619 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.37
                            PAS_10   4 lLnstpieltflDdnlqirrFtpaakklfklipadv 39 
                                       +L+s ++++  lD+  ++ + ++  + +f + ++d+
  gi|298676132|ref|YP_003727881.1| 251 VLDSSKVGIFILDSCFHVVWINEPMEDYFGIDREDI 286
                                       79999************************9999885 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00077
                            PAS_10   6 nstpieltflDdnlqirrFtpaa........kklfklipadvGrpladihpk...kavknveeviealrtgekdeve 71 
                                       ++ pi +t +D+n  i + ++aa        +k+ +++ +dv  +++d+  +   +++  +e v + l    ++++ 
  gi|298676132|ref|YP_003727881.1| 386 DTSPICITKVDRNGYIVYANHAAemvlglskSKIQERTYDDVKWKITDFDGNyypQEELPFELVQKYLEPVYDVRHA 462
                                       67899999*************87111211114555555566666666664333336666678899999999999999 PP

                            PAS_10  72 vvvp.kngkwvlvrylpyrdedgeiaGvvetfvDi 105
                                       ++ p  + k+  ++  p+ d+ ++++G+v  + +i
  gi|298676132|ref|YP_003727881.1| 463 IQWPdGQRKLLSINAAPIFDDYNRFDGLVAAIENI 497
                                       9998789999********************99998 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.2
                            PAS_10  42 pladihpkkavknveeviealrtgekdevevvv.pkngkwvlv 83 
                                       +l d+hp++ ++++ +  + l ++ k  ve +  +k+ ++ + 
  gi|298676132|ref|YP_003727881.1| 556 NLIDLHPQDVLEQIYQAYNYLVENGKTSVELPFiTKKSELRYF 598
                                       5667777777777777777777777766666553344333333 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       9.3   1.1e+04      86     112 ..     615     645 ..     571     655 .. 0.55
   2 ?   14.2   0.0   2.7e-05     0.033      41     113 ..     888     968 ..     877     985 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 9.3
                       HATPase_c_2  86 pteeep....keslkegGrGlalikglvDev 112
                                        + +e     +e ++++Gr   +i++ +D +
  gi|298676132|ref|YP_003727881.1| 615 TDITERkkveDELKESEGRFRTVIEQAADAI 645
                                       3333333343456666666666666666665 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.7e-05
                       HATPase_c_2  41 tNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep........keslkegGrGlalikglv 109
                                       +N +  a +  ++g+v+v+++++++a +++v D G g +  ++++  e  +        +      G+Glal+k+lv
  gi|298676132|ref|YP_003727881.1| 888 YNLIYNAIKFTNKGSVTVTVRQKNDAYQFSVIDTGIGIPEDKQDEIFE--SfrqldtgaSRRYAGTGLGLALVKRLV 962
                                       555555555556699*********************976665444333..2357788778888999**********9 PP

                       HATPase_c_2 110 Dev..e 113
                                       +    +
  gi|298676132|ref|YP_003727881.1| 963 EIHggQ 968
                                       866554 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.5      0.47   5.6e+02      62      85 ..       6      29 ..       2      31 .. 0.83
   2 ?    7.5   0.1    0.0028       3.3      21      52 ..      80     111 ..      68     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.47
                                      HHHTXXXXXXXXXXXXXXXXXXXX CS
                     Synaptobrevin 62 wwknmkliiililvvlililiiii 85
                                      ++kn k +ii++l++ ++i++i i
  gi|298676132|ref|YP_003727881.1|  6 YFKNKKSVIIVTLMLGFFIILIDI 29
                                      579999999999999999998855 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0028
                                       CHHHHCHCCCCCHHHHCCCCHHHHHHHHHHHH CS
                     Synaptobrevin  21 eNidkvlergekldeLvdktenLqssaqqFkk 52 
                                       +++++++ r++++++L ++t ++ +++++F++
  gi|298676132|ref|YP_003727881.1|  80 SDVNQLIIREKNVEQLLQRTCDILTNSRTFES 111
                                       679999************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (995 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 0.84u 0.69s 00:00:01.52 Elapsed: 00:00:00.88
# Mc/sec: 3413.63
//
Query:       gi|298676133|ref|YP_003727882.1|  [L=569]
Description: von Willebrand factor type A [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-17   64.2   1.6    3.6e-17   63.2   1.6    1.5  1  VWA              von Willebrand factor type A domain
    5.8e-17   61.6   0.0      1e-16   60.8   0.0    1.4  1  DUF1194          Protein of unknown function (DUF1194)
    4.4e-09   37.0   0.5    7.6e-09   36.2   0.5    1.4  1  VWA_2            von Willebrand factor type A domain
    1.2e-05   25.5  27.4      0.033   14.4   1.4    4.3  4  CARDB            CARDB
    0.00022   21.5  14.8       0.23   11.8   1.0    4.2  3  DUF11            Domain of unknown function DUF11
     0.0012   18.8   2.9       0.38   10.7   0.1    3.3  3  DUF2393          Protein of unknown function (DUF2393)
      0.003   17.5   8.9       0.22   11.6   0.8    3.8  3  DUF1573          Protein of unknown function (DUF1573)
     0.0054   16.3   0.5      0.085   12.4   0.1    2.3  2  Glucodextran_N   Glucodextranase, domain N
     0.0074   15.7  10.6       0.12   11.8   0.1    3.8  3  TRAP_beta        Translocon-associated protein beta (TRAPB)
  ------ inclusion threshold ------
      0.053   12.4   0.5        1.6    7.5   0.1    2.4  2  Integrin_alpha2  Integrin alpha
       0.19   12.0   5.7         26    5.1   0.1    4.6  5  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
       0.82    9.9   3.4       0.55   10.4   1.1    1.9  2  Ecm33            GPI-anchored cell wall organization protein


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   1.6   2.4e-20   3.6e-17       1     173 [.      22     201 ..      22     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 2.4e-20
                                       EEEEEEE-STTSCHHHHHHHHHHHHHHHHHHTB..TTTTEEEEEEEESSSEEEEEETTSHC...HHHHHHHHHHTGS CS
                               VWA   1 DivfvlDgSgsmgeenfekvkefikklveklev..gpegtrvglvqfssevktefslndys...skeellsalnnlk 72 
                                       D+++++DgSgs++ ++fe  +e + + +++ ++  +  +++++++qfs+ +++e++l++ +   + + + s++ +++
  gi|298676133|ref|YP_003727882.1|  22 DLYLLVDGSGSISSSDFELQLEGMANTINNSSIvpQDGSVSISVIQFSNIAQVEIPLTTINsqsDADNISSDIIAIN 98 
                                       9*******************************768999999******************887877799999999999 PP

                                       GGGGSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CS.S.....HTHHHHHHHHGCTEEEEEEEESSSH CS
                               VWA  73 ysgggttntgkalkyaleklfkssagaRenakkviilltdGksnd.g.....dpkeaaneakeqgikvfavGvgnad 143
                                       + gg+t+ +  a++  ++kl +  +g     k++i l tdG +n  g     d +++an+   +  ++ ++Gvg  +
  gi|298676133|ref|YP_003727882.1|  99 QVGGSTN-ISGAINLSVQKLPDDLSG-----KQIIDLSTDGVPNVnGiqasyDARDNANNSGFE--ELNTLGVGIGV 167
                                       9999999.******************.....************994587655555555555544..57777777788 PP

                                       HHHHHHHHSSSSC....HHCEEEESSHHHHHHHH CS
                               VWA 144 ekelLnkiasepg....eghvftvtdfeeleelf 173
                                       ++++L+++         +g++ ++ df+++++ f
  gi|298676133|ref|YP_003727882.1| 168 NETFLKELVFPQPsdeyPGFYTFAGDFDTFQKEF 201
                                       8999****44333356689999999999888655 PP

>> DUF1194  Protein of unknown function (DUF1194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.0   6.8e-20     1e-16       4     203 ..      21     210 ..      18     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 6.8e-20
                           DUF1194   4 leLvLavDvSgSvdeeElrlQreGyaaAlrdpevleallagalgriavtyveWsgeseqevvvdWtviesaedaeaf 80 
                                       ++L L+vD SgS+++++++lQ eG a+ +++ +++ +      g++++++++ s+    +v ++ t+i+s++da+++
  gi|298676133|ref|YP_003727882.1|  21 VDLYLLVDGSGSISSSDFELQLEGMANTINNSSIVPQ-----DGSVSISVIQFSNI--AQVEIPLTTINSQSDADNI 90 
                                       78*****************************998753.....489*********95..5688999************ PP

                           DUF1194  81 aaklaaapraaarrtaigeAlefaaallaenpveglrrviDvSGDGpnn.eglepvtaardaaeakgv.tingLaie 155
                                       ++ + a + +  ++t i++A++ +++ l +      +++iD+S DG  n +g++   +ard+a+++g    n L ++
  gi|298676133|ref|YP_003727882.1|  91 SSDIIAIN-QVGGSTNISGAINLSVQKLPDDLS--GKQIIDLSTDGVPNvNGIQASYDARDNANNSGFeELNTLGVG 164
                                       ****9876.56778**************98665..9**********88868999999**********9889999998 PP

                           DUF1194 156 tkeaeasaeldayyeeevigGpgaFvltanefedfaeairrKLvrEia 203
                                          +e++   +  + +   + pg F   a +f++f++  ++K   E+ 
  gi|298676133|ref|YP_003727882.1| 165 IGVNETFL-KELVFPQPSDEYPG-FYTFAGDFDTFQKEFEKKAGKEVG 210
                                       87764322.12245555555555.777777777777777777777765 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.5   5.1e-12   7.6e-09       2     106 ..      24     133 ..      23     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 5.1e-12
                             VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallksl.....pgd.rvglvtfsdgpevliplt.....kdkakilnalr 67 
                                        +++D+SgS++++d     +e + + + + +++      +g+  +++++fs+ ++v+iplt     +d + i + + 
  gi|298676133|ref|YP_003727882.1|  24 YLLVDGSGSISSSD-----FELQLEGMANTINNSsivpqDGSvSISVIQFSNIAQVEIPLTtinsqSDADNISSDII 95 
                                       69***********7.....777777777777744456434446*****************87867788999999999 PP

                             VWA_2  68 nleakgggtnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                       ++++ gg tn+  a++l  + l+++  + k++i l tDg
  gi|298676133|ref|YP_003727882.1|  96 AINQVGGSTNISGAINLSVQKLPDDL-SGKQIIDLSTDG 133
                                       99999*************99999885.666666666677 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.5      0.14   2.1e+02      11      72 ..      11      81 ..       5      98 .. 0.64
   2 !   14.4   1.4   2.2e-05     0.033      10      79 ..     228     292 ..     225     310 .. 0.81
   3 !    9.0   0.6    0.0011       1.6      14      78 ..     339     398 ..     331     411 .. 0.78
   4 !   13.7   5.1   3.8e-05     0.057      14      92 ..     446     522 ..     440     529 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.14
                                      C-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.........EEEEESEE-CTEEEEEEEEEE-S CS
                             CARDB 11 npseafvgeentitvtvkNqGtaasgatkvalyldgelv.........gtvtvpsLaagesttvsftwtte 72
                                      + s+  ++e++ +++ v  +G+++s +++++l    ++          g+v+++ ++ ++ ++v++  tt+
  gi|298676133|ref|YP_003727882.1| 11 TGSASAANEKVDLYLLVDGSGSISSSDFELQLEGMANTInnssivpqdGSVSISVIQFSNIAQVEIPLTTI 81
                                      55677889999999999999999999999998655555521222333333333555555555555555554 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.2e-05
                                       EC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEE CS
                             CARDB  10 lnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevt 79 
                                        + ++  vge++t +++v+NqG+++ ++++++  + g    t +  +L +ge  +v+++ t+e  +g+++
  gi|298676133|ref|YP_003727882.1| 228 KPGQQILVGETVTWSYNVTNQGDKNLTNVTIKDDVTG---FTHDCGKLVPGEWCNVTYSSTAE--KGQYE 292
                                       56788999******************99998755555...45789999999999999999997..66665 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0011
                                       EEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEE CS
                             CARDB  14 eafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategev 78 
                                       e  +++++t +++v+N+G+ + +++ ++   d+e+  t +  +L++ge  +v+ + ++e  +g++
  gi|298676133|ref|YP_003727882.1| 339 EILENDTVTWSYNVTNNGNVNLTDVIIK---DDETGFTHYCGKLEPGEWCNVTNSSKAE--KGQY 398
                                       5678999************998776544...6666678899999999999998888876..5554 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 3.8e-05
                                       EEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEESTT-SS CS
                             CARDB  14 eafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtltvvvDpdnev 90 
                                       ++ vg+e+t t++++N+G+ + +++  +++ +g+  +t +  +L++ges t s+t + ++ ++++  +v++  +ne 
  gi|298676133|ref|YP_003727882.1| 446 AVQVGNEVTWTYEITNTGNVNLTEI--NITKNGSIEKTYPNINLEPGESFTYSTTGVSKLGQQNYNGNVTAVYENEM 520
                                       67899*************9998665..567899998899999*****************999999999999999987 PP

                                       -- CS
                             CARDB  91 aE 92 
                                        +
  gi|298676133|ref|YP_003727882.1| 521 YD 522
                                       65 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   1.0   0.00016      0.23       9      40 ..     232     274 ..     220     312 .. 0.73
   2 !    7.9   0.2    0.0025       3.8      10      37 ..     340     367 ..     329     395 .. 0.91
   3 !    7.5   2.3    0.0034       5.1       9      36 ..     446     473 ..     437     512 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtl...........P 40 
                                       ++  G+tvt    vtN+g +++++v+++D +           P
  gi|298676133|ref|YP_003727882.1| 232 QILVGETVTWSYNVTNQGDKNLTNVTIKDDVtgfthdcgklvP 274
                                       7889*************************76444444444443 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0025
                             DUF11  10 vrpGdtvtytltvtNtgpasangvvvtD 37 
                                       +   dtvt    vtN+g++++++v ++D
  gi|298676133|ref|YP_003727882.1| 340 ILENDTVTWSYNVTNNGNVNLTDVIIKD 367
                                       5567999*****************9998 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0034
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvt 36 
                                       +v+ G +vt t   tNtg+++++++ +t
  gi|298676133|ref|YP_003727882.1| 446 AVQVGNEVTWTYEITNTGNVNLTEINIT 473
                                       799*******************998776 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00025      0.38      42      90 ..     218     266 ..     213     298 .. 0.81
   2 ?    2.8   0.1     0.073   1.1e+02      56      82 ..     339     365 ..     320     374 .. 0.80
   3 ?    3.8   0.1     0.035        52      56      83 ..     446     473 ..     430     526 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                           DUF2393  42 kylkkaeltilsqkrllyteafvvdgtitNeGkftikeCkleiklvnks 90 
                                       ky+   +      +++l+ e++  + ++tN+G++++++++++ ++  + 
  gi|298676133|ref|YP_003727882.1| 218 KYTNGKDSDTKPGQQILVGETVTWSYNVTNQGDKNLTNVTIKDDVTGFT 266
                                       55555555555667899***********************987666555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.073
                           DUF2393  56 rllyteafvvdgtitNeGkftikeCkl 82 
                                        +l ++++  + ++tN+G+ +++ +++
  gi|298676133|ref|YP_003727882.1| 339 EILENDTVTWSYNVTNNGNVNLTDVII 365
                                       5667899999*************9987 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.035
                           DUF2393  56 rllyteafvvdgtitNeGkftikeCkle 83 
                                       ++++ + +  + +itN+G+ +++e  ++
  gi|298676133|ref|YP_003727882.1| 446 AVQVGNEVTWTYEITNTGNVNLTEINIT 473
                                       57899999999************99886 PP

>> DUF1573  Protein of unknown function (DUF1573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.3    0.0062       9.3      12      70 ..     232     286 ..     223     297 .. 0.70
   2 ?    2.8   0.1     0.082   1.2e+02      13      33 ..     340     360 ..     336     405 .. 0.84
   3 !   11.6   0.8   0.00015      0.22      14      70 ..     448     503 ..     442     530 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0062
                           DUF1573  12 kieegekvtatFeftNtgkaplvitnvktsCgCttpeypkepiapGesgkikvtfnakg 70 
                                       +i  ge+vt ++++tN+g+++l  tnv+ + + t  + +  ++ pGe ++  vt+++++
  gi|298676133|ref|YP_003727882.1| 232 QILVGETVTWSYNVTNQGDKNL--TNVTIKDDVTGFTHDCGKLVPGEWCN--VTYSSTA 286
                                       457799**************87..56666666666666666666776654..4455554 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.082
                           DUF1573  13 ieegekvtatFeftNtgkapl 33 
                                       i e+++vt ++++tN+g+ +l
  gi|298676133|ref|YP_003727882.1| 340 ILENDTVTWSYNVTNNGNVNL 360
                                       668999***********9876 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00015
                           DUF1573  14 eegekvtatFeftNtgkaplvitnvktsCgCttpeypkepiapGesgkikvtfnakg 70 
                                       + g++vt t+e+tNtg+ +l+  n++++ g ++ +yp+  ++pGes++ + t  +k 
  gi|298676133|ref|YP_003727882.1| 448 QVGNEVTWTYEITNTGNVNLTEINITKN-GSIEKTYPNINLEPGESFTYSTTGVSKL 503
                                       66899*************9998888765.9999*************98776655554 PP

>> Glucodextran_N  Glucodextranase, domain N
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   5.7e-05     0.085     139     223 ..     289     373 ..     278     377 .. 0.81
   2 ?    1.7   0.0       0.1   1.5e+02     190     212 ..     447     469 ..     388     481 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.7e-05
                    Glucodextran_N 139 sgagdsasvveakggkalvAsdgsvalAlaasvpferasvGyvGasDgltdLkadgtltweyesasdGnvaltgeld 215
                                          ++ + ++ + +++    +d+s +   + s ++e++++G+  +s    ++ ++ t+tw+y+ +++Gnv lt  + 
  gi|298676133|ref|YP_003727882.1| 289 GQYENIGNATGQYNDTNYSDQDSSYYFGANPSIDMEKYTNGMNASSPTGPEILENDTVTWSYNVTNNGNVNLTDVII 365
                                       55667777766666666666667899999999*****************************************9887 PP

                    Glucodextran_N 216 lgtskeft 223
                                        ++++ ft
  gi|298676133|ref|YP_003727882.1| 366 KDDETGFT 373
                                       76666665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.1
                    Glucodextran_N 190 LkadgtltweyesasdGnvaltg 212
                                        +  +++tw+ye +++Gnv lt+
  gi|298676133|ref|YP_003727882.1| 447 VQVGNEVTWTYEITNTGNVNLTE 469
                                       5667899************9985 PP

>> TRAP_beta  Translocon-associated protein beta (TRAPB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1     8e-05      0.12      32      70 ..     235     274 ..     230     289 .. 0.80
   2 ?    3.3   0.4     0.032        48      33      60 ..     342     369 ..     340     374 .. 0.88
   3 ?    3.8   1.7     0.022        33      33      63 ..     449     479 ..     445     540 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8e-05
                         TRAP_beta  32 vegedltveytiyNvGssaAldVslvD..dsfpeeaFevvs 70 
                                       v ge +t +y+++N+G+   ++V+++D  ++f  +  ++v 
  gi|298676133|ref|YP_003727882.1| 235 V-GETVTWSYNVTNQGDKNLTNVTIKDdvTGFTHDCGKLVP 274
                                       4.899**********************55577776666555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.032
                         TRAP_beta  33 egedltveytiyNvGssaAldVslvDds 60 
                                       e+  +t +y+++N G+   +dV ++Dd 
  gi|298676133|ref|YP_003727882.1| 342 ENDTVTWSYNVTNNGNVNLTDVIIKDDE 369
                                       5677999*******************74 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.022
                         TRAP_beta  33 egedltveytiyNvGssaAldVslvDdsfpe 63 
                                        g+++t +y+i+N G+   ++++++ ++  e
  gi|298676133|ref|YP_003727882.1| 449 VGNEVTWTYEITNTGNVNLTEINITKNGSIE 479
                                       588999999****999998888888776444 PP

>> Integrin_alpha2  Integrin alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.037        55     345     370 ..     233     258 ..     211     259 .. 0.80
   2 ?    7.5   0.1    0.0011       1.6     337     368 ..     436     470 ..     426     473 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.037
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Integrin_alpha2 345 deiGseVehtyeiqNkGpstvpeael 370
                                         +G+ V+  y+++N+G++++ ++++
  gi|298676133|ref|YP_003727882.1| 233 ILVGETVTWSYNVTNQGDKNLTNVTI 258
                                       558****************9999875 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0011
                                       XXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Integrin_alpha2 337 gesame...sedeiGseVehtyeiqNkGpstvpea 368
                                       ge+a+e      ++G+eV+ tyei+N+G+ ++ e 
  gi|298676133|ref|YP_003727882.1| 436 GEDADEpqgPAVQVGNEVTWTYEITNTGNVNLTEI 470
                                       5555555557789***************9888765 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 ?    5.1   0.1     0.018        26       4      27 ..     236     259 ..     233     262 .. 0.92
   2 ?   -1.6   0.0       2.2   3.3e+03      58      71 ..     279     292 ..     276     298 .. 0.84
   3 ?    0.1   0.1      0.68     1e+03       5      25 ..     344     364 ..     342     366 .. 0.86
   4 ?   -1.5   0.0         2     3e+03      58      71 ..     386     399 ..     381     405 .. 0.86
   5 ?    4.8   0.2     0.022        33       2      27 ..     448     473 ..     447     476 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.018
                       NPCBM_assoc   4 Getvtltltvtndgtaaatnvsls 27 
                                       Getvt    vtn+g++ +tnv ++
  gi|298676133|ref|YP_003727882.1| 236 GETVTWSYNVTNQGDKNLTNVTIK 259
                                       99*******************985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                       NPCBM_assoc  58 kVtppagaaaGdye 71 
                                       +Vt +++a+ G+ye
  gi|298676133|ref|YP_003727882.1| 279 NVTYSSTAEKGQYE 292
                                       7999********97 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.68
                       NPCBM_assoc   5 etvtltltvtndgtaaatnvs 25 
                                       +tvt    vtn+g+  +t+v 
  gi|298676133|ref|YP_003727882.1| 344 DTVTWSYNVTNNGNVNLTDVI 364
                                       68899999*******999985 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 2
                       NPCBM_assoc  58 kVtppagaaaGdye 71 
                                       +Vt +++a+ G+ye
  gi|298676133|ref|YP_003727882.1| 386 NVTNSSKAEKGQYE 399
                                       69999*******97 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.022
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvsls 27 
                                       + G +vt t ++tn+g+  +t+++++
  gi|298676133|ref|YP_003727882.1| 448 QVGNEVTWTYEITNTGNVNLTEINIT 473
                                       6699******************9986 PP

>> Ecm33  GPI-anchored cell wall organization protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.1   0.00037      0.55      28      40 .]      79      91 ..      78      91 .. 0.94
   2 ?   -3.1   0.0       6.3   9.5e+03      30      35 ..     245     250 ..     243     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00037
                             Ecm33 28 ttIenQgDAdgLa 40
                                      ttI++Q+DAd+++
  gi|298676133|ref|YP_003727882.1| 79 TTINSQSDADNIS 91
                                      8*********998 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.3
                             Ecm33  30 IenQgD 35 
                                       ++nQgD
  gi|298676133|ref|YP_003727882.1| 245 VTNQGD 250
                                       79***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.64u 0.66s 00:00:01.30 Elapsed: 00:00:00.63
# Mc/sec: 2722.52
//
Query:       gi|298676134|ref|YP_003727883.1|  [L=410]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete 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-22   78.7   0.2    1.6e-21   76.7   0.0    2.1  2  OrfB_IS605      Probable transposase
    4.9e-10   39.2   0.3    1.8e-09   37.4   0.1    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0046   17.3   0.0      0.011   16.1   0.0    1.6  1  RuvX            Holliday junction resolvase
     0.0055   16.5   0.4      0.015   15.1   0.4    1.7  1  DUF919          Nucleopolyhedrovirus protein of unknown funct


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2      0.86   3.9e+03      37      52 ..      39      54 ..      18      70 .. 0.51
   2 !   76.7   0.0   3.7e-25   1.6e-21      10     119 ..     185     292 ..     176     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.86
                        OrfB_IS605 37 twflykgrrlksdyky 52
                                      + f+++g+ l ++  y
  gi|298676134|ref|YP_003727883.1| 39 QYFFNNGKYLNKNTAY 54
                                      2234444444444444 PP

  == domain 2  score: 76.7 bits;  conditional E-value: 3.7e-25
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                        ++ + n++++iDlG+ n+at+vt++gt+f+ +gr +ks +++++ke+ +lqs ++k++       k+   + kr  
  gi|298676134|ref|YP_003727883.1| 185 IAELDYNNHLSIDLGVDNFATCVTTSGTAFILDGRGIKSYNRWWNKEKSRLQSVYDKQN--VDDGLKMNQFSWKRFW 259
                                       6667789***************************************************9..9*************** PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       ++++++++ ++h++k++ e+ ++++++g++k+i
  gi|298676134|ref|YP_003727883.1| 260 KINDYMNQCVNHIVKHCLENRIGNVVIGELKEI 292
                                       ******************************987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.3     6e+03       9      21 ..     167     179 ..     164     181 .. 0.88
   2 !   37.4   0.1   4.1e-13   1.8e-09       1      69 []     311     385 ..     311     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                    OrfB_Zn_ribbon   9 eykakeyGikvee 21 
                                       +yk +++ i++++
  gi|298676134|ref|YP_003727883.1| 167 KYKGRWFEIEFVY 179
                                       79*******9987 PP

  == domain 2  score: 37.4 bits;  conditional E-value: 4.1e-13
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+++k++l+ k+k +Gik++ev++a+TSk  +   +  ++      ++s+r    ++ g  +++D+n+a+Nil++
  gi|298676134|ref|YP_003727883.1| 311 FARFKQKLASKCKYHGIKYHEVDEAFTSKVDALALEPIRKhkkylgKRSKRGIFQSSTGRLINADINGALNILRK 385
                                       899**************************8766655544445588*99************************986 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.4e-06     0.011      37     106 ..     266     345 ..     253     367 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.4e-06
                                       HHHHHHHHHHHHHTT--EEEEE--........----SSS---SSTTHHHHHHHHHT....T-EEEEE--S----XXX CS
                              RuvX  37 ekdleelkelvkeeeveeiVvGlP........lnldgsegesakkvrkfaeeLakrl..kklpvelvDErlttveae 103
                                       ++ ++++ + + e+++ ++V+G          +  +++++ ++  +++f ++La+++  ++++ + vDE +t++  +
  gi|298676134|ref|YP_003727883.1| 266 NQCVNHIVKHCLENRIGNVVIGELkeinqeqnIGKENTQNFQTIPFARFKQKLASKCkyHGIKYHEVDEAFTSKVDA 342
                                       78999*****************98666666555566777778888899******99977889***********9766 PP

                                       XXX CS
                              RuvX 104 ril 106
                                        +l
  gi|298676134|ref|YP_003727883.1| 343 LAL 345
                                       555 PP

>> DUF919  Nucleopolyhedrovirus protein of unknown function (DUF919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4   3.5e-06     0.015      15      58 ..       4      45 ..       2      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.5e-06
                            DUF919 15 qaKrkltiksqHfErlkkitKnpkElqdlekklnklRqeFLnfg 58
                                       +K  l+ + q +E lk++tK +k l +   +l ++Rq+F+n g
  gi|298676134|ref|YP_003727883.1|  4 TQKNHLRADKQTYETLKRLTKLSKNLYNF--TLYNIRQYFFNNG 45
                                      58999******************888765..8**********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.48s 00:00:01.02 Elapsed: 00:00:00.75
# Mc/sec: 1655.40
//
Query:       gi|298676135|ref|YP_003727884.1|  [L=284]
Description: undecaprenyl diphosphate synthase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-69  234.3   0.1    1.5e-69  234.0   0.1    1.1  1  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.0   0.1   8.4e-74   1.5e-69       1     219 [.      33     255 ..      33     260 .. 0.93

  Alignments for each domain:
  == domain 1  score: 234.0 bits;  conditional E-value: 8.4e-74
                                       EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHH...HHHHHH CS
                      Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellk...eellke 74 
                                       imDGNrR+Ak+ g +   +Ghk G ++ ++++e++ e+g++ +tvYafSteNf+R++ee ++l+el++   +e++++
  gi|298676135|ref|YP_003727884.1|  33 IMDGNRRYAKNMG-KAGYYGHKLGSDTTEKVIEWACEIGIEEMTVYAFSTENFSRPPEETEKLFELIDtrlNEMVED 108
                                       9************.99999************************************************8777778877 PP

                                       HHHHHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GG CS
                      Prenyltransf  75 elkellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.ee 150
                                       e  +++++++++r++Gd+++lp+ +++++e+ae+at + ++ ++ln+a++Yg+r++i++av+e+++++++ + + e+
  gi|298676135|ref|YP_003727884.1| 109 E--RTHNRQMKIRAVGDRKRLPQYLQDSIERAEKATCHYEN-FKLNVALAYGGRQDIIQAVQEIARKVKRGDLTvEK 182
                                       7..99999*****************************7766.**********************9999776666566 PP

                                       HSHHHHHCTSTT..T..SSS-SEEEEESS--S-TTSSTTTTTT-E..EEEESSSGGG--HHHHHHHHHHHHHC CS
                      Prenyltransf 151 ideetlekhlytaka..lpdpDlliRtsGeeRlSnFllwqlayse..lyfldvlWPdfskedllealleyqkr 219
                                       ++e+t+++hly   +  + d+D+++Rt+G+eR+SnFl wq+  +e   yf+  +WP f+k d+l+a++ yq+r
  gi|298676135|ref|YP_003727884.1| 183 VNESTISNHLYPDCEqpVSDVDMIVRTGGNERVSNFLPWQANGNEctAYFCAPYWPMFRKIDFLRAIRVYQAR 255
                                       79*********64336799*********************99998999***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 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:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.56s 00:00:01.11 Elapsed: 00:00:00.61
# Mc/sec: 1405.00
//
Query:       gi|298676136|ref|YP_003727885.1|  [L=1914]
Description: APHP domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-39  133.3  20.6    7.8e-10   38.4   0.3    8.7  9  PD40             WD40-like Beta Propeller Repeat
      6e-18   65.0  12.6    7.7e-17   61.4   1.6    3.5  3  CARDB            CARDB
    5.6e-11   42.6   0.6    2.1e-08   34.3   0.0    3.5  3  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    5.9e-08   32.6   6.7    6.1e-07   29.3   0.3    3.4  3  CarbopepD_reg_2  CarboxypepD_reg-like domain
    7.4e-08   31.5  23.0      0.017   13.9   0.3    6.8  6  DPPIV_N          Dipeptidyl peptidase IV (DPP IV) N-terminal 
    1.5e-06   27.2   4.4       0.03   13.0   0.0    3.9  4  Pectate_lyase22  Oligogalacturonate lyase
    5.1e-06   26.7   0.2    5.1e-06   26.7   0.2    4.5  5  SdrD_B           SdrD B-like domain
      2e-05   24.7   0.0      8e-05   22.7   0.0    2.1  1  DUF2012          Protein of unknown function (DUF2012)
  ------ inclusion threshold ------
       0.42   11.0   4.2       0.77   10.1   0.5    3.2  2  SpaA             Prealbumin-like fold domain
        9.2    6.6  14.0        1.5    9.1   0.5    5.1  5  Glyco_hydro_30C  Glycosyl hydrolase family 30 beta sandwich d


Domain annotation for each model (and alignments):
>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00047      0.85       3      37 ..     491     526 ..     489     527 .. 0.86
   2 !   18.3   0.1   8.8e-07    0.0016       4      25 ..     538     559 ..     536     571 .. 0.93
   3 !    5.8   0.0    0.0077        14       5      25 ..     584     603 ..     580     603 .. 0.79
   4 !   11.2   0.0   0.00015      0.28       4      24 ..     628     648 ..     626     651 .. 0.83
   5 !   19.9   0.1   2.9e-07   0.00052      16      38 .]     688     709 ..     687     709 .. 0.96
   6 !   38.4   0.3   4.4e-13   7.8e-10       2      38 .]     718     753 ..     717     753 .. 0.96
   7 !   37.6   0.2   8.2e-13   1.5e-09       3      37 ..     763     796 ..     761     797 .. 0.93
   8 ?   -2.3   0.0       2.6   4.7e+03      20      34 ..     855     870 ..     855     872 .. 0.80
   9 ?   -3.0   0.1       4.5     8e+03      23      32 ..    1832    1840 ..    1831    1843 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00047
                                       E--SSSS.EEEEEE-TTSSEEEEEEECT..TCEEEE CS
                              PD40   3 rltntpgnegaPsfSPDGkrlaFsSdRg.sGkpdIy 37 
                                       + t++p+ + +P +SP G+ ++F  + + + k+dIy
  gi|298676136|ref|YP_003727885.1| 491 QFTFNPEKDSNPVWSPTGNEIVFGKSIPtEEKYDIY 526
                                       6799999************99998887788888887 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 8.8e-07
                                       --SSSS.EEEEEE-TTSSEEEE CS
                              PD40   4 ltntpgnegaPsfSPDGkrlaF 25 
                                       ltn p +eg P++SPDG+++ +
  gi|298676136|ref|YP_003727885.1| 538 LTNLPNIEGHPRWSPDGNKILY 559
                                       7999****************87 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0077
                                       -SSSS.EEEEEE-TTSSEEEE CS
                              PD40   5 tntpgnegaPsfSPDGkrlaF 25 
                                       tn  +  ++  +SP G+++++
  gi|298676136|ref|YP_003727885.1| 584 TNDAQ-SECAVWSPSGSKIVY 603
                                       44444.899**********98 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00015
                                       --SSSS.EEEEEE-TTSSEEE CS
                              PD40   4 ltntpgnegaPsfSPDGkrla 24 
                                       +++++++   +s+SPDG+++a
  gi|298676136|ref|YP_003727885.1| 628 ILTGQKYANRFSWSPDGSKIA 648
                                       56777788899*********8 PP

  == domain 5  score: 19.9 bits;  conditional E-value: 2.9e-07
                                       E-TTSSEEEEEEECT.TCEEEEE CS
                              PD40  16 fSPDGkrlaFsSdRgsGkpdIyv 38 
                                       +SPDG+++++ Sd + G+ dIy+
  gi|298676136|ref|YP_003727885.1| 688 WSPDGSKIVYHSDEN-GNRDIYT 709
                                       ***************.******5 PP

  == domain 6  score: 38.4 bits;  conditional E-value: 4.4e-13
                                       EE--SSSS.EEEEEE-TTSSEEEEEEECT.TCEEEEE CS
                              PD40   2 krltntpgnegaPsfSPDGkrlaFsSdRgsGkpdIyv 38 
                                       ++lt++++ +++ +fSPDG++++F+S+R+ G+ dI++
  gi|298676136|ref|YP_003727885.1| 718 TQLTTNSAKDTDSFFSPDGSKIVFVSNRE-GNNDIWM 753
                                       79***************************.******7 PP

  == domain 7  score: 37.6 bits;  conditional E-value: 8.2e-13
                                       E--SSSS.EEEEEE-TTSSEEEEEEECT.TCEEEE CS
                              PD40   3 rltntpgnegaPsfSPDGkrlaFsSdRgsGkpdIy 37 
                                       +lt ++++++ P++ PDG+++aFsS+R  G++dI+
  gi|298676136|ref|YP_003727885.1| 763 QLTVNSADDMYPTWNPDGTKIAFSSNRA-GNYDIW 796
                                       6777899*********************.****** PP

  == domain 8  score: -2.3 bits;  conditional E-value: 2.6
                                       SSEEEEEEECT..TCE CS
                              PD40  20 GkrlaFsSdRg.sGkp 34 
                                       G + +++Sd+   G p
  gi|298676136|ref|YP_003727885.1| 855 GDKVTWTSDKAsPGEP 870
                                       77899****9887776 PP

  == domain 9  score: -3.0 bits;  conditional E-value: 4.5
                                        EEEEEECT.T CS
                              PD40   23 laFsSdRgsG 32  
                                        ++F Sd + G
  gi|298676136|ref|YP_003727885.1| 1832 MYFESDTP-G 1840
                                        67777766.5 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   1.6   4.3e-20   7.7e-17       1     102 []     906    1008 ..     906    1008 .. 0.93
   2 !   10.0   0.3   0.00044      0.78      16      73 ..    1116    1180 ..    1102    1192 .. 0.68
   3 ?   -3.4   0.3       6.4   1.2e+04      49      70 ..    1614    1636 ..    1598    1659 .. 0.50

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 4.3e-20
                                        S--EEE..EEEC-SEEETTSEEEEEEEEEE-SSS-.EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S- CS
                             CARDB    1 tpDLtv.tntlnpseafvgeentitvtvkNqGtaa.sgatkvalyldgelvgtvtvpsLaagesttvsftwttea 73  
                                        +pDLt+ + ++  +++  g+e+t++++vkN G+a+   +++ +ly+++el +t++   La+ges++  ft t++a
  gi|298676136|ref|YP_003727885.1|  906 KPDLTItNISWDKENPKIGDELTFSYEVKNLGKADtKSKFTNKLYINDELWDTSQC-TLASGESKKNIFTRTWKA 979 
                                        69****777888999********************8999***********999998.9****************6 PP

                                        S-CEEEEEEEESTT-SS--SSCCCSEEEE CS
                             CARDB   74 tegevtltvvvDpdnevaEsnEtNNeltk 102 
                                        t +e+ +++v+D+++e+++++ +NN+ltk
  gi|298676136|ref|YP_003727885.1|  980 TGSEYIIKIVADESGEIDDTDNSNNTLTK 1008
                                        667777********************986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00044
                                        ETTSEEEEEEEEEE-SSS-...EEEEEEEEEETTEEE.EEEEESEE-CTEEEEEEEEEE-S...- CS
                             CARDB   16 fvgeentitvtvkNqGtaa...sgatkvalyldgelv.gtvtvpsLaagesttvsftwtte...a 73  
                                          g+e+ +t+t+kN+G+ +       ++++  + e   +  +   L+++e+++v++tw+++   a
  gi|298676136|ref|YP_003727885.1| 1116 IIGDEIPVTYTIKNTGNVKhkfYAGYSTRCAFSNEIWdAPYKAITLEPSETEDVTLTWKVQnnvA 1180
                                        568999*********986622233455555555555545555589*************9984322 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 6.4
                                        E.EEEEESEE-CTEEEEEEEEEE CS
                             CARDB   49 v.gtvtvpsLaagesttvsftwt 70  
                                        + +t+t ++++ +e+tt ++++ 
  gi|298676136|ref|YP_003727885.1| 1614 AiKTATYKNISINENTTAKVNVN 1636
                                        33444444555555555444443 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.6   4.6e+03      18      56 ..     105     142 ..      95     149 .. 0.71
   2 !   34.3   0.0   1.2e-11   2.1e-08       2      75 ..    1015    1084 ..    1014    1088 .. 0.87
   3 ?    4.3   0.1     0.028        50      40      79 ..    1593    1635 ..    1592    1637 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.6
                   CarboxypepD_reg  18 tVtvtnadtgtvastttdadGafrlrglppgtysvtvsa 56 
                                       +++++++ +  + +ttt  +G+     l pg+y+  +++
  gi|298676136|ref|YP_003727885.1| 105 QISFYDN-SANKPYTTTVVKGSTERLELVPGDYNWIAEK 142
                                       6666632.2334557777888888888999999988875 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 1.2e-11
                   CarboxypepD_reg    2 isGrVt.dasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtt 75  
                                        ++G+V  d+s+++i+ +tV +t        + tt ++G++++++lp g+y++ ++++Gy+  +  +v ++   tt
  gi|298676136|ref|YP_003727885.1| 1015 LEGKVLlDSSKNGISDVTVKLT----PGDITKTTYPNGYYSFKNLPSGKYNILAEKNGYKFNSL-DVKISSSSTT 1084
                                        689996489*************....88899999*************************98886.5888777666 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.028
                   CarboxypepD_reg   40 frlrglppgtysvtv...sapGyatatreevtltagqtttldi 79  
                                        f +++l  g++++t    +++  +tat++++++++++t+ +++
  gi|298676136|ref|YP_003727885.1| 1593 FEIDALDKGNFTLTLtqkTKSAIKTATYKNISINENTTAKVNV 1635
                                        9999***********877788889**************99998 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.3   3.4e-10   6.1e-07       2      71 ..    1016    1085 ..    1015    1093 .. 0.95
   2 ?    5.0   0.5     0.014        24      33      84 ..    1600    1645 ..    1589    1646 .. 0.65
   3 ?   -3.5   0.0       6.1   1.1e+04      30      68 ..    1826    1864 ..    1820    1877 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 3.4e-10
                   CarbopepD_reg_2    2 sGtVvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektld 71  
                                        +G+V+ +++k+ +  +tV ++      +T  nG++++knlp+gky + ++  Gyk  +  v++s+ +t++
  gi|298676136|ref|YP_003727885.1| 1016 EGKVLLDSSKNGISDVTVKLTPGDITKTTYPNGYYSFKNLPSGKYNILAEKNGYKFNSLDVKISSSSTTK 1085
                                        7**************************************************************9988765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.014
                   CarbopepD_reg_2   33 nGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnillkeealele 84  
                                        +GnF+l+  ++ k     s++   t  k++++++++t +vn+++++e+  ++
  gi|298676136|ref|YP_003727885.1| 1600 KGNFTLTLTQKTK-----SAIKTAT-YKNISINENTTAKVNVNQSDESYLMD 1645
                                        5566665322222.....3444444.467999999*******9999998776 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 6.1
                   CarbopepD_reg_2   30 TdenGnFelknlpagkytLvvsyvGyktqekkvtvskek 68  
                                        ++++G+  +++ ++g   + ++++G ++++k  t s+e+
  gi|298676136|ref|YP_003727885.1| 1826 SEDEGYMYFESDTPGFSPFAITAMGIEEESKATTGSNES 1864
                                        566777777777777777889999999999888877765 PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.019        34      33      60 ..     487     514 ..     469     517 .. 0.79
   2 !   12.1   5.0   3.5e-05     0.062      21     136 ..     519     622 ..     516     650 .. 0.83
   3 !    8.4   0.3   0.00045      0.82      35      82 ..     676     724 ..     641     731 .. 0.74
   4 !   13.9   0.3   9.7e-06     0.017      35      85 ..     717     771 ..     706     773 .. 0.80
   5 !   13.2   0.2   1.6e-05     0.028       2      74 ..     734     805 ..     733     825 .. 0.75
   6 ?   -3.3   0.1       1.6   2.8e+03     232     267 ..    1391    1426 ..    1379    1437 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.019
                                       EECEEEETTTT.BSEEEEESSTTEEEEE CS
                           DPPIV_N  33 neveelspgeeklqlakwSPagdklafv 60 
                                       +++e+ + + ek + + wSP+g+ ++f 
  gi|298676136|ref|YP_003727885.1| 487 KKIEQFTFNPEKDSNPVWSPTGNEIVFG 514
                                       56777777789***************96 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.5e-05
                                       ETTEEEEEETTT.EECEEEETT.TT.BSEEEEESSTTEEEEEETT.....EEEEESTTTSEEEECES-STTTEEESB CS
                           DPPIV_N  21 ytaeyyiydlet.neveelspg.eeklqlakwSPagdklafvrnn.....nLyvrelatgkeiqlTsdgsagifnGv 90 
                                       ++++y+iy+++  n+ e++  +  +    ++wSP+g+k+ + ++n     n+++ ++  +++++lT+d         
  gi|298676136|ref|YP_003727885.1| 519 TEEKYDIYKVSVdNKYESVLTNlPNIEGHPRWSPDGNKILYKKDNtngwyNVWIMNSDGSSQTALTNDA-------- 587
                                       57899999999768888888887888999**************9888888*******999********9........ PP

                                       --HHHHHHTSSSSBEEEE-TTSSEEEEEEEECTTS-EEEEEESSSS CS
                           DPPIV_N  91 adWvyeEEvlgsnsavwWspdgsrlaylrfdeseVpeitlpsytde 136
                                            + E         Wsp+gs+++y   d s  pe  + +  d 
  gi|298676136|ref|YP_003727885.1| 588 -----QSE------CAVWSPSGSKIVYKHSDNSDLPEDVIIMNPDG 622
                                       .....667......77888888888888888888877666655555 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00045
                                       CEEEETTTT.BSEEEEESSTTEEEEEE....TTEEEEESTTTSEEEECES-S CS
                           DPPIV_N  35 veelspgeeklqlakwSPagdklafvr....nnnLyvrelatgkeiqlTsdg 82 
                                       ++++++   + q   wSP+g k+++      n+++y  ++    ++qlT++ 
  gi|298676136|ref|YP_003727885.1| 676 FRPQTQ---PWQSQIWSPDGSKIVYHSdengNRDIYTINIDGTDRTQLTTNS 724
                                       444444...4888899999999999872222457999999999999999987 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 9.7e-06
                                       CEEEETTTT.BSEEEEESSTTEEEEEE....TTEEEEESTTTSEEEECES-STTT CS
                           DPPIV_N  35 veelspgeeklqlakwSPagdklafvr....nnnLyvrelatgkeiqlTsdgsag 85 
                                        ++l+ +++k ++  +SP+g k++fv     nn++++ ++  ++++qlT +  ++
  gi|298676136|ref|YP_003727885.1| 717 RTQLTTNSAKDTDSFFSPDGSKIVFVSnregNNDIWMMNVDGSNKTQLTVNSADD 771
                                       4667777899****************8444459****************988555 PP

  == domain 5  score: 13.2 bits;  conditional E-value: 1.6e-05
                                       TTSSEEEEEECEEEESSSEETTEEEEEETTTEECEEEETTTT.BSEEEEESSTTEEEEEE....TTEEEEESTTTS. CS
                           DPPIV_N   2 pdgkflllatnaeknwRhsytaeyyiydletneveelspgeeklqlakwSPagdklafvr....nnnLyvrelatg. 73 
                                       pdg+++++ +n       ++ ++ ++ ++   + ++l+ ++++ ++++w+P+g+k+af      n ++++ el+++ 
  gi|298676136|ref|YP_003727885.1| 734 PDGSKIVFVSN------REGNNDIWMMNVDGSNKTQLTVNSADDMYPTWNPDGTKIAFSSnragNYDIWLIELKEDi 804
                                       56666666444......467899999999999999999999*****************8622225799999988774 PP

                                       E CS
                           DPPIV_N  74 k 74 
                                       +
  gi|298676136|ref|YP_003727885.1| 805 N 805
                                       4 PP

  == domain 6  score: -3.3 bits;  conditional E-value: 1.6
                                        S-SSS-S-EEE-TTTSSEEEEEEETTSSEEEEEEES CS
                           DPPIV_N  232 gWvelhdevhflkrdesgflwisekdGfkHLylfdl 267 
                                         W +  ++ h+ +++ ++ ++++e+++ +++y ++ 
  gi|298676136|ref|YP_003727885.1| 1391 LWADSVHKLHLASNNLDNAIKVIENHDKNKVYTYQE 1426
                                        699999999999999999*************99986 PP

>> Pectate_lyase22  Oligogalacturonate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0014       2.5     169     256 ..     524     605 ..     500     629 .. 0.72
   2 ?   -0.9   0.0      0.27   4.9e+02     218     267 ..     615     662 ..     603     673 .. 0.70
   3 !   13.0   0.0   1.7e-05      0.03      41     101 ..     686     745 ..     671     749 .. 0.90
   4 !    5.8   0.1    0.0026       4.6     217     313 ..     750     837 ..     745     843 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0014
                   Pectate_lyase22 169 rlirvdlktgeaevilkenqwlghpiyrpfddstvafchegphdlvdarmwlinedgsnlrkvkehaegescthevw 245
                                        + +v ++    +v+ +  +  ghp + p d + + + ++         +w++n dgs    + + a+ e     vw
  gi|298676136|ref|YP_003727885.1| 524 DIYKVSVDNKYESVLTNLPNIEGHPRWSP-DGNKILYKKDNTNGW--YNVWIMNSDGSSQTALTNDAQSEC---AVW 594
                                       55666666666666666667777777777.555666666655554..468*****************9985...48* PP

                   Pectate_lyase22 246 vpdgsalayvs 256
                                        p gs ++y  
  gi|298676136|ref|YP_003727885.1| 595 SPSGSKIVYKH 605
                                       ********964 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.27
                   Pectate_lyase22 218 mwlinedgsnlrkvkehaegesc.thevwvpdgsalayvsylkgsterviy 267
                                       + ++n dgsn   + +   g+       w pdgs +a   ++  +  r+i 
  gi|298676136|ref|YP_003727885.1| 615 VIIMNPDGSNKETILT---GQKYaNRFSWSPDGSKIAVSGHIGNQGIRIIN 662
                                       4578999999888865...444404556*******9987777777666653 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 1.7e-05
                   Pectate_lyase22  41 kcftrdgskllfggafdgprnyylldlntqqavqltegkgdntfggflssdddalfyvkne 101
                                       + ++ dgsk+++  + +g+r+ y ++++    +qlt     +t   f+s+d   + +v n 
  gi|298676136|ref|YP_003727885.1| 686 QIWSPDGSKIVYHSDENGNRDIYTINIDGTDRTQLTTNSAKDT-DSFFSPDGSKIVFVSNR 745
                                       56899*******************************9999888.6799***9999999875 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.0026
                   Pectate_lyase22 217 rmwlinedgsnlrkvkehaegescthevwvpdgsalayvsylkgsterviysadpvtlenreltempacshlmsnyd 293
                                        +w++n dgsn  ++   +      +  w pdg+ +a+ s   g+ +  +++ +      +++ + p    +  n  
  gi|298676136|ref|YP_003727885.1| 750 DIWMMNVDGSNKTQLTVNSAD--DMYPTWNPDGTKIAFSSNRAGNYDIWLIELK------EDINHRPVINDIQVN-P 817
                                       58*********8887765554..46789************99999887776654......345555656665555.4 PP

                   Pectate_lyase22 294 gtlmvgdgsdapvdvkddsg 313
                                        t++ g+ +d  vd  d  g
  gi|298676136|ref|YP_003727885.1| 818 STIFEGNSCDIIVDASDPDG 837
                                       56777777777777777666 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       2.4   4.4e+03      72      98 ..      25      51 ..      16      59 .. 0.73
   2 !   26.7   0.2   2.9e-09   5.1e-06      17      82 ..    1021    1081 ..    1013    1110 .. 0.73
   3 ?   -2.8   0.0       4.1   7.3e+03      52      88 ..    1595    1634 ..    1589    1646 .. 0.62
   4 ?    0.7   0.4      0.34   6.2e+02      10      38 ..    1647    1673 ..    1643    1685 .. 0.72
   5 ?   -2.7   0.0       3.7   6.7e+03      23      84 ..    1801    1866 ..    1798    1884 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.4
                            SdrD_B 72 vtakkaGsddaldSdadpatgltktvt 98
                                       +++k +++++ +Sd ++at++ + ++
  gi|298676136|ref|YP_003727885.1| 25 ESSSKFSVNENFESDTKKATDKYNNIN 51
                                      56677889999*****99998776664 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 2.9e-09
                            SdrD_B   17 qdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakkaGsdda 82  
                                         d+ ++gis+vtV+L  + g++  t tT  +G+Y+F+nl +G+Y++   + +gy++ + +    ++
  gi|298676136|ref|YP_003727885.1| 1021 LDSSKNGISDVTVKL--TPGDI--TKTTYPNGYYSFKNLPSGKYNILA-EKNGYKFNSLDVKISSS 1081
                                        49999**********..44444..688999***************977.55677776655544444 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.1
                            SdrD_B   52 FtnltpGeYkVefta.pagy..tvtakkaGsddaldSdad 88  
                                         + l++G++++++t+ ++    t+t+k+ + ++++ + ++
  gi|298676136|ref|YP_003727885.1| 1595 IDALDKGNFTLTLTQkTKSAikTATYKNISINENTTAKVN 1634
                                        5677888888888664333334666666666666555544 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.34
                            SdrD_B   10 DanknGiqdagekgisgvtVtLkdakgev 38  
                                        D n++Gi+d +e+    ++ tL+++++++
  gi|298676136|ref|YP_003727885.1| 1647 DDNGDGIKDRTENP--HIKTTLIEKDDKQ 1673
                                        99*********964..4555555555554 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 3.7
                            SdrD_B   23 gisgvtVtLkdakgevvatttTd....asGkYkFtnltpGeYkVeftapagytvtakkaGsddald 84  
                                         i+  t++L + ++ + +  tT      +G+  F++ tpG    ++ta    + +++++Gs++++ 
  gi|298676136|ref|YP_003727885.1| 1801 NIDESTIRLCRCNDGTWDPLTTRklseDEGYMYFESDTPGFSPFAITAMGIEEESKATTGSNESMY 1866
                                        566677888777776665444443333789999999999975555544433366677777777655 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   4.5e-08     8e-05      19      76 ..    1037    1095 ..    1009    1140 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.5e-08
                           DUF2012   19 qrkfkalvrrDGsFifrdlpegsYlLevespeyvFepyrVdvkdkgkaka.sklrivet 76  
                                          +++  +  +G ++f++lp+g+Y++ +e+ +y F+ + V+++++ + ka ++++ + +
  gi|298676136|ref|YP_003727885.1| 1037 PGDITKTTYPNGYYSFKNLPSGKYNILAEKNGYKFNSLDVKISSSSTTKAdPIIGNIDE 1095
                                        44567888899********************************5555544044444444 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.5   0.00043      0.77      35      58 ..    1013    1062 ..     939    1080 .. 0.72
   2 ?   -0.6   0.2      0.99   1.8e+03      45      81 ..    1592    1628 ..    1566    1651 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00043
                                        E..........................SEEE-BTTSEEEEEEEESEEEEE CS
                              SpaA   35 v..........................ttlttdenGkatfegLplGtYll 58  
                                        +                           t+tt  nG+ +f++Lp G+Y +
  gi|298676136|ref|YP_003727885.1| 1013 InlegkvlldsskngisdvtvkltpgdITKTTYPNGYYSFKNLPSGKYNI 1062
                                        13333333444444445555556666699*******************76 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.99
                                        EEEEEEEESEEEEEEEEE-STTEEE-SSEEEEEECEE CS
                              SpaA   45 katfegLplGtYllvEtkaPegYvldkepfevtvtat 81  
                                        ++++++L+ G+++l+ t+  +   ++++   ++++++
  gi|298676136|ref|YP_003727885.1| 1592 NFEIDALDKGNFTLTLTQKTKSAIKTATYKNISINEN 1628
                                        5666666666666666666666666666666665554 PP

>> Glyco_hydro_30C  Glycosyl hydrolase family 30 beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.6   2.9e+03      25      49 ..     564     588 ..     562     602 .. 0.61
   2 ?    9.1   0.5   0.00085       1.5      16      41 ..     725     751 ..     714     770 .. 0.66
   3 ?   -2.1   0.0       2.5   4.5e+03      24      37 ..     777     790 ..     776     795 .. 0.81
   4 ?    1.9   0.1      0.15   2.6e+02      31      64 ..    1582    1617 ..    1579    1618 .. 0.77
   5 ?    0.7   1.7      0.35   6.3e+02      11      50 ..    1609    1651 ..    1603    1666 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                   Glyco_hydro_30C  25 pDGsivvvilNrsessvtitvsdss 49 
                                       ++G + v i+N+ +ss+t+  +d +
  gi|298676136|ref|YP_003727885.1| 564 TNGWYNVWIMNSDGSSQTALTNDAQ 588
                                       5566667788887777776555543 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00085
                   Glyco_hydro_30C  16 nvetvAFlnpDGsivvvilNr.sessv 41 
                                         +t +F +pDGs++v + Nr +++++
  gi|298676136|ref|YP_003727885.1| 725 AKDTDSFFSPDGSKIVFVSNReGNNDI 751
                                       447779***************655544 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.5
                   Glyco_hydro_30C  24 npDGsivvvilNrs 37 
                                       npDG++++   Nr+
  gi|298676136|ref|YP_003727885.1| 777 NPDGTKIAFSSNRA 790
                                       9******9998885 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.15
                   Glyco_hydro_30C   31 vvilNrsessvtitvsdsskskgslsv...parSivT 64  
                                        ++i+N+s ++++++++   k++++l++    + +i T
  gi|298676136|ref|YP_003727885.1| 1582 IIIFNQS-EDINFEIDALDKGNFTLTLtqkTKSAIKT 1617
                                        699**88.99999998666677999987755555655 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.35
                   Glyco_hydro_30C   11 psvssnvetvAFln...pDGsivvvilNrsessvtitvsdssk 50  
                                        ++++s ++t  ++n    +++++ v +N+s++s   +v+d+++
  gi|298676136|ref|YP_003727885.1| 1609 QKTKSAIKTATYKNisiNENTTAKVNVNQSDESYLMDVDDNGD 1651
                                        3445789999999999999*******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1914 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 1.12u 0.41s 00:00:01.53 Elapsed: 00:00:00.70
# Mc/sec: 8198.95
//
Query:       gi|298676137|ref|YP_003727886.1|  [L=303]
Description: hypothetical protein Metev_2272 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-09   36.0   0.1     0.0051   16.7   0.0    3.1  3  TrmB           Sugar-specific transcriptional regulator TrmB
    1.1e-05   25.2   1.3      0.015   15.2   0.0    3.4  4  MarR           MarR family
    0.00048   20.0   0.1        0.7    9.9   0.0    2.8  2  HTH_11         HTH domain
    0.00064   19.2   0.0     0.0012   18.3   0.0    1.5  1  Aph-1          Aph-1 protein
    0.00069   19.5   0.1        0.4   10.7   0.0    2.9  2  HTH_36         Helix-turn-helix domain
    0.00075   19.3   0.0      0.082   12.8   0.0    2.5  2  MarR_2         MarR family
     0.0072   16.2   0.8        1.3    9.0   0.0    2.7  2  HTH_5          Bacterial regulatory protein, arsR family
     0.0076   16.2   0.2      0.017   15.0   0.1    1.6  1  DUF1441        Protein of unknown function (DUF1441)
  ------ inclusion threshold ------
      0.018   15.7   0.2        5.5    7.7   0.1    2.5  2  RPA_C          Replication protein A C terminal
      0.022   14.7   0.0      0.045   13.7   0.0    1.5  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
      0.035   14.0   0.0       0.14   12.2   0.0    1.8  2  HTH_43         Winged helix-turn helix
      0.045   14.2   0.0        4.9    7.7   0.0    2.6  2  HTH_27         Winged helix DNA-binding domain
      0.053   13.3   0.0        1.6    8.6   0.0    2.4  2  HTH_IclR       IclR helix-turn-helix domain
      0.065   13.7   0.1         13    6.3   0.0    2.6  2  HTH_40         Helix-turn-helix domain
       0.11   12.9   0.9        1.7    9.0   0.1    2.7  3  Rrf2           Transcriptional regulator
       0.13   12.2   0.1        1.1    9.3   0.0    2.3  2  HTH_Crp_2      Crp-like helix-turn-helix domain
       0.18   11.4   3.1         16    5.1   0.0    3.8  3  HTH_24         Winged helix-turn-helix DNA-binding


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 !   15.3   0.0   1.3e-05     0.013      17      56 ..      12      50 ..       2      59 .. 0.81
   2 !   16.7   0.0   4.9e-06    0.0051      17      58 ..      94     135 ..      92     141 .. 0.91
   3 ?   -0.9   0.0       1.5   1.5e+03      41      63 ..     158     180 ..     157     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                                      HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      L+ ++p++++++ +el++++s+v  +++sL++ G+  +  
  gi|298676137|ref|YP_003727886.1| 12 LV-SEPKNISQLKNELKLDHSTVSLAVKSLISNGFAIKYS 50
                                      44.89******************************87755 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 4.9e-06
                                       HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                       +lk+++++++ei+  +g+ r+++ +v++sL+  G++ ++ g 
  gi|298676137|ref|YP_003727886.1|  94 VLKNDSLNIKEISYVTGLHRNTISSVINSLSMYGVILKSNGC 135
                                       799*******************************99887765 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.5
                                       HHHHHHHHCTSEEEESSTTTEEE CS
                              TrmB  41 evLrsLedkGlVerekgrpklYr 63 
                                       + L++L + G +  ++g+  l++
  gi|298676137|ref|YP_003727886.1| 158 KKLKKLAKEGTIIWQRGSEFLFK 180
                                       5699*******999998877765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.4e-05     0.015      15      46 ..      14      45 ..       2      51 .. 0.90
   2 ?    0.2   0.0      0.68   7.2e+02      11      34 ..      71      94 ..      70      96 .. 0.89
   3 !    6.9   0.1    0.0055       5.8       4      48 ..      87     130 ..      84     133 .. 0.81
   4 ?   -2.0   0.0       3.4   3.6e+03      37      47 ..     159     169 ..     156     172 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGl 46
                                      ++p ++s+L + l+++ stv+ +++ L+ +G+
  gi|298676137|ref|YP_003727886.1| 14 SEPKNISQLKNELKLDHSTVSLAVKSLISNGF 45
                                      47899**************************9 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.68
                                      HHHHSTTEEHHHHHHHHTS-HHHH CS
                              MarR 11 ilyeqgplsvseLakklgvskstv 34
                                      +l+e + l  s+L +k++++ ++v
  gi|298676137|ref|YP_003727886.1| 71 LLKEYPRLPWSKLLNKSSLHVMSV 94
                                      6899999***********999887 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0055
                                       HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR   4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48 
                                       + ++++  l+ +++l+++e+    g+++ t++ v+  L   G i 
  gi|298676137|ref|YP_003727886.1|  87 SSLHVMSVLK-NDSLNIKEISYVTGLHRNTISSVINSLSMYGVIL 130
                                       5566666655.589**********************998888775 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 3.4
                                       HHHHHHHTTSE CS
                              MarR  37 vldrLekkGli 47 
                                        l++L k+G i
  gi|298676137|ref|YP_003727886.1| 159 KLKKLAKEGTI 169
                                       57888888865 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0057         6      17      52 ..      18      53 ..       5      53 .. 0.87
   2 !    9.9   0.0   0.00066       0.7       7      48 ..      93     132 ..      88     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0057
                            HTH_11 17 sgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr 52
                                      ++++L+ eL++  +tv   +k+L + g+ I  ++g+
  gi|298676137|ref|YP_003727886.1| 18 NISQLKNELKLDHSTVSLAVKSLISNGFAIKYSQGK 53
                                      5789**************************988875 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00066
                            HTH_11   7 elLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIes 48 
                                         L ++++ ++++e++  +++ r t+   I +L++ gv + s
  gi|298676137|ref|YP_003727886.1|  93 SVL-KNDS-LNIKEISYVTGLHRNTISSVINSLSMYGVILKS 132
                                       556.6776.9***************************88776 PP

>> Aph-1  Aph-1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.2e-06    0.0012      59     127 ..      59     125 ..      53     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                             Aph-1  59 reqlafgvvfsvlfqelfRylfykllkkaeegLkkisessklkeskhqlayvsGlGfGvmsgvfslvni 127
                                       +++la ++v+svl+ e+ R+   kll+k +  + ++ +  + + + ++++yv+Gl   ++s+v+  +++
  gi|298676137|ref|YP_003727886.1|  59 QSELAHSIVLSVLLKEYPRLPWSKLLNKSSLHVMSVLK--NDSLNIKEISYVTGLHRNTISSVINSLSM 125
                                       678999********************998766655555..66678999***************998876 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.014        15      29      54 ..      20      45 ..      16      46 .. 0.88
   2 !   10.7   0.0   0.00038       0.4      31      54 ..     105     128 ..      90     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.014
                            HTH_36 29 etlakrlglsknTvsraikeLeqlGy 54
                                      + l + l+l+ +Tvs a+k+L+  G+
  gi|298676137|ref|YP_003727886.1| 20 SQLKNELKLDHSTVSLAVKSLISNGF 45
                                      6788899***************9985 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00038
                            HTH_36  31 lakrlglsknTvsraikeLeqlGy 54 
                                       ++  +gl++nT+s+ i++L  +G 
  gi|298676137|ref|YP_003727886.1| 105 ISYVTGLHRNTISSVINSLSMYGV 128
                                       55568**************98886 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   7.8e-05     0.082      12      51 ..      10      46 ..       2      53 .. 0.87
   2 ?    4.0   0.0     0.042        45      16      46 ..      96     124 ..      61     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.8e-05
                                      HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                      ++L  +p    ++++l  +l+l++s+vs ++k L + G+ 
  gi|298676137|ref|YP_003727886.1| 10 FNLVSEPK---NISQLKNELKLDHSTVSLAVKSLISNGFA 46
                                      67777776...99***********************9986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.042
                                       CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHH CS
                            MarR_2  16 rrpgrdltvgelarrlglsksavsrilkrLv 46 
                                        ++   l+++e+   +gl + ++s +++ L+
  gi|298676137|ref|YP_003727886.1|  96 KNDS--LNIKEISYVTGLHRNTISSVINSLS 124
                                       3343..99********************998 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 !    9.0   0.0    0.0012       1.3      11      33 ..      12      34 ..       7      48 .. 0.85
   2 ?    5.0   0.1     0.022        23       6      33 ..      90     117 ..      85     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                                      HTTSSEEHHHHHHHHTS-HHHHH CS
                             HTH_5 11 LaegelcvcelaeelglsqstvS 33
                                      L ++++ +++l +el+l  stvS
  gi|298676137|ref|YP_003727886.1| 12 LVSEPKNISQLKNELKLDHSTVS 34
                                      66789*****************9 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.022
                                       HHHHHHTTSSEEHHHHHHHHTS-HHHHH CS
                             HTH_5   6 kILklLaegelcvcelaeelglsqstvS 33 
                                        +++ L + +l + e++  +gl + t+S
  gi|298676137|ref|YP_003727886.1|  90 HVMSVLKNDSLNIKEISYVTGLHRNTIS 117
                                       67899999**************999998 PP

>> DUF1441  Protein of unknown function (DUF1441)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.6e-05     0.017       2      42 ..     100     140 ..      99     145 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                           DUF1441   2 lnitqlaeitglhRqtvkkRlkgvepaagsnkknkvYaltd 42 
                                       lni++++ +tglhR+t+++ ++ +++ +   k n  Y+l +
  gi|298676137|ref|YP_003727886.1| 100 LNIKEISYVTGLHRNTISSVINSLSMYGVILKSNGCYYLNQ 140
                                       79**********************99999999999999875 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.025        26      69      96 ..      18      45 ..      14      66 .. 0.95
   2 ?    7.7   0.1    0.0052       5.5      64      97 ..      96     129 ..      82     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.025
                                      EHHHHHHHSTSXHHHHHHHHHHHHHTTS CS
                             RPA_C 69 hvdeiaqklrlsvndvkqavdeLsneGi 96
                                      ++++++++l+l+ ++v  av++L+++G 
  gi|298676137|ref|YP_003727886.1| 18 NISQLKNELKLDHSTVSLAVKSLISNGF 45
                                      6889*********************995 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0052
                                       STTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C  64 seeGvhvdeiaqklrlsvndvkqavdeLsneGii 97 
                                       +++ ++++ei+  ++l  n++ +++++Ls  G+i
  gi|298676137|ref|YP_003727886.1|  96 KNDSLNIKEISYVTGLHRNTISSVINSLSMYGVI 129
                                       45889***************************99 PP

>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.2e-05     0.045      33      81 ..      50     103 ..      42     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.2e-05
                                       SS-B-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH........ CS
                     BPL_LplA_LipB  33 tgGrnvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealg......y 81 
                                       + G+n++++ ++el+ s++ls+  k++++ + + + + ++l v+ +l+      +
  gi|298676137|ref|YP_003727886.1|  50 SQGKNTFVH-QSELAHSIVLSVLLKEYPRLPWSKLLNKSSLHVMSVLKndslniK 103
                                       689******.77***********************************86543221 PP

>> HTH_43  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.3   2.4e+03      18      55 ..      14      51 ..       8      60 .. 0.80
   2 ?   12.2   0.0   0.00013      0.14      10      77 ..      89     152 ..      84     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.3
                                      HS-B-HHHHHHHH---HHHHHHHHHGGGGGT-EEEEE- CS
                            HTH_43 18 eeeanvpklieltgmPRRtlqDtlkalaeldielefvq 55
                                      +e +n+ +l +  ++   t+  ++k+l   +  +++ q
  gi|298676137|ref|YP_003727886.1| 14 SEPKNISQLKNELKLDHSTVSLAVKSLISNGFAIKYSQ 51
                                      56679999999999999999999999998888888877 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHS-B-HHHHHHHH---HHHHHHHHHGGGGGT-EEEEE--TTS-S--EEEEEE-TTB-HHH CS
                            HTH_43  10 lylaylideeeanvpklieltgmPRRtlqDtlkalaeldielefvqegernnaGyyrisdWGpidkeW 77 
                                       l+++ ++++++ n+ ++  +tg+ R t+  ++++l+  ++ l+   +g    + ++risd+   d  W
  gi|298676137|ref|YP_003727886.1|  89 LHVMSVLKNDSLNIKEISYVTGLHRNTISSVINSLSMYGVILK--SNGCYYLNQKHRISDFI--DYYW 152
                                       778889999999************************9999887..67777777778888763..3333 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 ?    7.7   0.0    0.0046       4.9      16      47 ..      14      45 ..       2      57 .. 0.86
   2 ?    3.8   0.0      0.08        85      16      48 ..      97     129 ..      88     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0046
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGL 47
                                       ++k +++l   l+++ s++s ++k L+ +G+
  gi|298676137|ref|YP_003727886.1| 14 SEPKNISQLKNELKLDHSTVSLAVKSLISNGF 45
                                      489*************************9997 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.08
                            HTH_27  16 rrrkkladlcgrlnvedshisyslkkLtekGLv 48 
                                       ++   +++++ ++ +   +is++++ L  +G++
  gi|298676137|ref|YP_003727886.1|  97 NDSLNIKEISYVTGLHRNTISSVINSLSMYGVI 129
                                       6777899********************999998 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.16   1.7e+02      20      47 ..      18      45 ..       8      47 .. 0.88
   2 ?    8.6   0.0    0.0015       1.6      18      46 ..      99     127 ..      85     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.16
                                      BHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                          HTH_IclR 20 tlselArrtglpkStvhRlLqtLvelGy 47
                                      ++s+l +++ l  Stv+  +++L+  G+
  gi|298676137|ref|YP_003727886.1| 18 NISQLKNELKLDHSTVSLAVKSLISNGF 45
                                      58999999***************99998 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0015
                                       S-BHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                          HTH_IclR  18 eltlselArrtglpkStvhRlLqtLvelG 46 
                                        l+++e++  tgl++ t +  +++L   G
  gi|298676137|ref|YP_003727886.1|  99 SLNIKEISYVTGLHRNTISSVINSLSMYG 127
                                       5899****************999998766 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.036        38       6      47 ..      10      51 ..       5      76 .. 0.83
   2 ?    6.3   0.0     0.012        13      10      71 ..      97     162 ..      88     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.036
                            HTH_40  6 lelleeglsieeIAkerglkesTIegHLaelieegeeidler 47
                                      ++l+ e ++i +  +e +l  sT+   + +li +g  i++++
  gi|298676137|ref|YP_003727886.1| 10 FNLVSEPKNISQLKNELKLDHSTVSLAVKSLISNGFAIKYSQ 51
                                      6889999****************************9999854 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.012
                            HTH_40  10 eeglsieeIAkerglkesTIegHLaelieegeeidlerlvseeeekeIeeaiek....vgseklkp 71 
                                       +++l+i+eI+   gl ++TI + + +l   g  ++ +  +  +++ +I + i+     ++++klk+
  gi|298676137|ref|YP_003727886.1|  97 NDSLNIKEISYVTGLHRNTISSVINSLSMYGVILKSNGCYYLNQKHRISDFIDYywnyINNKKLKK 162
                                       789******************999998888865555555444444444444443333455555555 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.2   5.5e+03      27      54 ..      18      45 ..      13      57 .. 0.71
   2 ?    9.0   0.1    0.0017       1.7      16      60 ..      91     134 ..      86     143 .. 0.80
   3 ?    1.1   0.0       0.5   5.3e+02      44      61 ..     158     175 ..     143     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.2
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                              Rrf2 27 sseeiaerqnispsylekilakLrkagl 54
                                      +++++ ++ ++ +s ++  ++ L  +g+
  gi|298676137|ref|YP_003727886.1| 18 NISQLKNELKLDHSTVSLAVKSLISNGF 45
                                      6777888888888888888888888876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0017
                                       HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              Rrf2  16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrG 60 
                                       +++  ++++ ++++ei+  ++++++ ++ +++ L+  g++    G
  gi|298676137|ref|YP_003727886.1|  91 VMSVLKNDS-LNIKEISYVTGLHRNTISSVINSLSMYGVILKSNG 134
                                       444445555.99************************999977666 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.5
                                       HHHHHHHHTTSEEEETTT CS
                              Rrf2  44 kilakLrkaglvksvrGk 61 
                                       k l+kL+k+g +  +rG 
  gi|298676137|ref|YP_003727886.1| 158 KKLKKLAKEGTIIWQRGS 175
                                       7799***********996 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0011       1.1      23      53 ..     101     131 ..      83     145 .. 0.85
   2 ?   -0.5   0.0       1.2   1.2e+03      39      53 ..     157     172 ..     157     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                                       HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2  23 tqeelAsmlGltretvsrilseLkreglisr 53 
                                       + +e++   Gl+r t+s +++ L+  g+i +
  gi|298676137|ref|YP_003727886.1| 101 NIKEISYVTGLHRNTISSVINSLSMYGVILK 131
                                       5689999********************9975 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                                       HHHHHHHHHTTSEE.E CS
                         HTH_Crp_2  39 srilseLkreglis.r 53 
                                       ++ l++L +eg i  +
  gi|298676137|ref|YP_003727886.1| 157 NKKLKKLAKEGTIIwQ 172
                                       5789*******99754 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 ?    4.3   0.1     0.028        29      20      46 ..      19      45 ..       2      46 .. 0.72
   2 ?    5.1   0.0     0.016        16      13      47 ..      95     129 ..      71     129 .. 0.92
   3 ?   -0.9   0.1       1.1   1.2e+03      36      47 ..     158     169 ..     157     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.028
                            HTH_24 20 qreLAerlglSpstvnrrlkrLeeeGl 46
                                      +++L  +l l  stv+  +k L+++G+
  gi|298676137|ref|YP_003727886.1| 19 ISQLKNELKLDHSTVSLAVKSLISNGF 45
                                      455667899999***********9996 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.016
                            HTH_24  13 qknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                        kn +++++e++  +gl ++t++  ++ L   G+I
  gi|298676137|ref|YP_003727886.1|  95 LKNDSLNIKEISYVTGLHRNTISSVINSLSMYGVI 129
                                       689*********************99999877776 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.1
                            HTH_24  36 rrlkrLeeeGlI 47 
                                       + lk+L +eG I
  gi|298676137|ref|YP_003727886.1| 158 KKLKKLAKEGTI 169
                                       569*******88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); 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: 0.51u 0.41s 00:00:00.92 Elapsed: 00:00:00.57
# Mc/sec: 1611.45
//
Query:       gi|298676138|ref|YP_003727887.1|  [L=268]
Description: hypothetical protein Metev_2273 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00011   22.1   0.1     0.0002   21.1   0.1    1.4  1  TrmB           Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
       0.01   15.7   0.2       0.11   12.4   0.1    2.4  3  AhpC-TSA       AhpC/TSA family
      0.018   15.5   0.4      0.073   13.6   0.1    2.0  2  PCI            PCI domain
      0.062   13.6   0.0       0.14   12.5   0.0    1.6  1  PG_binding_2   Putative peptidoglycan binding domain
       0.11   12.5   0.0       0.29   11.2   0.0    1.7  1  Dimerisation2  Dimerisation 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 !   21.1   0.1   5.7e-08    0.0002      15      58 ..     219     262 ..     216     267 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.7e-08
                                       HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                       + Llk++p++ ++++ +l+v +    ++L++L+ k+++e+  ++
  gi|298676138|ref|YP_003727887.1| 219 IDLLKEKPSDLETVSTRLNVNKKETDKILKNLLAKDIIEKTASS 262
                                       57*************************************99776 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.1e-05      0.11      48      98 ..      36      84 ..      32     120 .. 0.86
   2 ?   -1.5   0.0      0.62   2.2e+03      56      89 ..     120     165 ..     111     168 .. 0.74
   3 ?   -0.3   0.0      0.26   9.3e+02      74      91 ..     189     206 ..     186     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.1e-05
                                      HHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE-TTSHHHHHT CS
                          AhpC-TSA 48 laklyeefkergvevigvsvdspeshkkfiekeslnfpllsDeegkvakay 98
                                      ++kl ++ k  +++v+ +svd+++s+kk     +++ p lsDe +k++ ++
  gi|298676138|ref|YP_003727887.1| 36 FQKLKDATK--DIDVVVLSVDELKSLKKSLSSLGYKKPHLSDEYNKLSANL 84
                                      555555555..899*****************************99998876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.62
                                       CCTTEEEEEEESSSCHHHHHHHHH-H.............SSEEEE- CS
                          AhpC-TSA  56 kergvevigvsvdspeshkkfiekes............lnfpllsD 89 
                                       +  ++ v+ +++++ +  k+   +e             l f+++ D
  gi|298676138|ref|YP_003727887.1| 120 DLTNISVYSITPEDIFIFKSITSREHdlldmytlfssgLDFEIIKD 165
                                       5568889999999999877777766667777777777777777777 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.26
                                       HHHHHH-H.SSEEEE-TT CS
                          AhpC-TSA  74 kkfiekeslnfpllsDee 91 
                                       ++f ++++l  pl+sD  
  gi|298676138|ref|YP_003727887.1| 189 EEFLDEYNLSHPLFSDLR 206
                                       6899************65 PP

>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.91   3.3e+03      30      51 ..      68      89 ..      43      90 .. 0.67
   2 ?   13.6   0.1     2e-05     0.073      15      90 ..     185     256 ..     180     260 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.91
                                      HHHTTHHHHHHHHHHHHHHHHH CS
                               PCI 30 laddglaqllesLekkvrerll 51
                                       ++++l++ +++L  +++++++
  gi|298676138|ref|YP_003727887.1| 68 YKKPHLSDEYNKLSANLILENI 89
                                      4567777777777777777776 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHCESEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSS CS
                               PCI  15 lsgfseelkdleeelladdglaqllesLekkvrerllrqvskiyssislerlaklldlsvdevEkilvklIrdgei 90 
                                       ++gf+e+l ++    l ++  ++l ++ ++++ e+ ++ + k  +  +le++++ l+++++e++kil +l +++ i
  gi|298676138|ref|YP_003727887.1| 185 YTGFEEFLDEY---NLSHPLFSDLRDMAYENMMEQMIIDLLK-EKPSDLETVSTRLNVNKKETDKILKNLLAKDII 256
                                       57888888888...5677777888888888888888888888.7778***********************999887 PP

>> PG_binding_2  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     4e-05      0.14       6      35 ..      44      71 ..      39      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                      PG_binding_2  6 kpeeervlaedvaeevqaaLsrLGyydgea 35
                                      k+ + +vl  d+ ++++++Ls+LGy++  +
  gi|298676138|ref|YP_003727887.1| 44 KDIDVVVLSVDELKSLKKSLSSLGYKK--P 71
                                      6778999******************54..3 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     8e-05      0.29      22      76 ..     217     266 ..     208     268 .] 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8e-05
                     Dimerisation2  22 gvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsn 76 
                                        + dlLke +p ++e+v+++l+++ k t+ +l+ + a ++ e  k+ +  + Y+n
  gi|298676138|ref|YP_003727887.1| 217 MIIDLLKE-KPSDLETVSTRLNVNKKETDKILKNLLAKDIIE--KTAS--SCYKN 266
                                       688*****.**************************9999999..4444..47777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1137  (0.0634168); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.67s 00:00:01.14 Elapsed: 00:00:00.66
# Mc/sec: 1222.87
//
Query:       gi|298676139|ref|YP_003727888.1|  [L=395]
Description: nucleotidyl transferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-47  162.0   0.0    2.8e-47  161.4   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    2.8e-15   55.4  28.7    1.3e-08   34.2   3.0    5.1  6  Hexapep          Bacterial transferase hexapeptide (six repea
    2.1e-12   47.7   0.0    2.9e-12   47.2   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    1.6e-06   27.7  16.8    0.00013   21.6   2.7    4.5  5  Hexapep_2        Hexapeptide repeat of succinyl-transferase
    0.00012   21.9   0.0    0.00031   20.6   0.0    1.7  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
     0.0039   15.4   4.4     0.0081   14.3   4.4    1.5  1  DUF4954          Domain of unknown function (DUF4954)
  ------ inclusion threshold ------
       0.16   10.9   0.0       0.36    9.7   0.0    1.7  2  Fucokinase       L-fucokinase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.4   0.0   1.1e-50   2.8e-47       1     247 [.       2     231 ..       2     232 .. 0.92

  Alignments for each domain:
  == domain 1  score: 161.4 bits;  conditional E-value: 1.1e-50
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       kavILa G+GtR++PLt + +k +++v++k +++++ + + + +gi+e  v +t +h+  v+e++++gs +gv++++
  gi|298676139|ref|YP_003727888.1|   2 KAVILAAGEGTRMRPLTYSCPKVMLTVANK-PILEHIMDATIGAGIDE-FVFITGFHENAVKEYFGDGSSWGVDIQY 76 
                                       79****************************.*****************.555566********************** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       +++ e+kgtAdA++ a  +++ ++     +vL+gD+l+++   +++kk ++k++  ++++ +++v++++e+Gvi ++
  gi|298676139|ref|YP_003727888.1|  77 VTQLEQKGTADAIKHADGYVDGHF-----IVLNGDVLVTK---DYLKKLVSKKS--DAVITAKEVDNPSEFGVIDVS 143
                                       ****************99999766.....9*********5...55778888888..7999****************9 PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                       + ++v+++vEK ++++ ++la++GiY+f  ++++++ +    ++rge eitd ++ ++++gk+  +    d+e W D
  gi|298676139|ref|YP_003727888.1| 144 G-DNVTQIVEKSSNPP-TNLANTGIYLFHDSIFEYI-DRTPLSERGELEITDSMQMMIDDGKQVTY-KLLDNE-WID 215
                                       7.69************.*******************.66788899***************988766.666665.*** PP

                                       XSSHHHHHHHHHHHHH CS
                   NTP_transferase 232 vGtldslleaneklae 247
                                       +G + ++l+an+ l++
  gi|298676139|ref|YP_003727888.1| 216 IGRPWDMLDANKLLLQ 231
                                       ***********98765 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       2.3   5.8e+03       9      21 ..      96     108 ..      91     111 .. 0.79
   2 !   18.1   0.5   6.2e-07    0.0016      10      36 .]     241     267 ..     240     267 .. 0.93
   3 !   34.2   3.0   5.1e-12   1.3e-08       2      35 ..     251     284 ..     250     285 .. 0.96
   4 !   26.7   3.7   1.2e-09   3.1e-06       2      35 ..     269     302 ..     268     303 .. 0.91
   5 !   14.4   0.9   9.3e-06     0.024       1      35 [.     303     336 ..     303     337 .. 0.87
   6 ?    1.3   0.6      0.12   3.2e+02       7      26 ..     368     387 ..     362     388 .. 0.55

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.3
                                       EE-TTEEEETTEE CS
                           Hexapep   9 lIgpfaviggnVk 21 
                                       + g+f v+ g+V 
  gi|298676139|ref|YP_003727888.1|  96 VDGHFIVLNGDVL 108
                                       6789999999995 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 6.2e-07
                                       E-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  10 IgpfaviggnVkIGdnvkIgagvvigg 36 
                                       + p+a+i g V+IG+n+++ +g++i g
  gi|298676139|ref|YP_003727888.1| 241 VEPYATIKGEVVIGKNTVVKNGSYIEG 267
                                       679*********************976 PP

  == domain 3  score: 34.2 bits;  conditional E-value: 5.1e-12
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +vIG+n+++ ++++i g+V+IG+++ Ig++++i+
  gi|298676139|ref|YP_003727888.1| 251 VVIGKNTVVKNGSYIEGPVVIGEDCDIGPNCYIR 284
                                       79******************************97 PP

  == domain 4  score: 26.7 bits;  conditional E-value: 1.2e-09
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +vIG+++ Igp+++i++ + IG++vkIg+ v ++
  gi|298676139|ref|YP_003727888.1| 269 VVIGEDCDIGPNCYIRPSTCIGNHVKIGNAVEVK 302
                                       89**************************977775 PP

  == domain 5  score: 14.4 bits;  conditional E-value: 9.3e-06
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +t++ + + Ig+ a++ g+ ++G+++  gag+ ++
  gi|298676139|ref|YP_003727888.1| 303 NTIVMDATNIGHLAYV-GDSVVGKRCNFGAGTKVA 336
                                       57889999********.5555***********987 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 0.12
                                       TEEE-TTEEEETTEEE-TTE CS
                           Hexapep   7 nvlIgpfaviggnVkIGdnv 26 
                                       +v+ g ++ i  +V++ +n+
  gi|298676139|ref|YP_003727888.1| 368 DVHTGINTSINVGVVLERNT 387
                                       55555555555555555554 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 !   47.2   0.0   1.1e-15   2.9e-12       1     122 [.       3     129 ..       3     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 1.1e-15
                                       EEEEEESS-TTTT..T...THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCH..HHHHHTTC......TS-EEE CS
                      NTP_transf_3   1 aviLAGGrSsRmg..g...dKallplggkpllervldalraagvdevvvvggdee..vlaalarl......gvrvve 64 
                                       aviLA+G+++Rm   +   +K +l +++kp+le+++da   ag+de v ++g +e  v++++         ++++v+
  gi|298676139|ref|YP_003727888.1|   3 AVILAAGEGTRMRplTyscPKVMLTVANKPILEHIMDATIGAGIDEFVFITGFHEnaVKEYFG-DgsswgvDIQYVT 78 
                                       79**********8551559********************************997511444333.2355533455666 PP

                                       -TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEE CS
                      NTP_transf_3  65 dedpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvpt 122
                                       +  ++kg++ ++++a   +  + +++vl +D+ l+t++ +++l+ +    +++v+ ++
  gi|298676139|ref|YP_003727888.1|  79 QL-EQKGTADAIKHADGYV--DGHFIVLNGDV-LVTKDYLKKLVSKK---SDAVITAK 129
                                       65.5899999999999987..89*********.88*********984...34444444 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.5   6.4e+03      23      30 ..      39      46 ..      39      46 .. 0.70
   2 !    9.3   0.1   0.00036      0.93      14      32 ..     245     265 ..     243     266 .. 0.87
   3 !   21.6   2.7   5.1e-08   0.00013       1      28 [.     268     297 ..     268     302 .. 0.93
   4 ?    4.7   0.1      0.01        26       4      13 ..     323     332 ..     322     335 .. 0.88
   5 ?   -1.4   0.1      0.79     2e+03      11      23 ..     372     386 ..     367     387 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.5
                                      T-EE-TT- CS
                         Hexapep_2 23 ncvvgaGv 30
                                      ++++gaG+
  gi|298676139|ref|YP_003727888.1| 39 DATIGAGI 46
                                      57788885 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00036
                                       -EE.S.EEE-TT-EE-TT-EE CS
                         Hexapep_2  14 agi.G.vslGdncvvgaGvvi 32 
                                       a+i G v +G+n vv +G++i
  gi|298676139|ref|YP_003727888.1| 245 ATIkGeVVIGKNTVVKNGSYI 265
                                       5677779*************9 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 5.1e-08
                                       .EEE-TT-EE-TT-EE..SEEE-TT-EE-T CS
                         Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvga 28 
                                       pv IG++C iG+n++i   + +G+ +++g+
  gi|298676139|ref|YP_003727888.1| 268 PVVIGEDCDIGPNCYIrpSTCIGNHVKIGN 297
                                       8****************99*****999998 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.01
                                       E-TT-EE-TT CS
                         Hexapep_2   4 IGdnCliGan 13 
                                       +G++C++Ga 
  gi|298676139|ref|YP_003727888.1| 323 VGKRCNFGAG 332
                                       8*******96 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 0.79
                                       -TT.-E.ESEEE-TT CS
                         Hexapep_2  11 Gan.ag.iGvslGdn 23 
                                       G n ++ +Gv l++n
  gi|298676139|ref|YP_003727888.1| 372 GINtSInVGVVLERN 386
                                       556344458888776 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 !   20.6   0.0   1.2e-07   0.00031       2      42 ..       2      45 ..       1      66 [. 0.81

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.2e-07
                                      EEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTT CS
                              IspD  2 vvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallask 42
                                       +vi AAG+G+Rm+     +pK  l+++++++leh +da  + +
  gi|298676139|ref|YP_003727888.1|  2 KAVILAAGEGTRMRpltYSCPKVMLTVANKPILEHIMDATIGAG 45
                                      69**********9633369*******************998744 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   4.4   3.2e-06    0.0081     175     259 ..     252     334 ..     220     339 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-06
                           DUF4954 175 eigekvkilnaglikN.vkigdyatiegasklengtinSskeapveiGegViledfiissGskikdgavisrcfvGq 250
                                       +ig++++++n ++i+  v ig+ + i     ++  t + +    v+iG+ V+++++i++  ++i + a + +++vG+
  gi|298676139|ref|YP_003727888.1| 252 VIGKNTVVKNGSYIEGpVVIGEDCDIGPNCYIRPSTCIGN---HVKIGNAVEVKNTIVMDATNIGHLAYVGDSVVGK 325
                                       5899999999999985489999999999999999998876...599******************************* PP

                           DUF4954 251 avklkkqfs 259
                                        ++++ + +
  gi|298676139|ref|YP_003727888.1| 326 RCNFGAGTK 334
                                       **9987765 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       0.7   1.8e+03     105     153 ..      72     119 ..      66     138 .. 0.70
   2 ?    9.7   0.0   0.00014      0.36     271     334 ..     237     311 ..     159     345 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.7
                        Fucokinase 105 leirsvkkflhKpseeelqasgavlkdekvlldsGvvffdhktaekLlk 153
                                       + i++v ++ +K++++ +++    ++  + +l    v++ ++  +kL++
  gi|298676139|ref|YP_003727888.1|  72 VDIQYVTQLEQKGTADAIKHADGYVDGHFIVLNG-DVLVTKDYLKKLVS 119
                                       5678888888888888888776666665555554.66666666666665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00014
                        Fucokinase 271 kesavvinSvlessvsvgegsvieh.sslkgnvsigsnsiv.sglelessee.........slelpddtilqtls 334
                                       ++++v   + ++++v +g+++v+++ s ++g+v ig+ + +  +++++ s++          +e+++ +++  ++
  gi|298676139|ref|YP_003727888.1| 237 NKGSVEPYATIKGEVVIGKNTVVKNgSYIEGPVVIGEDCDIgPNCYIRPSTCignhvkignAVEVKNTIVMDATN 311
                                       555556677888899999999998536777888888888662578888887777766666667777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.49s 00:00:01.16 Elapsed: 00:00:00.60
# Mc/sec: 1998.60
//
Query:       gi|298676140|ref|YP_003727889.1|  [L=434]
Description: phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain I [Methanohalobium evestigatum Z-7303]
Scores for 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-35  119.7   0.0    1.3e-34  118.9   0.0    1.3  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.8e-28   99.1   0.1    4.2e-28   98.0   0.1    1.6  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    4.1e-20   72.1   0.0    7.6e-20   71.2   0.0    1.4  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    5.2e-12   45.8   0.0    1.2e-11   44.6   0.0    1.6  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
  ------ inclusion threshold ------
      0.045   13.9   0.1        7.8    6.7   0.0    3.0  2  CinA_KH      Damage-inducible protein CinA KH domain
        0.1   11.4   0.0       0.17   10.7   0.0    1.3  1  DUF2957      Protein of unknown function (DUF2957)


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.0   4.2e-38   1.3e-34       2     134 ..       2     125 ..       1     128 [. 0.95

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 4.2e-38
                                       GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB- CS
                         PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllp 78 
                                       ++fg sG+Rg ++++ +t el++klg+ +++  k+      +v+G+D Rvs ++++ a+++gl+++G +v+++gl++
  gi|298676140|ref|YP_003727889.1|   2 KLFGSSGIRGMANKD-VTVELALKLGHVLGKKYKN------IVIGKDPRVSAEMIEYAMISGLTSSGGSVMRTGLVT 71 
                                       68***********55.9******999999998887......************************************ PP

                                       HHHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT CS
                         PGM_PMM_I  79 tPavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiieke 134
                                       tP +++a++   +d+g+mitaSHnp+ey giK+ +++G+ ++++++e+Ie++ie +
  gi|298676140|ref|YP_003727889.1|  72 TPTLAYAAKD--YDCGVMITASHNPAEYIGIKLWNPDGMAFDSSQQEEIEQEIEDY 125
                                       *********9..799*************************************9976 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.0   0.1   1.4e-31   4.2e-28      10     103 .]     152     244 ..     145     244 .. 0.92

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 1.4e-31
                                       TS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGGG-SEE CS
                        PGM_PMM_II  10 kvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkkegadlg 86 
                                       ++d++    +++kvv+d++ Gag++i++ ll+elg++v++lna+ d++fp + p+p+e ++l+ll e+vk+ +adlg
  gi|298676140|ref|YP_003727889.1| 152 IMDKTNPVTKPVKVVVDCGSGAGSTITPYLLRELGCEVITLNAQLDGHFPARKPEPNE-KNLQLLKETVKSADADLG 227
                                       445555667899**********************************************.****************** PP

                                       EEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  87 lafDgDaDRlgvvderG 103
                                       +a+DgDaDR+++vd++G
  gi|298676140|ref|YP_003727889.1| 228 IAHDGDADRMMAVDKNG 244
                                       ***************98 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.0   2.5e-23   7.6e-20       2     112 ..     249     350 ..     248     352 .. 0.92

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 2.5e-23
                                       HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETT CS
                       PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifld 78 
                                       gd++la++a +++ +   ++ +v+++v ts++l+++   l++++ +t+vGd yv+ee+k++ga +GgE Sg +if++
  gi|298676140|ref|YP_003727889.1| 249 GDEMLAIFAMNVCGS---DS-TVIAPVDTSMILDDA---LDCEIKRTRVGDVYVAEEIKRTGADFGGEASGSWIFPK 318
                                       9***********873...44.5*************9...89************************************ PP

                                       TBSS--HHHHHHHHHHHHHHHTS-HHHHHHHHHH CS
                       PGM_PMM_III  79 eattkDGilaallvleilaetgkslselleellk 112
                                        +++ DGi+aa++++ei+++  ++l el e+l++
  gi|298676140|ref|YP_003727889.1| 319 ISYCPDGIYAAAKLVEIVQD--RPLGELREQLPE 350
                                       ******************77..699999977654 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   4.1e-15   1.2e-11      23      71 ..     375     430 ..     357     432 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 4.1e-15
                                       H.......HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEES.SHHHHHHHHHHHHH CS
                        PGM_PMM_IV  23 a.......sikeglkilledGrrlavRpSGTepllrvyvEak.sdeelarlaeevae 71 
                                       +       + ++g++i+   G++l vRpSGTep++r+ vE++ + eel +lae+ ++
  gi|298676140|ref|YP_003727889.1| 375 QlsqygeiNSIDGVRIDMDGGWVL-VRPSGTEPKIRITVESRdDVEELYQLAEDTIK 430
                                       23334455789*************.*****************999999999998765 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0026       7.8      25      47 ..      71      93 ..      62      97 .. 0.86
   2 ?    3.8   0.0     0.022        65      34      64 ..     402     433 ..     397     434 .] 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0026
                                      SSSEEEEEEETTEEEEEEE...E CS
                           CinA_KH 25 enptlAiyakegevtvRltakaa 47
                                      + ptlA+ ak+ ++ v +ta+ +
  gi|298676140|ref|YP_003727889.1| 71 TTPTLAYAAKDYDCGVMITASHN 93
                                      789****************9876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.022
                                       ETTEEEEEEE....EEHHHHHHHHH....HHH CS
                           CinA_KH  34 kegevtvRlta.kaaneeeaealiapveeeir 64 
                                       +  e ++R+t+ + ++ ee  +l++++++e++
  gi|298676140|ref|YP_003727889.1| 402 SGTEPKIRITVeSRDDVEELYQLAEDTIKEVM 433
                                       56678999998556777888888888888775 PP

>> DUF2957  Protein of unknown function (DUF2957)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.8e-05      0.17     245     332 ..     216     303 ..     208     316 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.8e-05
                           DUF2957 245 nllalvaDdeigisilapataiaagslkGeyiGvdssfnYrstalqgataalldPleasaslasalklDytqavpGv 321
                                       +++   aD++ gi+    a  + a   +Ge++  d  +   +  + g++ +++ P+++s+ l  al+ +  ++  G 
  gi|298676140|ref|YP_003727889.1| 216 KETVKSADADLGIAHDGDADRMMAVDKNGEFVSGDEMLAIFAMNVCGSDSTVIAPVDTSMILDDALDCEIKRTRVGD 292
                                       556778***************************************************99999999999998888888 PP

                           DUF2957 322 vttveksaptG 332
                                       v  +e+   tG
  gi|298676140|ref|YP_003727889.1| 293 VYVAEEIKRTG 303
                                       88777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.45s 00:00:01.03 Elapsed: 00:00:00.57
# Mc/sec: 2301.46
//
Query:       gi|298676141|ref|YP_003727890.1|  [L=609]
Description: glucosamine/fructose-6-phosphate aminotransferase, isomerizing [Methanohalobium evestigatum Z-7303]
Scores for complete 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-60  202.0   3.7    2.8e-30  104.8   0.1    3.6  4  SIS       SIS domain
    6.4e-22   78.2   0.0    1.2e-21   77.3   0.0    1.4  1  GATase_6  Glutamine amidotransferase domain
    1.2e-15   57.6   0.0    3.2e-15   56.1   0.0    1.8  1  GATase_7  Glutamine amidotransferase domain
    0.00079   19.4   0.1      0.072   13.1   0.0    2.6  2  SIS_2     SIS domain
     0.0057   15.6   0.0     0.0095   14.9   0.0    1.2  1  GATase_4  Glutamine amidotransferases class-II
  ------ inclusion threshold ------
        0.1   13.4   0.0       0.26   12.1   0.0    1.7  1  DUF5124   Domain of unknown function (DUF5124)


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.58   1.7e+03      65      91 ..      13      39 ..       8      44 .. 0.83
   2 ?   -0.1   0.0      0.26   7.7e+02      84      95 ..     166     177 ..     156     202 .. 0.86
   3 !   95.3   0.2   8.4e-31   2.5e-27       3     130 ..     289     417 ..     287     418 .. 0.96
   4 !  104.8   0.1   9.4e-34   2.8e-30       7     129 ..     467     590 ..     461     592 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.58
                                      HHHHHHHHHHHHHHTTSEEEEEESSTT CS
                               SIS 65 etkdlvaaaelakergakiiaITdskg 91
                                       + +l+++++++  rg   ++IT  ++
  gi|298676141|ref|YP_003727890.1| 13 AKQELIDSLKKLEYRGYDSVGITILNS 39
                                      578999*************99997654 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.26
                                       EEEESSTTSHHH CS
                               SIS  84 iaITdskgspla 95 
                                       i+IT++k+spl+
  gi|298676141|ref|YP_003727890.1| 166 IIITGKKNSPLV 177
                                       99*******996 PP

  == domain 3  score: 95.3 bits;  conditional E-value: 8.4e-31
                                       CTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEE.EEEESSSHHHHHHHHHHHHHH CS
                               SIS   3 akakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlv.ilisfsgetkdlvaaaelake 78 
                                       ++  ri ++++Gtsy++++ +++ +e+++gi+  ++  se+++++   +d+dd++ i+is+sget+d++aa++ +k+
  gi|298676141|ref|YP_003727890.1| 289 RNLTRIELIACGTSYNAGLIAKYLFEQLAGIHTNIDTGSEYRYRYPVFCDSDDVLsIAISQSGETADTIAALQSLKS 365
                                       5667999*************************************999999999877********************* PP

                                       TTSEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHHH CS
                               SIS  79 rgakiiaITdskgsplareadlalyinaepetlvastksltaqlaaldalav 130
                                        g +++aIT+  gs++ r+ad ++yi a+pe +va+tk++t+ql+ l++lav
  gi|298676141|ref|YP_003727890.1| 366 SGCRTLAITNVMGSSITRDADDVMYIKAGPELGVAATKTFTSQLTILYLLAV 417
                                       ************************************************9986 PP

  == domain 4  score: 104.8 bits;  conditional E-value: 9.4e-34
                                       EEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHH.HHHHTTSE CS
                               SIS   7 riyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaae.lakergak 82 
                                         +++G+  +y++a+e+alkl+ei++i++e+++a+elkhg+lali+ed++v++i++sg+t d++ ++  ++k+r+a+
  gi|298676141|ref|YP_003727890.1| 467 DYFFIGRYMNYPVALEGALKLKEISYIHAEGYAAGELKHGPLALITEDTPVVAIATSGHTYDKIISNImEVKARNAT 543
                                       5699************************************************************99999******** PP

                                       EEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHH CS
                               SIS  83 iiaITdskgsplareadlalyinaepetlvastksltaqlaaldala 129
                                       +ia++ ++++ + ++ dl+l+i++ +e l ++++++++ql+a+++++
  gi|298676141|ref|YP_003727890.1| 544 VIAVAEEDDNEIEKYVDLVLRIPKTDELLSPILSNIVLQLLAYYTAL 590
                                       *******************************************9987 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.0     4e-25   1.2e-21      11     123 ..      62     179 ..      51     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 4e-25
                          GATase_6  11 edevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall....ee 83 
                                       ++ ++++H+R+a++g ++++ a+P    +g++++vhNG i+ny++l+eel + +g++frs++Dtev+++ll    ++
  gi|298676141|ref|YP_003727890.1|  62 DGYTGIGHTRWATHGQPTKQNAHPH--LSGNISIVHNGIIENYQQLKEELIE-AGYEFRSETDTEVIAHLLnsyyQQ 135
                                       55689************88888***..*************************.****************99888833 PP

                          GATase_6  84 lG......eevlerlrGmfafaiwdkrentlilardrlgvkplyya 123
                                        +      + +l+rl+G +a+a++  +   +i++  +  ++pl+++
  gi|298676141|ref|YP_003727890.1| 136 NDdfhtafQNTLKRLDGSYAVAAVCDDMPDIIITGKK--NSPLVVG 179
                                       335767889999*********9988877777776333..6777776 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0   1.1e-18   3.2e-15      10     122 ..      80     195 ..      69     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 1.1e-18
                          GATase_7  10 eagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnGm 77 
                                       +++a P +   +g++ iv+nG i Ny++l+eeL ++g++fr+++Dtev+++ll++            +++l+rl+G+
  gi|298676141|ref|YP_003727890.1|  80 KQNAHPHL---SGNISIVHNGIIENYQQLKEELIEAGYEFRSETDTEVIAHLLNSyyqqnddfhTAFQNTLKRLDGS 153
                                       44445555...699***************************************999*******999*********** PP

                          GATase_7  78 fAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       +A+a + ++  ++++   +    PL +g  +g   + aS + a+l
  gi|298676141|ref|YP_003727890.1| 154 YAVAAVCDDMPDIIITGKK--NSPLVVGLGNG-CNFAASDITAFL 195
                                       ***9887777766665554..67888888864.777777777765 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   2.4e-05     0.072     102     137 ..     338     374 ..     303     375 .. 0.87
   2 ?    3.8   0.1     0.019        56     107     136 ..     517     547 ..     475     549 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.4e-05
                                       -TT-EE.EEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                             SIS_2 102 kpgDvL.lviSnsGnnavvveaaeaakergmkviAlt 137
                                       ++ DvL + iS+sG+ a  ++a++  k+ g+++ A+t
  gi|298676141|ref|YP_003727890.1| 338 DSDDVLsIAISQSGETADTIAALQSLKSSGCRTLAIT 374
                                       7889995669**************************9 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.019
                                       EEEE-SS--S.HHHHHHHHHHHHHT-EEEEE CS
                             SIS_2 107 LlviSnsGnn.avvveaaeaakergmkviAl 136
                                        + i +sG+    ++  ++++k+r ++viA+
  gi|298676141|ref|YP_003727890.1| 517 VVAIATSGHTyDKIISNIMEVKARNATVIAV 547
                                       46688899987899****************8 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.2e-06    0.0095      68     146 ..      60     137 ..      41     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.2e-06
                          GATase_4  68 piksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElafCellee 140
                                       +i     + H R at+G+ +++n+hp    l g ++ + HnG +++y++      e  +e   +TD+E++  +ll++
  gi|298676141|ref|YP_003727890.1|  60 DIDGYTGIGHTRWATHGQPTKQNAHPH---LSG-NISIVHNGIIENYQQLKeeliEAGYEFRSETDTEVI-AHLLNS 131
                                       577777899*****************6...455.56678*****99877655557788999999***976.577777 PP

                          GATase_4 141 lasrfe 146
                                         ++++
  gi|298676141|ref|YP_003727890.1| 132 YYQQND 137
                                       666664 PP

>> DUF5124  Domain of unknown function (DUF5124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.7e-05      0.26      21      67 ..     455     504 ..     439     534 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.7e-05
                           DUF5124  21 iydclekyskaevyylvGdfmql...essdaklscialvdtkGsvagkwn 67 
                                       + + + ++s+   y+ +G +m+     ++  kl+ i+++  +G  ag+ +
  gi|298676141|ref|YP_003727890.1| 455 VRKYAKQFSEVSDYFFIGRYMNYpvaLEGALKLKEISYIHAEGYAAGELK 504
                                       55667899*************976667999****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 3913.42
//
Query:       gi|298676142|ref|YP_003727891.1|  [L=404]
Description: nucleotidyl transferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-45  153.9   0.2    8.2e-45  153.3   0.2    1.3  1  NTP_transferase  Nucleotidyl transferase
    1.6e-22   78.3  20.6    2.3e-08   33.4   0.3    4.7  4  Hexapep          Bacterial transferase hexapeptide (six repea
    2.6e-15   57.1   0.0    3.7e-15   56.7   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    5.4e-09   35.6  21.0    4.7e-07   29.4   0.7    4.8  4  Hexapep_2        Hexapeptide repeat of succinyl-transferase
    8.2e-06   25.7   0.1      2e-05   24.5   0.1    1.7  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    1.6e-05   24.8   0.1    2.7e-05   24.0   0.1    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    0.00015   21.8   0.9    0.00026   21.0   0.9    1.3  1  CTP_transf_3     Cytidylyltransferase
     0.0011   19.0   0.1     0.0021   18.0   0.1    1.4  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.075   13.3   1.0        0.5   10.6   0.1    2.9  3  DapH_N           Tetrahydrodipicolinate succinyltransferase N


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.3   0.2   4.1e-48   8.2e-45       1     231 [.       2     218 ..       2     232 .. 0.92

  Alignments for each domain:
  == domain 1  score: 153.3 bits;  conditional E-value: 4.1e-48
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       kavILa G+G+R +PLt t +k ++pv++k +++++ ++ l + +i++ii+++ +++++++ +++++g++fgv++++
  gi|298676142|ref|YP_003727891.1|   2 KAVILAAGEGSRCRPLTLTKSKVMLPVANK-PVLEHIIESLEKCSITDIILIV-DYEKERIMDHFEDGKDFGVNITY 76 
                                       79****************************.*****************66665.578889999************** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       ++++ + gtA+A+++ +e ++de++   +lvL+gD +++    e++ + ie+a+ g++++++++ ++ ++yGv+ +d
  gi|298676142|ref|YP_003727891.1|  77 IHQSAQLGTAHALLQTQEHVKDENQ---FLVLNGDNVVE---PETISDLIEDAE-GDASVLTQKMKNTSNYGVVITD 146
                                       ************************7...***********...667777777777.7888***************999 PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                       + +++e++vEKP+e+  s+l+++GiY+f++++++++ k+   +++ge  itd+l+ +++ g++  ++  k    W D
  gi|298676142|ref|YP_003727891.1| 147 N-KKIEKIVEKPEEKI-SNLVNTGIYLFTPNIFQII-KQTPISEKGEYAITDTLQLMIDYGYQVTNVNTKS--RWID 218
                                       8.6**********988.*******************.87999999*******************9987777..5988 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   1.2   3.2e-08   6.4e-05      10      36 .]     245     271 ..     245     271 .. 0.93
   2 !   33.4   0.3   1.2e-11   2.3e-08       2      33 ..     273     304 ..     272     307 .. 0.92
   3 !   10.2   0.4   0.00024      0.49       2      30 ..     308     335 ..     307     336 .. 0.87
   4 !   24.2   0.9   9.2e-09   1.8e-05       1      34 [.     360     393 ..     360     394 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.2e-08
                                       E-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  10 IgpfaviggnVkIGdnvkIgagvvigg 36 
                                       I  +avi g+V+IG+n++I +g++i g
  gi|298676142|ref|YP_003727891.1| 245 IEDGAVIKGDVEIGENTTIRSGCYIIG 271
                                       7889********************975 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 1.2e-11
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvv 33 
                                       ++IG+n+ Igp+avi++ ++IG n+ +++++ 
  gi|298676142|ref|YP_003727891.1| 273 VIIGDNCEIGPNAVILPSTTIGHNSSVESFTH 304
                                       79**************************9876 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00024
                                       EEEETTEEE-TTEEEETTEEE-TTEEEET CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIga 30 
                                       +++ +++ I   +++ +n +IG+n +Ig 
  gi|298676142|ref|YP_003727891.1| 308 AIVMNDTRISTHSYL-SNSVIGNNNTIGT 335
                                       78899999999****.7788*******96 PP

  == domain 4  score: 24.2 bits;  conditional E-value: 9.2e-09
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       +t+IG+++lI+ ++ + +++ IG ++++++g v+
  gi|298676142|ref|YP_003727891.1| 360 GTIIGDDNLIRDNVLVKAGTLIGTDCRVESGNVV 393
                                       699****************************997 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   1.8e-18   3.7e-15       1     115 [.       3     127 ..       3     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 1.8e-18
                                       EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTCTS-EEE-TT CS
                      NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevlaal...arlgvrvveded 67 
                                       aviLA+G++sR       + K +lp+++kp+le+++++l+++++ ++++++++  e + +++   +++gv +++  +
  gi|298676142|ref|YP_003727891.1|   3 AVILAAGEGSRCRpltltKSKVMLPVANKPVLEHIIESLEKCSITDIILIVDYekERIMDHFedgKDFGVNITYIHQ 79 
                                       79**********7554435********************************99444566655222555766655444 PP

                                       S.S-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHT CS
                      NTP_transf_3  68 p.gkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasg 115
                                       + + g++++l+   ++++d+ ++lvl +D + ++pe++  l++ a+ + 
  gi|298676142|ref|YP_003727891.1|  80 SaQLGTAHALLQTQEHVKDENQFLVLNGDNV-VEPETISDLIEDAEGDA 127
                                       4289**************************6.6***********87332 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.8    0.0028       5.6      14      32 ..     249     269 ..     247     270 .. 0.88
   2 !   29.4   0.7   2.4e-10   4.7e-07       1      27 [.     272     300 ..     272     301 .. 0.95
   3 ?   -0.1   0.2      0.41   8.2e+02       7      16 ..     324     333 ..     323     336 .. 0.47
   4 !   10.6   1.5   0.00018      0.36       2      32 ..     361     393 ..     360     395 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0028
                                       -EE.S.EEE-TT-EE-TT-EE CS
                         Hexapep_2  14 agi.G.vslGdncvvgaGvvi 32 
                                       a+i G v++G+n ++ +G++i
  gi|298676142|ref|YP_003727891.1| 249 AVIkGdVEIGENTTIRSGCYI 269
                                       788855*************98 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 2.4e-10
                                       .EEE-TT-EE-TT-EE..SEEE-TT-EE- CS
                         Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvg 27 
                                       pviIGdnC iG+na+i   +++G n+ v+
  gi|298676142|ref|YP_003727891.1| 272 PVIIGDNCEIGPNAVIlpSTTIGHNSSVE 300
                                       8***************999******9997 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.41
                                       T-EE-TT-EE CS
                         Hexapep_2   7 nCliGanagi 16 
                                       n++iG n +i
  gi|298676142|ref|YP_003727891.1| 324 NSVIGNNNTI 333
                                       4444444444 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00018
                                       EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE CS
                         Hexapep_2   2 viIGdnCliGanagi..GvslGdncvvgaGvvi 32 
                                       +iIGd+ li  n  +  G+ +G +c v++G v+
  gi|298676142|ref|YP_003727891.1| 361 TIIGDDNLIRDNVLVkaGTLIGTDCRVESGNVV 393
                                       79************888*************888 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 !   24.5   0.1   9.9e-09     2e-05       2     219 ..       2     232 ..       1     234 [. 0.70

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 9.9e-09
                                       EEEEECTTSSCT...T-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG.....CCEEE CS
                              IspD   2 vvvipAAGsGkR...mkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld.....ksiql 70 
                                        +vi AAG+G+R   +   + K  l ++++++leh +++l +  ++  i+++v+ ++ e++++   d      +i+ 
  gi|298676142|ref|YP_003727891.1|   2 KAVILAAGEGSRcrpLTLTKSKVMLPVANKPVLEHIIESLEK-CSITDIILIVDYEK-ERIMDHFEDgkdfgVNITY 76 
                                       69**********44445799*******************998.67777777777666.5565555555666766777 PP

                                       EE--SS..HHHHHHHHHHTTSSTTSEEEE--TT-TT--HHHHHHHHHHHHTTCSEEEEEEE-SSE....EEEEETTT CS
                              IspD  71 vaGGde..RaesVlnglkalegeakfVLvHDaARpllkaadiaellaaaeqstqgailalpvkDt....ikrveadg 141
                                       ++   +   a++ l++ + +++e++f Lv ++   ++++++i +l++ ae    + +l   +k+t    + ++++++
  gi|298676142|ref|YP_003727891.1|  77 IHQSAQlgTAHALLQTQEHVKDENQF-LVLNGDN-VVEPETISDLIEDAEG--DASVLTQKMKNTsnygVVITDNKK 149
                                       77655422578888888888888765.6667776.99*********99996..788888888887444444566554 PP

                                       ..BEEEEETG..TTEEEE....EEEEEEEHHHHHHHHHHHHHCT---SSHHHHHHHTT--EEEEE--TTG----SHH CS
                              IspD 142 ..lvaetedR..egLwaa....qtPqgFrvdlllaahakgeqegaeitDdaslvekiGlsvkvVeGeednlKittpe 210
                                          ++e ++   ++L +      tP  F++  ++++     +  + itD  +l+   G +v  V+ ++  +    + 
  gi|298676142|ref|YP_003727891.1| 150 ieKIVEKPEEkiSNLVNTgiylFTPNIFQI--IKQTPISE-KGEYAITDTLQLMIDYGYQVTNVNTKSRWIDAIFAW 223
                                       444555554412334332111145666543..33333333.334789999999999999999999999999999999 PP

                                       HHHHHHHHH CS
                              IspD 211 DlalAeail 219
                                       Dl++A+ i+
  gi|298676142|ref|YP_003727891.1| 224 DLLTANSIV 232
                                       999999886 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   1.4e-08   2.7e-05      11     132 ..      32     150 ..      24     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.4e-08
                                       TTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS.EEEEE CS
                   Glycos_transf_2  11 ktlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd.yilfl 86 
                                       + l+  +esl +    +  +ii++ D ++++  +  e+  + + ++++i+++   G a al +  ++++ +  +l+l
  gi|298676142|ref|YP_003727891.1|  32 PVLEHIIESLEKC---SITDIILIVDYEKERIMDHFEDGKDFGVNITYIHQSAQLGTAHALLQTQEHVKDEnQFLVL 105
                                       6666677766665...7889999999999999999999989************************************ PP

                                       ESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS CS
                   Glycos_transf_2  87 DaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv 132
                                       + D +++p+++++l+e +e  +a+v  ++   ++     i+ nk++
  gi|298676142|ref|YP_003727891.1| 106 NGDNVVEPETISDLIEDAEG-DASVLTQKMKNTSNYGVVITDNKKI 150
                                       *******************9.8878777777777766666666654 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.9   1.3e-07   0.00026      14     149 ..      21     157 ..      20     220 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.3e-07
                                       TTGGGSEETTEEHHHHHHHHHHHTTTTSE.EEEEES-HHHHHHHHHTT...SEEEE--TTCSSHHHHHHHHHHHHTT CS
                      CTP_transf_3  14 pgKnlldlggkpliayvleaalkskafek.vivaTDseeiknvakefg...asvlvtrsslesdterflevvkaflm 86 
                                       + K++l+ ++kp +++++e + k+   +  +iv+  +e+i+++ ++     + +  + +s++ +t+  l   +++  
  gi|298676142|ref|YP_003727891.1|  21 KSKVMLPVANKPVLEHIIESLEKCSITDIiLIVDYEKERIMDHFEDGKdfgVNITYIHQSAQLGTAHALLQTQEHVK 97 
                                       67**********************9988878999********99754441177777777777777777777777666 PP

                                       T.TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTTSSEEEEEEETTSHH.HHTSTTSTEEEETTT CS
                      CTP_transf_3  87 seneeiivnlqGdnPllqeevikkaietlkenqedylstlvkkvgkee.evlnandlkvlldda 149
                                       +  e+  + l Gdn+ +++e+i+ +ie+ +   +  l+++ k++ +    +++ ++++++++++
  gi|298676142|ref|YP_003727891.1|  98 D--ENQFLVLNGDNV-VEPETISDLIEDAEGDAS-VLTQKMKNTSNYGvVITDNKKIEKIVEKP 157
                                       6..556666779996.8999*******9988855.44444444444330334444455555544 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 !   18.0   0.1     1e-06    0.0021       6     107 ..      24     118 ..      22     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1e-06
                   Glyco_tranf_2_3   6 vlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                       v+ p++n  +vl+ ++esl ++  + ++++++vd +++   + +e   ++++   +++++++ +lg   +++al ++
  gi|298676142|ref|YP_003727891.1|  24 VMLPVANK-PVLEHIIESLEKC--SITDIILIVDYEKERIMDHFED-GKDFGV-NITYIHQSAQLG---TAHALLQT 92 
                                       56677666.7788888888776..6699999999999999999987.899988.7******99888...5899**** PP

                   Glyco_tranf_2_3  83 lravksd.lvllvDdDtvvePdtlkr 107
                                        ++vk++   l++++D+vveP+t+  
  gi|298676142|ref|YP_003727891.1|  93 QEHVKDEnQFLVLNGDNVVEPETISD 118
                                       *****5559999***********975 PP

>> DapH_N  Tetrahydrodipicolinate succinyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00025       0.5      39      70 ..     133     164 ..     112     166 .. 0.85
   2 ?   -2.1   0.0       2.4   4.7e+03      47      58 ..     230     241 ..     226     256 .. 0.81
   3 ?   -1.8   0.0         2   3.9e+03      22      56 ..     337     369 ..     320     388 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                                       EEEE-SSEEEEEEEHHHHHHHHHHTTTTEEEE CS
                            DapH_N  39 kvfgsedsgvvfGdwkeieevleenkdkiedy 70 
                                       k+  +++ gvv++d k+ie+++e+ ++ki+++
  gi|298676142|ref|YP_003727891.1| 133 KMKNTSNYGVVITDNKKIEKIVEKPEEKISNL 164
                                       55678899*********************875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                                       EEEEEEHHHHHH CS
                            DapH_N  47 gvvfGdwkeiee 58 
                                        +v+G+++++++
  gi|298676142|ref|YP_003727891.1| 230 SIVLGEYEDFKR 241
                                       689999999875 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2
                                       EEEE-.C.TC----TTSEEEE-SSEEEEEEEHHHH CS
                            DapH_N  22 YvkgelkeeelefpeevkvfgsedsgvvfGdwkei 56 
                                       ++ +e+++ ++e+  +      ++ g+++Gd + i
  gi|298676142|ref|YP_003727891.1| 337 FITEEKDSLKIEI--KGMLHKADRLGTIIGDDNLI 369
                                       4555544444443..23444556677777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.36s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 2309.72
//
Query:       gi|298676143|ref|YP_003727892.1|  [L=363]
Description: transposase [Methanohalobium evestigatum Z-7303]
Scores for 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-25   86.7   3.4    1.4e-24   85.7   1.0    2.5  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    6.4e-10   39.3   1.6    6.4e-10   39.3   1.6    1.7  2  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.058   13.4   0.1       0.14   12.2   0.1    1.6  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.13   12.4   1.6       0.88    9.7   0.1    2.3  2  UPF0547         Uncharacterised protein family UPF0547
       0.88    9.3   6.7        3.4    7.4   6.7    2.0  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
          1    9.4   4.8        2.7    8.1   4.8    1.7  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        1.8    8.8   5.8         13    6.0   1.9    3.0  2  DUF2387         Probable metal-binding protein (DUF2387)
        2.2    8.1   4.5         21    4.9   0.4    2.4  2  Rubredoxin_2    Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.38   8.5e+02      15      30 ..     187     202 ..     183     230 .. 0.83
   2 !   85.7   1.0   6.4e-28   1.4e-24       1      69 []     277     346 ..     277     346 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.38
                    OrfB_Zn_ribbon  15 yGikveevnpayTSkt 30 
                                       +G k  e+ ++yTS +
  gi|298676143|ref|YP_003727892.1| 187 KGTKADEIRERYTSLK 202
                                       5788889999999965 PP

  == domain 2  score: 85.7 bits;  conditional E-value: 6.4e-28
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l+ ++ ykak +G++v+ +np yTS++CseCg+++k+ ++++ +fkC++Cg++ ++D+nA+ Ni++r
  gi|298676143|ref|YP_003727892.1| 277 FSELTDFILYKAKLEGVPVVIINPMYTSQQCSECGYIDKNnRQKQANFKCKRCGHRENADYNASKNIAHR 346
                                       899*************************************9**************************997 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   1.6   2.9e-13   6.4e-10      15     106 ..     164     246 ..     151     256 .. 0.87
   2 ?   -3.2   0.1       4.1   9.3e+03      40      68 ..     313     341 ..     304     347 .. 0.64

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 2.9e-13
                        OrfB_IS605  15 gnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrkhl 91 
                                        + + g+DlG+ n+at+++++    +ykg ++++  ++++  + +lqsk   s     a++ l++l++k +r+ ++l
  gi|298676143|ref|YP_003727892.1| 164 YEDVMGVDLGVVNIATTSDNE----VYKGTKADEIRERYTSLKSRLQSKGTWS-----AKKHLKKLSKKERRFKRDL 231
                                       56789****************....************************6665.....7999*************** PP

                        OrfB_IS605  92 lhklathliktlkev 106
                                        h +a++l+++ k++
  gi|298676143|ref|YP_003727892.1| 232 NHRVAKQLVERAKDT 246
                                       *********998765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.1
                        OrfB_IS605  40 lykgrrlksdykylakeiaelqsklkksk 68 
                                       + k +r k+++++ +++  +    ++ sk
  gi|298676143|ref|YP_003727892.1| 313 IDKNNRQKQANFKCKRCGHRENADYNASK 341
                                       55556666666666666666555555555 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   6.2e-05      0.14      60      96 ..     288     333 ..     259     343 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.2e-05
                                       -EEE......EEEE--EEEETTTS-EEECHH..H.HHS-TTTSSS- CS
                              HypA  60 aeLe......ieevpvkvrCreCgkefelee..k.alrCpkCgsad 96 
                                       a+Le      i+ +  + +C+eCg+  + ++  + +++C++Cg+++
  gi|298676143|ref|YP_003727892.1| 288 AKLEgvpvviINPMYTSQQCSECGYIDKNNRqkQaNFKCKRCGHRE 333
                                       5555555555777788999*****9888555333788*****9874 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00039      0.88      15      25 ..     305     315 ..     303     316 .. 0.87
   2 ?    1.5   0.2      0.15   3.3e+02      16      22 ..     325     331 ..     322     332 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00039
                           UPF0547  15 qfCphCGyvFq 25 
                                       q C++CGy+++
  gi|298676143|ref|YP_003727892.1| 305 QQCSECGYIDK 315
                                       89******986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.15
                           UPF0547  16 fCphCGy 22 
                                       +C  CG+
  gi|298676143|ref|YP_003727892.1| 325 KCKRCGH 331
                                       5777887 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   6.7    0.0015       3.4       3      26 ..     307     332 ..     306     333 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0015
                                       -SSS-..-B----SSS----SSS--- CS
                    DNA_RNApol_7kD   3 CgeCg..aevslkkgdpiRCkeCGhR 26 
                                       C eCg  +++  +k++  +Ck CGhR
  gi|298676143|ref|YP_003727892.1| 307 CSECGyiDKNNRQKQANFKCKRCGHR 332
                                       9999966788899999*********9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.8    0.0012       2.7      19      45 ..     305     331 ..     301     332 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0012
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCrk 45 
                                       + C  Cg+  k  r k+   f+Ck+C++
  gi|298676143|ref|YP_003727892.1| 305 QQCSECGYIdKNNRQKQ-ANFKCKRCGH 331
                                       57*******77777777.********98 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.046     1e+02      38      72 ..     216     250 ..     213     253 .. 0.86
   2 ?    6.0   1.9    0.0059        13      31      49 ..     305     323 ..     299     350 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.046
                           DUF2387  38 ftdelsekgqsvakelktrvnkdeekeasakvqtv 72 
                                       ++ +ls+k++ ++++l+ rv+k+  ++a+++ +++
  gi|298676143|ref|YP_003727892.1| 216 HLKKLSKKERRFKRDLNHRVAKQLVERAKDTSRSI 250
                                       7889999****************998888887766 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0059
                           DUF2387  31 rECvsCgftdelsekgqsv 49 
                                         C +Cg++d+ + ++q+ 
  gi|298676143|ref|YP_003727892.1| 305 QQCSECGYIDKNNRQKQAN 323
                                       57999*****999995543 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3     0.014        31       2       8 ..     306     312 ..     306     315 .. 0.89
   2 ?    4.9   0.4    0.0096        21       1      10 [.     324     333 ..     324     335 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.014
                      Rubredoxin_2   2 vCsqCGf 8  
                                       +Cs+CG+
  gi|298676143|ref|YP_003727892.1| 306 QCSECGY 312
                                       7*****9 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0096
                      Rubredoxin_2   1 YvCsqCGfes 10 
                                       + C++CG++ 
  gi|298676143|ref|YP_003727892.1| 324 FKCKRCGHRE 333
                                       78*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1052  (0.0586759); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.37s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2164.57
//
Query:       gi|298676144|ref|YP_003727893.1|  [L=108]
Description: hypothetical protein Metev_2279 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0099   14.7   0.4      0.013   14.3   0.4    1.1  1  DUF2207   Predicted membrane protein (DUF2207)
  ------ inclusion threshold ------
      0.013   15.5   0.3      0.014   15.3   0.3    1.0  1  DsbD_2    Cytochrome C biogenesis protein transmembrane regio
       0.11   12.4   0.4       0.15   12.0   0.4    1.2  1  TraQ      Type-F conjugative transfer system pilin chaperone 
        7.4    6.4   6.8         61    3.4   6.5    2.2  2  DUF3188   Protein of unknown function (DUF3188)


Domain annotation for each model (and alignments):
>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.4   2.8e-06     0.013     391     450 ..      18      83 ..       8      85 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.8e-06
                           DUF2207 391 iilglilillallllvll......lvfllilllillliaiivlllfsrllgrrteeGaellakwkg 450
                                       ++lg++++l++ ++++l         +++i++++l+ i+i++++++ +++  +++  +++++k++g
  gi|298676144|ref|YP_003727893.1|  18 LVLGILFVLVGGVFYQLYrmdaysDPIFSIPMFVLGGILIVYYFFSGAFVVNLSAGNKDYRYKIDG 83 
                                       333333333333333333566778**********************99999999998888888887 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.3   3.1e-06     0.014      42      95 ..      13      67 ..       5      95 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.1e-06
                            DsbD_2 42 RilsYallGalvgllgsvlqlagel.eglrallgvllgllllllglklllkkkll 95
                                      R  +Y +lG+l++l+g v+ +  ++ ++   ++++ + +l+ +l++++++++ ++
  gi|298676144|ref|YP_003727893.1| 13 RNGAYLVLGILFVLVGGVFYQLYRMdAYSDPIFSIPMFVLGGILIVYYFFSGAFV 67
                                      7789***************998777556677777777777777777777655443 PP

>> TraQ  Type-F conjugative transfer system pilin chaperone (TraQ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   3.3e-05      0.15      19      59 ..      18      58 ..      12      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.3e-05
                              TraQ 19 lslGvwfhlvarlvyrkPelavllaeilavglvliGgyril 59
                                      l lG+ f lv+++ y+   +      i+++ + ++Gg  i+
  gi|298676144|ref|YP_003727893.1| 18 LVLGILFVLVGGVFYQLYRMDAYSDPIFSIPMFVLGGILIV 58
                                      579*********************************98776 PP

>> DUF3188  Protein of unknown function (DUF3188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.0      0.03   1.4e+02      27      45 ..      18      33 ..      10      38 .. 0.79
   2 ?    3.4   6.5     0.014        61       4      38 ..      23      58 ..      18      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.03
                           DUF3188 27 lPallvGlgLivsgavgrg 45
                                      l   + G++ +++g+v++ 
  gi|298676144|ref|YP_003727893.1| 18 L---VLGILFVLVGGVFYQ 33
                                      4...889999999999886 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.014
                           DUF3188  4 lLillgllill.ysqrqgsdrlqslPallvGlgLiv 38
                                      l +l+g +  + y +   sd ++s+P ++ G  Liv
  gi|298676144|ref|YP_003727893.1| 23 LFVLVGGVFYQlYRMDAYSDPIFSIPMFVLGGILIV 58
                                      556666665555777777888**********99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.53s 00:00:01.06 Elapsed: 00:00:00.67
# Mc/sec: 483.45
//
Query:       gi|298676145|ref|YP_003727894.1|  [L=294]
Description: NAD-dependent epimerase/dehydratase [Methanohalobium evestigatum Z-7303]
Scores for complete 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-56  191.9   0.0    1.5e-56  191.6   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.1e-49  168.2   0.1    7.8e-49  166.8   0.1    1.6  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.7e-22   79.9   0.6    4.7e-21   75.2   0.6    2.6  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.2e-21   77.0   0.0    1.7e-21   76.5   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.7e-11   43.8   0.0    2.2e-11   43.4   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    6.9e-09   35.3   0.0      2e-05   23.9   0.0    2.4  2  NAD_binding_4    Male sterility protein
      4e-06   26.8   0.0    4.6e-05   23.4   0.0    2.4  2  NAD_binding_10   NAD(P)H-binding
     0.0003   20.3   0.0     0.0028   17.2   0.0    2.3  2  adh_short        short chain dehydrogenase
    0.00031   20.4   0.2    0.00084   19.0   0.0    1.8  2  NmrA             NmrA-like family
     0.0042   17.0   0.0     0.0085   16.0   0.0    1.6  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
  ------ inclusion threshold ------
       0.08   13.5   0.0       0.27   11.8   0.0    1.9  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.098   12.6   0.0          1    9.2   0.0    2.3  2  KR               KR domain


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.6   0.0     1e-59   1.5e-56       1     241 []       3     231 ..       3     231 .. 0.94

  Alignments for each domain:
  == domain 1  score: 191.6 bits;  conditional E-value: 1e-59
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       ilVtG++GfiGs++++++l++g++v  +d+lss+ +++  e +e+v+ d+   s   ++f+  ++d+v+h Aa  +v
  gi|298676145|ref|YP_003727894.1|   3 ILVTGGAGFIGSHIAEYFLSEGHNVRIVDNLSSGYQENIPESAEFVNEDIYSVS--PDVFE--GVDYVFHEAALVSV 75 
                                       8**************************************9999*******9755..89999..9************* PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklve 154
                                       ++s ++p++ +++n+ gt+n+l+ + +agv++++ +sS++vYG+++  pk e++     +p spYa++K+  e l+ 
  gi|298676145|ref|YP_003727894.1|  76 PVSCQQPEEAFRINTLGTMNVLQNSLDAGVEKVVLASSAAVYGNNPILPKMEDM---LPEPASPYAISKMDCEYLAG 149
                                       *******************************************99988*99998...5699***************9 PP

                                       HHHHHHT-EEEEEEESEEESTT.S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHT CS
                         Epimerase 155 ayaaqyglnaiilrlfnlyGpr.ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvd 230
                                        +++++ l++++lr+fn+yGpr ++++  + vip ++++++egk +++++gdgt+ Rdf+ ++Dv++a+++++++  
  gi|298676145|ref|YP_003727894.1| 150 MFHDKG-LRTTCLRYFNVYGPRqDPNSPYAAVIPIFMKRAKEGK-DLVIYGDGTQTRDFVNIQDVVRANVAAMDN-- 222
                                       997776.***************555555****************.******************************.. PP

                                       T-STTEEEEES CS
                         Epimerase 231 agdkgeiyniG 241
                                          +g+++n++
  gi|298676145|ref|YP_003727894.1| 223 --GDGDVFNVA 231
                                       ..567899986 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.8   0.1   5.2e-52   7.8e-49       1     328 [.       4     288 ..       4     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 5.2e-52
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiGs++ae++l++g++v +++++ss  + ++i +           + ++++ D+   s   ++++ v  d
  gi|298676145|ref|YP_003727894.1|   4 LVTGGAGFIGSHIAEYFLSEGHNVRIVDNLSSG-YQENIPE-----------SAEFVNEDIYSVS--PDVFEGV--D 64 
                                       9***********************988887776.5455543...........3479*****8755..8999998..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                        v++ AA   V+vs ++Pe+ +++n lGt+++L+   ++g+e   +++ aS++ vYG+    p  E+   +P sPYa
  gi|298676145|ref|YP_003727894.1|  65 YVFHEAALVSVPVSCQQPEEAFRINTLGTMNVLQNSLDAGVE---KVVLASSAAVYGNNPILPKMEDMLPEPASPYA 138
                                       ****************************************97...8999**************************** PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCC.HHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtr.kitravarialgkqevlylGnldakRdwghvkDyv 230
                                       ++K+ +++++  +++  gl ++  ++fn ++pr+ ++ +    i+ ++ r+++gk + +++G++ ++Rd+  ++D+v
  gi|298676145|ref|YP_003727894.1| 139 ISKMDCEYLAGMFHD-KGLRTTCLRYFNVYGPRQDPNSPYAaVIPIFMKRAKEGK-DLVIYGDGTQTRDFVNIQDVV 213
                                       **********99887.8999999*************9887715555556666665.8999***************** PP

                                       HHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB-- CS
                     GDP_Man_Dehyd 231 eamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlll 307
                                       +a ++++ ++  + +++atg+++sv+e++e  ++ +g + +                     + ++  r+g+ +  +
  gi|298676145|ref|YP_003727894.1| 214 RANVAAMDNGDGDVFNVATGTSVSVQEIAETIIEITGSSSD---------------------IVYEEEREGDIKDSV 269
                                       ***************************99965555554322.....................333445555555556 PP

                                       B-THHHHHHH----SS-HHHH CS
                     GDP_Man_Dehyd 308 gdaskakeeLgWkpkvsfeel 328
                                       +d sk+     W+ kv++ee+
  gi|298676145|ref|YP_003727894.1| 270 ADVSKISG--WWESKVDLEEG 288
                                       66666552..24555555555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.6   3.1e-24   4.7e-21       1     252 [.       3     254 ..       3     268 .. 0.77

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 3.1e-24
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES.-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.. CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiiller.dElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel 76 
                                       +lvtG++G iGs++ + +l++   +++++++ +   + +i ++   e+ +          i +v       +++e  
  gi|298676145|ref|YP_003727894.1|   3 ILVTGGAGFIGSHIAEYFLSEGH-NVRIVDNlSSGYQENIPESA--EFVN--------EDIYSVS-----PDVFE-- 61 
                                       89**************9999865.56666651444555555544..2222........2244554.....57899.. PP

                                       T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE..............GGGSS--SHHH CS
                   Polysacc_synt_2  77 kvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt..............DKAvnPtnvmG 139
                                       +vd+vfh AAl  VP+  ++p ea++ N lgt+nv++ +++agv+kvvl S+              D   +P + + 
  gi|298676145|ref|YP_003727894.1|  62 GVDYVFHEAALVSVPVSCQQPEEAFRINTLGTMNVLQNSLDAGVEKVVLASSaavygnnpilpkmeDMLPEPASPYA 138
                                       *************************************************9983333332333222233345666666 PP

                                       HHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTGT.......TSSHHHHHHHHHTTSSEEE.S-TT-EEEEE-HHH CS
                   Polysacc_synt_2 140 atKrlaekllqalakeseekktkfvvvRfGNVlgSr.......GSviplFkkqikeggpvtv.TdpemtRyfmtiee 208
                                       ++K+ +e l+  ++++      + ++ R+ NV g r         vip+F k+ keg+++ +  d + tR f+ i++
  gi|298676145|ref|YP_003727894.1| 139 ISKMDCEYLAGMFHDKG----LRTTCLRYFNVYGPRqdpnspyAAVIPIFMKRAKEGKDLVIyGDGTQTRDFVNIQD 211
                                       66666666666665555....999**********87444444458************99888468999********* PP

                                       HHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH......... CS
                   Polysacc_synt_2 209 avqLvlqalalakggeifvldmGepvkivdlakalielsgleek 252
                                        v+  + a+ ++ +g++f +  G +v+++++a+++ie++g +++
  gi|298676145|ref|YP_003727894.1| 212 VVRANVAAMDNG-DGDVFNVATGTSVSVQEIAETIIEITGSSSD 254
                                       ***998888776.589***********************97665 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0   1.1e-24   1.7e-21       1     229 [.       4     220 ..       4     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1.1e-24
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +vtGgaGF+G+++ + +++++  ++vr++D   s    e++ ++  +++++ D+ + +   ++ egvd v+h a+lv
  gi|298676145|ref|YP_003727894.1|   4 LVTGGAGFIGSHIAEYFLSEG--HNVRIVDNLSSGYQ-ENIPES--AEFVNEDIYSVS--PDVFEGVDYVFHEAALV 73 
                                       69*******************..5******7766655.444333..347899**9876..589************** PP

                         3Beta_HSD  78 dvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                        v    ++ +e  ++n  GT nvl+  ++agv+++v  Ssa v g+    ++il   E   + + + ++y+ sK   
  gi|298676145|ref|YP_003727894.1|  74 SVPVsCQQPEEAFRINTLGTMNVLQNSLDAGVEKVVLASSAAVYGN----NPILPKME--DMLPEPASPYAISKMDC 144
                                       99754889999***********************************....67774444..45567899********* PP

                         3Beta_HSD 154 EklvlkaNgrtlknggrlyTcaLRpagiyGegdk......llvpllkqlaklglalfkigdeevlsdrvYvgNvawa 224
                                       E l        +++   l T +LR   +yG++++       + p + + ak g+ l+ +gd  ++ d+v    v+ a
  gi|298676145|ref|YP_003727894.1| 145 EYLAGM-----FHDK-GLRTTCLRYFNVYGPRQDpnspyaAVIPIFMKRAKEGKDLVIYGDGTQTRDFVNIQDVVRA 215
                                       *99644.....4444.599************9972222224566778999*************************** PP

                         3Beta_HSD 225 hilAa 229
                                        + A+
  gi|298676145|ref|YP_003727894.1| 216 NVAAM 220
                                       *9987 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 !   43.4   0.0   1.5e-14   2.2e-11       1     236 [.       1     254 [.       1     270 [. 0.78

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.5e-14
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....T--T.TSHHHHHHHHHHH--S......EEEE------HHH CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre....eldl.tdaeavaellkeakpd......vvvnaAAytavDk 66 
                                       m+ilvtG+ G +Gs++a+ + +eg++v  +++     + ++ + ae v+e + +++pd       v + AA   v  
  gi|298676145|ref|YP_003727894.1|   1 MNILVTGGAGFIGSHIAEYFLSEGHNVRIVDNLssgyQENIpESAEFVNEDIYSVSPDvfegvdYVFHEAALVSVPV 77 
                                       89**********************99988866567886776234566788887777774444447************ PP

                                       HHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHH...HHHH CS
                     RmlD_sub_bind  67 aEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqa...vlaa 139
                                         +++e+a+++n  +++++ +    +g+ +++  S+  V+  +   p  ed  ++P + Y+ +K++ E       ++
  gi|298676145|ref|YP_003727894.1|  78 SCQQPEEAFRINTLGTMNVLQNSLDAGVeKVVLASSAAVYGNNPILPKMEDMLPEPASPYAISKMDCEYLagmFHDK 154
                                       ***************************9458899*********999**********************861115669 PP

                                       -SSEEEEEE-SEESS.SSS-.....HHHHHHHHHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH..GGG-EE CS
                     RmlD_sub_bind 140 gkkalivRtswvyge.kgkn.....fvktmlrlakereelkvvaDqlgsPTsardlAevllqllekaae.ekelagv 209
                                       g +++ +R   vyg  ++ n      +  ++++ake + l +  D     T++rd  ++   + ++ a+ ++ +  v
  gi|298676145|ref|YP_003727894.1| 155 GLRTTCLRYFNVYGPrQDPNspyaaVIPIFMKRAKEGKDLVIYGD----GTQTRDFVNIQDVVRANVAAmDNGDGDV 227
                                       99***********98533332211134456888999999988665....566666555433332222220224489* PP

                                       EE---BS-EEHHHHHHHHHHHHCHTTS CS
                     RmlD_sub_bind 210 yHlanegetswlefArailkeagadse 236
                                       + +a   ++s  e+A+ i++ +g++s 
  gi|298676145|ref|YP_003727894.1| 228 FNVATGTSVSVQEIAETIIEITGSSSD 254
                                       *******************99988764 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00046      0.68       1      26 [.       5      30 ..       5      40 .. 0.92
   2 !   23.9   0.0   1.3e-08     2e-05      85     209 ..      60     172 ..      55     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00046
                                      EE-TTSHHHHHHHHHHHHHS-.TEEE CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiy 26
                                      +TG+ GF+G+++ e  L++  +v+i+
  gi|298676145|ref|YP_003727894.1|  5 VTGGAGFIGSHIAEYFLSEGHNVRIV 30
                                      7****************999998875 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 1.3e-08
                                       HHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H..... CS
                     NAD_binding_4  85 aeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegeke 158
                                        e vd ++h aA v++  + ++   ++r+N++Gt +vl+ +        ++  S+a+v+g++               
  gi|298676145|ref|YP_003727894.1|  60 FEGVDYVFHEAALVSVPVSCQQpeeAFRINTLGTMNVLQNSLDAGVE-KVVLASSAAVYGNNP-------------- 121
                                       6789***********9876554444***************9987777.799999999999999.............. PP

                                       .HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-...- CS
                     NAD_binding_4 159 ekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg...e 209
                                            ++++ l + +  Y  sK+  E+l    +++ gl+++ +R  +++g   +
  gi|298676145|ref|YP_003727894.1| 122 --ILPKMEDMLPEPASPYAISKMDCEYLAGMFHDK-GLRTTCLRYFNVYGprqD 172
                                       ..345667777888889999999999999999977.999999998888885542 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 !   23.4   0.0   3.1e-08   4.6e-05       1     142 [.       7     162 ..       7     223 .. 0.72
   2 ?   -0.0   0.1      0.48   7.1e+02     162     180 ..     230     248 ..     218     251 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.1e-08
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT.HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-........ CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn.peklaeleaeeglevvegdvtdvedlaealkgadaVvsal........ 68 
                                       G+ G +G+++++  l++ gh+v+++  n ++  +e    e +e v  d+ +v+   ++++g+d V+  +        
  gi|298676145|ref|YP_003727894.1|   7 GGAGFIGSHIAEYFLSE-GHNVRIV-DNlSSGYQENI-PESAEFVNEDIYSVS--PDVFEGVDYVFHEAalvsvpvs 78 
                                       99***************.5**9865.66144444433.478888888888765..4899******999966666654 PP

                                       ..--TCCHHHH.......HHHHHHHHHHCT--EEEEEEETTTTSGCG..CHHHHHHHHCCHHHHHHHHHHHHH...H CS
                    NAD_binding_10  69 ..ggggkdeeg.......aknivdaakeagvkRfvlvsaigvgdevp..gefgewnkellkaylaakraaeel...l 131
                                               ee+       + n+++    agv+++vl s++ v+ + p   + +++  e  ++y++ k   e l    
  gi|298676145|ref|YP_003727894.1|  79 cqQ----PEEAfrintlgTMNVLQNSLDAGVEKVVLASSAAVYGNNPilPKMEDMLPEPASPYAISKMDCEYLagmF 151
                                       431....11113445556************************97533113344444555567776666655552223 PP

                                       HHSSSEEEEEE CS
                    NAD_binding_10 132 rasgldwTivr 142
                                        ++gl  T +r
  gi|298676145|ref|YP_003727894.1| 152 HDKGLRTTCLR 162
                                       44666666655 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.48
                                       S----EEEHHHHHHHHHHH CS
                    NAD_binding_10 162 pfkggsisradVAdvlvav 180
                                         +g+s+s + +A++++++
  gi|298676145|ref|YP_003727894.1| 230 VATGTSVSVQEIAETIIEI 248
                                       457899*********9997 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.8e-06    0.0028       3      58 ..       3      59 ..       1      71 [. 0.86
   2 ?    0.8   0.0      0.19   2.8e+02      96     122 ..      77     103 ..      50     120 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.8e-06
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TT CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDv 58
                                      +lvtG+++ IG  ia+ +++eG +v +vd+ ++  +e + e  e  +++++ ++ Dv
  gi|298676145|ref|YP_003727894.1|  3 ILVTGGAGFIGSHIAEYFLSEGHNVRIVDNLSSGYQENIPESAEFvNEDIYSVSPDV 59
                                      8*****************************999998888887766666777666666 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.19
                                       CSHHHHHHHHHHHTHHHHHHHHHHHHH CS
                         adh_short  96 lseeewervievNltgvflltravlpa 122
                                       +s ++ e+ + +N  g++++ +  l+a
  gi|298676145|ref|YP_003727894.1|  77 VSCQQPEEAFRINTLGTMNVLQNSLDA 103
                                       4566778999*********99988776 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   5.6e-07   0.00084       1      73 [.       3      71 ..       3     114 .. 0.80
   2 ?   -1.3   0.0      0.87   1.3e+03     160     196 ..     187     222 ..     177     256 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.6e-07
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtg 73
                                      Ilv+G++G +G+++++++l++gh+vr++  ++ s   ++   + +e+v++d+++ +    +++gvd vf   +
  gi|298676145|ref|YP_003727894.1|  3 ILVTGGAGFIGSHIAEYFLSEGHNVRIV-DNL-SSGYQENIPESAEFVNEDIYSVS--PDVFEGVDYVFHEAA 71
                                      9*************************85.444.45555555567899999988654..578888888887655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.87
                                       E-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHH CS
                              NmrA 160 tappedkvtllgpgnpkavlldaeeDiGafvikilkd 196
                                        a++++ +++ g+g     ++ + +D+ ++ ++++++
  gi|298676145|ref|YP_003727894.1| 187 RAKEGKDLVIYGDGTQTRDFV-NIQDVVRANVAAMDN 222
                                       444455788888888777777.888888887777776 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   5.7e-06    0.0085       6      33 ..       8      35 ..       3      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.7e-06
                                      --SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N  6 GaGtmGagiaavfasagleVvlvdisee 33
                                      GaG +G+ ia+ f+s+g++V++vd  ++
  gi|298676145|ref|YP_003727894.1|  8 GAGFIGSHIAEYFLSEGHNVRIVDNLSS 35
                                      99*********************98444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.27       3      32 ..       5      34 ..       3      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                      EEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvversd 32
                                      v  G+G+ig   A+++   g++V +v++ +
  gi|298676145|ref|YP_003727894.1|  5 VTGGAGFIGSHIAEYFLSEGHNVRIVDNLS 34
                                      5569**********************9875 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00069         1       4      26 ..       4      27 ..       2      50 .. 0.84
   2 ?    0.5   0.0      0.32   4.8e+02     107     139 ..      84     116 ..      60     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00069
                                      EEETTTSHHHHHHHHHHHHHH.S- CS
                                KR  4 litGGlGgLGlelarwlaekg.ar 26
                                      l+tGG+G +G ++a+  +++g + 
  gi|298676145|ref|YP_003727894.1|  4 LVTGGAGFIGSHIAEYFLSEGhNV 27
                                      9***************99999444 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.32
                                       HHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHH CS
                                KR 107 qvlapKvkGawnLhelledesldffvlfSSiag 139
                                       ++++    G+ n+ + + d  ++ +vl SS+a 
  gi|298676145|ref|YP_003727894.1|  84 EAFRINTLGTMNVLQNSLDAGVEKVVLASSAAV 116
                                       556666678999999999999999999999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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: 0.59u 0.37s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1649.07
//
Query:       gi|298676146|ref|YP_003727895.1|  [L=296]
Description: glycosyl transferase family 2 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-24   85.1   0.2    7.8e-24   84.4   0.2    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    8.1e-05   22.6   0.1    0.00012   22.1   0.1    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0041   17.6   0.0      0.011   16.2   0.0    1.8  2  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
        3.6    7.0   6.1          1    8.7   0.8    2.1  2  DUF373           Domain of unknown function (DUF373)


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.2   1.7e-27   7.8e-24       4     168 ..       8     162 ..       6     164 .. 0.94

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 1.7e-27
                                       EEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
                   Glycos_transf_2   4 iptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                       +p+yNe++t+ e+++ + +      ++++vvDDgS D+t +i+e+l     +  v+r+++n+G++++l+  ++ a  
  gi|298676146|ref|YP_003727895.1|   8 MPAYNEANTIGEVIHGCQKY----VDKVVVVDDGSVDDTIKIAESL-----GAYVVRHPQNEGYGASLRDCFKTALK 75 
                                       9******************9....**********************.....9*********************9855 PP

                                       S...EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTC CS
                   Glycos_transf_2  81 d...yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfe 154
                                            ++++D+D ++dpd +  ++e+l++ g  v++g+r+ ++ ++d    +k      ++    +++  ++n+s+ 
  gi|298676146|ref|YP_003727895.1|  76 LdadMMVIIDSDGQHDPDEITHVLEPLDR-GINVAIGSRFINGNGDDVPAYRK---VGMKVLDVATNFVGGINVSDT 148
                                       4455*************************.999*********99999999997...59******************* PP

                                       STCCCEEEEHHHHH CS
                   Glycos_transf_2 155 igsaallrrealee 168
                                        ++++++ +ea+++
  gi|298676146|ref|YP_003727895.1| 149 QCGFRAYDKEAIKN 162
                                       **********9975 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   2.6e-08   0.00012       7     129 ..       7     119 ..       3     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.6e-08
                   Glyco_tranf_2_3   7 lVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralneal 83 
                                       + p++ne+ ++gev++   ++    ++vvvv+d+s ++t++ ae     l++    vv+ ++n g ++  r  + + 
  gi|298676146|ref|YP_003727895.1|   7 AMPAYNEANTIGEVIHGCQKY---VDKVVVVDDGSVDDTIKIAES----LGA---YVVRHPQNEGYGASLRDCFKTA 73 
                                       679**************9996...99***************9976....555...4677777788766666666666 PP

                   Glyco_tranf_2_3  84 ravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfll.nr 129
                                          + d+ +++D+D   +Pd +  +l  + ++++ ++ +++f + n+
  gi|298676146|ref|YP_003727895.1|  74 LKLDADMMVIIDSDGQHDPDEITHVLEPL-DRGINVAIGSRFINgNG 119
                                       6677*********************9998.88888887777776554 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 !   16.2   0.0   2.5e-06     0.011       1      81 [.      11      87 ..      11      94 .. 0.73
   2 ?   -0.1   0.0      0.32   1.4e+03       8      33 ..      67      92 ..      58     104 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                   Glyco_tranf_2_4  1 rneadiLpeflahhlalgfdrilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvlvvD 79
                                      +nea++++e++    ++ +d+++v+d++s D+t +i ++l ++ + h +++    +  ++  k++l+   +ad ++ +D
  gi|298676146|ref|YP_003727895.1| 11 YNEANTIGEVIHGCQKY-VDKVVVVDDGSVDDTIKIAESLGAYVVRHPQNEG-YGASLRDCFKTALKL--DADMMVIID 85
                                      69*********999999.*********************8665544444322.223334444444433..577777777 PP

                   Glyco_tranf_2_4 80 aD 81
                                      +D
  gi|298676146|ref|YP_003727895.1| 86 SD 87
                                      76 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.32
                   Glyco_tranf_2_4  8 peflahhlalgfdrilvydndstDgt 33
                                        + + +l+l++d ++++d d + + 
  gi|298676146|ref|YP_003727895.1| 67 RDCFKTALKLDADMMVIIDSDGQHDP 92
                                      55667788899999998887655444 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.4     0.063   2.8e+02      98     113 ..      28      43 ..      14      48 .. 0.76
   2 ?    8.7   0.8   0.00023         1     143     211 ..     213     294 ..     205     296 .] 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.063
                            DUF373  98 adsaivVsDGaeDesv 113
                                       +d+++vV DG+ D+++
  gi|298676146|ref|YP_003727895.1|  28 VDKVVVVDDGSVDDTI 43 
                                       489********99986 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00023
                            DUF373 143 llkkalkdpelrk..tiLvplGlllliyallll............lglpelalaiillllGlylllrGfgldellee 205
                                        l ++lkd e+r+  + ++ +Gll+ +++++l             l++    l+i+l+l+G ++ + G+ l+  +++
  gi|298676146|ref|YP_003727895.1| 213 ALVQILKDMEFRRplYYFTAPGLLMGLVGVFLGlsflqdfyhgdsLSFGPTLLMILLTLVGTFMAFTGIILHA-MSK 288
                                       5689999999999667899*******99999988999*****999777779999**************99997.777 PP

                            DUF373 206 lleklk 211
                                       l++++k
  gi|298676146|ref|YP_003727895.1| 289 LIRETK 294
                                       766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1751.27
//
Query:       gi|298676147|ref|YP_003727896.1|  [L=323]
Description: glycosyl transferase family 2 [Methanohalobium evestigatum Z-7303]
Scores for 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-27   94.5   0.1    9.3e-27   93.9   0.1    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    4.6e-16   59.4   0.0    6.8e-16   58.8   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    8.5e-12   45.1   2.6    7.3e-11   42.0   2.6    2.0  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    2.5e-09   37.3   0.1    3.8e-09   36.8   0.1    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    4.2e-05   24.0   0.3    0.00097   19.6   0.0    2.4  2  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.029   13.8   0.1      0.054   12.9   0.0    1.4  2  Anp1             Anp1
       0.32    9.7   3.2       0.43    9.3   3.2    1.2  1  DUF2207          Predicted membrane protein (DUF2207)


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 !   93.9   0.1   3.6e-30   9.3e-27       1     124 [.       7     125 ..       7     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 3.6e-30
                                       EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglr 76 
                                       s+v+ t Neek+++e+++sll+  +p++ fei++vD  StD+t++i++++     +v ++ +e+    a+a+n g++
  gi|298676147|ref|YP_003727896.1|   7 SIVVGTRNEEKYIAECINSLLNLnYPKDSFEILIVDGMSTDNTQNIVKNY-----PVNLLINEKI-NVASARNLGIK 77 
                                       89************************************************.....9999999977.9********** PP

                                       H--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCC CS
                   Glycos_transf_2  77 aatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetd 124
                                       +++gd+i+f D D+ ++  wl+ lv ++++ ++dv++++ p    ++d
  gi|298676147|ref|YP_003727896.1|  78 HSQGDLIAFTDGDCKVNNLWLKTLVYEIQNAPEDVACVGGPNLVIDND 125
                                       *************************************98766555555 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 !   58.8   0.0   2.7e-19   6.8e-16       1     226 [.       4     226 ..       4     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 2.7e-19
                   Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgk 75 
                                       p+ ++++V t nee+++ e+++sll+  yp   +e+ +v+ +s++ t + ++     +    v++++n++   ++++
  gi|298676147|ref|YP_003727896.1|   4 PF-VSIVVGTRNEEKYIAECINSLLNLNYPKdsFEILIVDGMSTDNTQNIVKN----Y---PVNLLINEK---INVA 69 
                                       67.9*********************99995556****************8875....6...556999999...4666 PP

                   Glyco_tranf_2_3  76 sralnealravksdlvllvDdDtvvePdtlkrllqff.ltp.kvgavgtpvfl.lnrstlvsalgalefaerhlrfl 149
                                       s   n ++++ ++dl+++ D+D+ v    lk l+  + ++p +v++vg+p ++ +n+  + +++g+++  e++l+  
  gi|298676147|ref|YP_003727896.1|  70 SA-RNLGIKHSQGDLIAFTDGDCKVNNLWLKTLVYEIqNAPeDVACVGGPNLViDNDPIFARVVGYVQ--ETFLSSG 143
                                       55.78***************************9999974446*********88679887777776643..5555333 PP

                   Glyco_tranf_2_3 150 aar....ralgv.ltlnGsg.slirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkay 220
                                         +    +++++ + + +++  l+  ++ ++ + +d+ f ++ D +l +r+ + g+r  y p+a v++ ++ +lk +
  gi|298676147|ref|YP_003727896.1| 144 GSAqchsYSKKQyVQSIPNCnALYKKSIIRNVGFFDEYFKVGQDGDLNFRISKIGYRFLYIPEAKVWHHRRGNLKSF 220
                                       3333333555543778887769**********99******************************************* PP

                   Glyco_tranf_2_3 221 ikqrnR 226
                                        kq++ 
  gi|298676147|ref|YP_003727896.1| 221 SKQMFK 226
                                       ***985 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   2.6   2.9e-14   7.3e-11       4     237 ..       8     236 ..       5     245 .. 0.69

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 2.9e-14
                   Glyco_tranf_2_2   4 iplraseerhyieerv..lqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGas 78 
                                       i +++ +e++yi e +  l++ +y  + +e+++vd+ S++++ + v++    nll+  ++        a arN+G++
  gi|298676147|ref|YP_003727896.1|   8 IVVGTRNEEKYIAECInsLLNLNYPKDSFEILIVDGMSTDNTQNIVKNY-PVNLLIN-EK-----INVASARNLGIK 77 
                                       77788888889*****97777777799**************99999986.5788887.33.....479********* PP

                   Glyco_tranf_2_2  79 kaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdl.nkedsevlkdvedltassrvledllaak 154
                                       ++++dl+ F D+Dc +    ++ ++      ++++ ++        +l +++d  + + v+++    +      a  
  gi|298676147|ref|YP_003727896.1|  78 HSQGDLIAFTDGDCKVNNLWLKTLVY-----EIQNAPEDVACVGGPNLvIDNDPIFARVVGYVQETFLSS-GGSAQC 148
                                       **************998777766666.....788887655555544441555555555555543322222.222222 PP

                   Glyco_tranf_2_2 155 stlvk.ffapss..ssilinrraflevGGyDErfrGhgaEDfdlllRlaka.ikslekmpvellykarakslsnykG 227
                                        ++ k  +++s    ++l ++  + +vG +DE f  +   D dl  R+ k  +++l   p    ++ r ++l++++ 
  gi|298676147|ref|YP_003727896.1| 149 HSYSKkQYVQSIpnCNALYKKSIIRNVGFFDEYF--KVGQDGDLNFRISKIgYRFL-YIPEAKVWHHRRGNLKSFSK 222
                                       23332233333223578999999999********..88899999999998725555.66666666899999987753 PP

                   Glyco_tranf_2_2 228 ....frrflealak 237
                                           + +++ +l k
  gi|298676147|ref|YP_003727896.1| 223 qmfkYGSWMAELFK 236
                                       22114466666655 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 !   36.8   0.1   1.5e-12   3.8e-09       2     193 ..      84     282 ..      83     309 .. 0.74

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.5e-12
                   Glyco_trans_2_3   2 illlDaDtvlppdclreiaaela.sp.evaivqgpvlvmnvanwleelaalf...faedhgkdilvrealgr..vvp 71 
                                       i++ D D  ++   l+ +++e++  p +va v gp lv  + ++++++  +    f ++ g +    +++++  v +
  gi|298676147|ref|YP_003727896.1|  84 IAFTDGDCKVNNLWLKTLVYEIQnAPeDVACVGGPNLVIDNDPIFARVVGYVqetF-LSSGGSAQCHSYSKKqyVQS 159
                                       77889999999999********955669*******999777899999999887754.33333444444555544889 PP

                   Glyco_trans_2_3  72 svGsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc.ele 147
                                       ++  +a+   s ++ vg++d   + v+ D d+ +r+ + Gyr+ ++pe+ v+ + + +l+ + +Q+ ++     el+
  gi|298676147|ref|YP_003727896.1| 160 IPNCNALYKKSIIRNVGFFD-EYFKVGQDGDLNFRISKIGYRFLYIPEAKVWHHRRGNLKSFSKQMFKYGSWMaELF 235
                                       9*******************.679********************************************865543556 PP

                   Glyco_trans_2_3 148 klillvrllgylgsllwsalplhlallllfsllalalvl.lllllla 193
                                       k+++ ++++  l  +++  ++l  +++ + +l+ l+ ++ ll+++ +
  gi|298676147|ref|YP_003727896.1| 236 KKHRDLVRWYALIPPIAILFSLVSIISSIVNLNLLYIFIcLLFTYII 282
                                       66665555544444444444443344444443332222212222222 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 !   19.6   0.0   3.8e-07   0.00097       1      41 [.      13      57 ..      13      91 .. 0.81
   2 ?    1.7   0.1      0.14   3.6e+02      41      76 ..     205     246 ..     198     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.8e-07
                   Glyco_tranf_2_4  1 rneadiLpeflahhlalgf..dr..ilvydndstDgtrailkelp 41
                                      rne++++ e++  +l+l +  d   il++d +stD+t +i+k++p
  gi|298676147|ref|YP_003727896.1| 13 RNEEKYIAECINSLLNLNYpkDSfeILIVDGMSTDNTQNIVKNYP 57
                                      8*****************7553244*****************975 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
                   Glyco_tranf_2_4  41 pevkllhvd....ksyederrq.vellkallaryaea.dwvl 76 
                                       pe+k++h++    ks++++ ++  +++ +l++++++  +w +
  gi|298676147|ref|YP_003727896.1| 205 PEAKVWHHRrgnlKSFSKQMFKyGSWMAELFKKHRDLvRWYA 246
                                       678999999888888888999944699999999988548875 PP

>> Anp1  Anp1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.1e-05     0.054      25      79 ..       8      60 ..       4      90 .. 0.83
   2 ?   -4.0   0.0         3   7.6e+03     170     191 ..     208     231 ..     207     234 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                              Anp1 25 iltplrdaekflpeyfenllkltyphelidLaflvsdtsegdktlealeeelkkl 79
                                      i++  r++ek++ e ++ ll+l+yp++ +++ ++ + ++  d+t++ ++++  +l
  gi|298676147|ref|YP_003727896.1|  8 IVVGTRNEEKYIAECINSLLNLNYPKDSFEILIVDGMST--DNTQNIVKNYPVNL 60
                                      88899************************9955555555..99999988876555 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3
                              Anp1 170 nvlrklpdelek..eqpYDlnsWv 191
                                       +v+ ++  +l++  +q + + sW+
  gi|298676147|ref|YP_003727896.1| 208 KVWHHRRGNLKSfsKQMFKYGSWM 231
                                       678877766664558999999997 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.2   0.00017      0.43     358     441 ..     218     300 ..     177     304 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00017
                           DUF2207 358 kkwksavkk..kergyfdkkgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivlllfsr 432
                                       k++ +   +  k+  ++ +  kk++  ++ ++l+  i++l+ ++ ++ ++v l+ ++ +++l++  i++i+l  +++
  gi|298676147|ref|YP_003727896.1| 218 KSFSK---QmfKYGSWMAELFKKHRDLVRWYALIPPIAILFSLVSIISSIVNLNLLYIFICLLFTYIILILLTALKI 291
                                       33333...244477788888888887777777777777777777777777766777777777777777777777777 PP

                           DUF2207 433 llgrrteeG 441
                                        ++  + +G
  gi|298676147|ref|YP_003727896.1| 292 SFKMKSVYG 300
                                       777666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1077  (0.0600703); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.36s 00:00:00.78 Elapsed: 00:00:00.73
# Mc/sec: 1337.92
//
Query:       gi|298676148|ref|YP_003727897.1|  [L=453]
Description: capsular polysaccharide biosynthesis protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0015   17.2   0.0     0.0021   16.8   0.0    1.2  1  AMP-binding  AMP-binding enzyme
  ------ inclusion threshold ------
      0.025   14.5   0.1      0.051   13.5   0.1    1.5  1  RNaseH_like  Ribonuclease H-like


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 !   16.8   0.0   2.3e-07    0.0021     219     369 ..     173     310 ..      41     316 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.3e-07
                                       HHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS CS
                       AMP-binding 219 lelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllgge 293
                                       + l+l ll+  +++ +  +++ +  ++ ++ i+k+k+ vi+g  + l al +     +  ++ +dl+ l+ +++  e
  gi|298676148|ref|YP_003727897.1| 173 AKLYLKLLRQKRLGTFGANDKiF--QRYVNIIKKFKPKVIYGYSSSLYALSKyL---Y-RYNINDLN-LKSIISDSE 242
                                       55666666666666666555533..47889********************8833...2.24455766.9999***** PP

                                       -EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEE CS
                       AMP-binding 294 plspellrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellv 369
                                        l p+  + +++ f ++v++ YG  E+t +     +ee+    g +  +  +v ++ +D + g++v +g+ G+++v
  gi|298676148|ref|YP_003727897.1| 243 TLYPHYRKMIEKQFNCKVYDHYGSKEATYAQE---CEEH---DG-YHIAAENVFLEFLDSN-GKRVNEGNFGKIFV 310
                                       ****************************8752...3333...22.4456668888888988.88888898898887 PP

>> RNaseH_like  Ribonuclease H-like
   #    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      55     118 ..     384     450 ..     353     452 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-06
                       RNaseH_like  55 kke.rkikslrekiflEtslslevaskleelllea..kkkkaelkleihiDiGengktkelikevvg 118
                                       + + + i++l  ki+ E ++  e+ +++++ l+e+  ++  +++++  +iD+ e+gk + +i++v++
  gi|298676148|ref|YP_003727897.1| 384 QIVqNSINELDIKIVPEENYNDEITKQIKNSLKEYfdEDCVIKFNFVEDIDVPESGKHRFIISNVID 450
                                       333489************************999994344557788888***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.42s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2510.13
//
Query:       gi|298676149|ref|YP_003727898.1|  [L=359]
Description: glycosyl transferase group 1 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-33  115.9   0.6    2.5e-33  115.0   0.6    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    6.4e-29  101.1   0.0    1.9e-28   99.6   0.0    1.7  2  Glyco_trans_1_4  Glycosyl transferases group 1
    8.1e-10   39.0   0.1    1.7e-09   37.9   0.1    1.6  1  Glyco_transf_4   Glycosyltransferase Family 4
    9.9e-08   32.3   0.0    2.2e-07   31.2   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
     0.0022   18.5   0.0     0.0032   17.9   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.0   0.6     7e-37   2.5e-33      17     170 ..     181     335 ..     169     337 .. 0.96

  Alignments for each domain:
  == domain 1  score: 115.0 bits;  conditional E-value: 7e-37
                                       EEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES...STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHH CS
                   Glycos_transf_1  17 iilsvgrlekeKgvdllikafallkkqlnpnvklviaG..ngeeekelkklaeelelsdnviflgevsredleellk 91 
                                        + +vgrlek Kg+  l+ a++++  +  + v++v++G  +++++ ++ +  +++++ +nv+++g +s+ ++ + l+
  gi|298676149|ref|YP_003727898.1| 181 NVTFVGRLEKSKGIYELLNAIPHVLNK-YKYVNFVLVGpyEKKDFIRINSFLKQHNICNNVFLTGPISKLKVYQELS 256
                                       578*********************988.************999********************************** PP

                                       CESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHH CS
                   Glycos_transf_1  92 nadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgen 168
                                       +++ifvlps+ E+f+i++lEAm +glp+ia+ +g ++e+v+++ +G+l+k+n+  ++a++i  l+e+eelr ++ +n
  gi|298676149|ref|YP_003727898.1| 257 KSKIFVLPSHVEAFPISILEAMGIGLPIIATPIGDVPEIVENNINGFLIKENDFLDMANKIMYLIENEELRLKMVNN 333
                                       **************************************************************************999 PP

                                       HH CS
                   Glycos_transf_1 169 ar 170
                                         
  gi|298676149|ref|YP_003727898.1| 334 NL 335
                                       75 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 ?   -1.6   0.0      0.94   3.4e+03       4      50 ..       7      55 ..       5      64 .. 0.62
   2 !   99.6   0.0   5.2e-32   1.9e-28       3     134 .]     181     323 ..     179     323 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.94
                                      EEEES---GG.GTHHHHHHHH.HHHH.HHEEEEEES---...HHHHHHH CS
                   Glyco_trans_1_4  4 ilfvGrleenvkgvdllleav.pllrkkdvrlvivGdgp.rpeeleela 50
                                      il +G   +++ g+  ++e+v +  +k++++l+ +  +  ++++l+e +
  gi|298676149|ref|YP_003727898.1|  7 ILILGPTPPPYGGIATFVEEVlKSNLKNEYNLLHINTNRnNSKSLKENI 55
                                      7778877558889999999997665545576665554433445565544 PP

  == domain 2  score: 99.6 bits;  conditional E-value: 5.2e-32
                                       EEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---.......HHHHHHHT..T-T.TEEEE---TH..HHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgprp.....eeleelaa..gleerveftGfved..lae 68 
                                       ++ fvGrl e+ kg+  ll+a+p++++k + v++v+vG  +++     +   + ++  ++ ++v +tG +++  + +
  gi|298676149|ref|YP_003727898.1| 181 NVTFVGRL-EKSKGIYELLNAIPHVLNKyKyVNFVLVGPYEKKdfiriN---SFLKqhNICNNVFLTGPISKlkVYQ 253
                                       689*****.667**************99658*******66533353332...3332457889********5445999 PP

                                       HHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  69 llaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                        l+++++fv+Ps  e f++++lEam  glp++at++g ++e+v  + ng+l++++d  ++a++i  L+e+
  gi|298676149|ref|YP_003727898.1| 254 ELSKSKIFVLPShvEAFPISILEAMGIGLPIIATPIGDVPEIVenNINGFLIKENDFLDMANKIMYLIEN 323
                                       9***********************************99*****9889********************986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.1   4.6e-13   1.7e-09      53     169 ..      54     168 ..      17     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 4.6e-13
                    Glyco_transf_4  53 rllrslaflrrlrrllkrekpDvvHah..spaalg...aallalrr.rlgiplVltvHglyekrllkarlkplsrll 123
                                       +    l+  ++l  ll   +p +vH+h  s+ +++   + ++      +  ++V+++Hg +      +++  ++ l+
  gi|298676149|ref|YP_003727898.1|  54 NINVFLRVTFQLLYLLSYKRPKLVHIHasSYLSFWektFFAFI--SkLYLRKVVYHIHGGA------FKQFYEQSLF 122
                                       4555677788999999999*****8883234444332222222..245999**********......5666677889 PP

                    Glyco_transf_4 124 ralerrllrradrviavSeatadelrerygvppekitVipnGvDle 169
                                       +++ r+ +   d +i+ S+  +++l+e     +eki V+ n vDl+
  gi|298676149|ref|YP_003727898.1| 123 KKIIRFCFYFFDGIIVLSDNWKNYLHEQNLTYKEKIFVVNNFVDLN 168
                                       9999999999*****************666777***********96 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   6.2e-11   2.2e-07       2      83 ..     261     344 ..     260     351 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 6.2e-11
                   Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarer 76 
                                       ++ ps+ e +   ++Ea++ G +++++++ +++e+++++  ++l++  d  ++a ki yl++n+e+r ++ +++ ++
  gi|298676149|ref|YP_003727898.1| 261 FVLPSHVEAFPISILEAMGIGLPIIATPIGDVPEIVENNINGFLIKenDFLDMANKIMYLIENEELRLKMVNNNLKK 337
                                       6778999999999*********************************9****************************99 PP

                   Glyco_trans_1_2  77 vlaehty 83 
                                       + ++++ 
  gi|298676149|ref|YP_003727898.1| 338 FNEKYNI 344
                                       9988875 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     9e-07    0.0032      57     159 ..      59     163 ..      36     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9e-07
                   Glyco_trans_4_4  57 laalralrrllrqrrerpdvvhahs.ptag.....laarlarrrrgiplvvtlhglllrrgsgavrrlyralerrll 127
                                       l+ +++l  ll     rp +vh+h  ++++     ++a + +     ++v+++hg ++ +    +++l++ + r+++
  gi|298676149|ref|YP_003727898.1|  59 LRVTFQLLYLL--SYKRPKLVHIHAsSYLSfwektFFAFISK-LYLRKVVYHIHGGAFKQ--FYEQSLFKKIIRFCF 130
                                       56677777777..889********955544123335555556.778899******99974..67899********** PP

                   Glyco_trans_4_4 128 rradavlvvseaeaeelralg.vpadrvvvvpn 159
                                         +d+++v+s+ +  +l++++    +++ vv n
  gi|298676149|ref|YP_003727898.1| 131 YFFDGIIVLSDNWKNYLHEQNlTYKEKIFVVNN 163
                                       *******************66367778877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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: 0.57u 0.44s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2020.98
//
Query:       gi|298676150|ref|YP_003727899.1|  [L=397]
Description: glycosyl transferase group 1 [Methanohalobium evestigatum Z-7303]
Scores for complete 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-36  125.7   0.2    2.8e-35  121.4   0.2    2.4  1  Glycos_transf_1  Glycosyl transferases group 1
    3.6e-24   85.7   0.0    6.4e-24   84.9   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.2e-12   47.3   0.0    3.2e-12   46.8   0.0    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
     0.0013   19.1   0.0     0.0051   17.2   0.0    2.0  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.02   14.9   0.1      0.052   13.5   0.1    1.8  1  DUF4649          Domain of unknown function (DUF4649)
      0.038   14.2   0.6       0.14   12.4   0.6    2.0  1  DUF1359          Protein of unknown function (DUF1359)
       0.12   12.8   0.0       0.17   12.3   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.4   0.2   1.1e-38   2.8e-35      14     167 ..     200     374 ..     190     379 .. 0.92

  Alignments for each domain:
  == domain 1  score: 121.4 bits;  conditional E-value: 1.1e-38
                                       T-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHH CS
                   Glycos_transf_1  14 kkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleell 90 
                                       + ++i+ vgrl+ +Kg+++likaf ++k++  +n+klv+ G ge e+elk+lae++ l+++++f g+++  +  +++
  gi|298676150|ref|YP_003727899.1| 200 ESPVIINVGRLVDVKGQNHLIKAFSKVKDE-VDNAKLVFLGRGELENELKELAEKYRLENDIFFMGFQK--NPFKFI 273
                                       5799***********************997.**************************************..9***** PP

                                       HCESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTT........................SEEEE-T CS
                   Glycos_transf_1  91 knadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdge........................tGllvkp 142
                                       kn+++fvl+s++Egf+ +++E+ma+g+p+i+++  +gp+e++++                          + l  k+
  gi|298676150|ref|YP_003727899.1| 274 KNSSVFVLSSTNEGFPNAIVESMACGIPIISTDcFSGPREILAPDTdinyqtnvveyapygiltpvcndgDRLSLKN 350
                                       *******************************************9999999999999999999988888766666665 PP

                                       T-HHHHHHHHHHHHHSHHHHHHHHH CS
                   Glycos_transf_1 143 nnaealaeairklledeelrerlge 167
                                       +   +l++ai+++l+++el e++g 
  gi|298676150|ref|YP_003727899.1| 351 E-ENMLSDAINQILKNDELKEKYGL 374
                                       5.89999999999999999988775 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 !   84.9   0.0   2.5e-27   6.4e-24       2     110 ..     202     317 ..     201     365 .. 0.89

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 2.5e-27
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHHT..T-T.TEEEE---THHHHHHHH- CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleelaa..gleerveftGfvedlaellaaa 73 
                                       pvi+ vGrl+  vkg+  l++a+ +++++ d ++lv+ G+g+ + +el+ela+  +le+++ f+Gf ++  ++++++
  gi|298676150|ref|YP_003727899.1| 202 PVIINVGRLV-DVKGQNHLIKAFSKVKDEvDnAKLVFLGRGElE-NELKELAEkyRLENDIFFMGFQKNPFKFIKNS 276
                                       89*******5.67**************99856*********955.699999976999999***************** PP

                                       SEEEE--..---SHHHHHHHHTT-EEEE-TGG.GTTT--.T CS
                   Glyco_trans_1_4  74 dvfvaPs..egfglkllEamaaglpvVatdvg.giaevv.g 110
                                       +vfv+ s  egf+++++E+ma+g+p+++td+  g++e++  
  gi|298676150|ref|YP_003727899.1| 277 SVFVLSStnEGFPNAIVESMACGIPIISTDCFsGPREILaP 317
                                       ********99*********************6598997652 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   1.3e-15   3.2e-12       2     169 ..      15     181 ..      14     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.3e-15
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeev....elvvrvprvplpllkrllrslaflr...rlrrllkre 71 
                                       GG+e +v +L+ +L+++ +++ + + ++d+  ++      +l +++p +   l++ + r ++f++   + +++ k++
  gi|298676150|ref|YP_003727899.1|  15 GGAEKVVSNLSINLPDK-YKIKLMVYHTDQIDYQYNgeiiDLNISIPEPDKSLKNMFIRVFTFFSliqKSKNIKKQY 90 
                                       9***************9.99998877777766666656787777777777778888888777755111556677777 PP

                    Glyco_transf_4  72 kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadel 148
                                       +p    +   a+ ++ l+     l   ++++vH+       ++ ++++ ++ + l + ++++a  +iavS+ ++++l
  gi|298676150|ref|YP_003727899.1|  91 EPQATISFLTAPNILNLFSK---LSDNVIISVHSQI----SQGLKGLEGKIHKQLIKLFYNHAYLIIAVSKGVKKDL 160
                                       99999888888887776654...578**********....68999999***************************** PP

                    Glyco_transf_4 149 rerygvppekitVipnGvDle 169
                                       + +++++peki Vi+n+  ++
  gi|298676150|ref|YP_003727899.1| 161 VNNFRIKPEKIKVIHNPYETD 181
                                       *****************9998 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 !   17.2   0.0     2e-06    0.0051       5      79 ..     282     381 ..     277     394 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2e-06
                   Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltdda.egleelftpgk.........................evilfedleelaek 55 
                                        s +e++   ++E +acG++++++d  +g++e++ p++                          + l  +++ l ++
  gi|298676150|ref|YP_003727899.1| 282 SSTNEGFPNAIVESMACGIPIISTDCfSGPREILAPDTdinyqtnvveyapygiltpvcndgdRLSLKNEENMLSDA 358
                                       556677888899************99************999999999999999999999988555555588888899 PP

                   Glyco_trans_1_2  56 iryllanpeerraiaeaarervla 79 
                                       i++ l+n+e+ ++ +  a++r  +
  gi|298676150|ref|YP_003727899.1| 359 INQILKNDELKEKYGLLAQKR-AE 381
                                       999999999988888888887.44 PP

>> DUF4649  Domain of unknown function (DUF4649)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1     2e-05     0.052      31      58 ..      26      55 ..      14      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                           DUF4649 31 vtvpDsypvtkltykgkkldYq..Gtygdl 58
                                      +++pD y+++ ++y   ++dYq  G++ dl
  gi|298676150|ref|YP_003727899.1| 26 INLPDKYKIKLMVYHTDQIDYQynGEIIDL 55
                                      99*****************98633666555 PP

>> DUF1359  Protein of unknown function (DUF1359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.6   5.4e-05      0.14      22      82 ..     158     217 ..     148     234 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.4e-05
                           DUF1359  22 kdvihdvkdqtelvklleddlksneikkddkleleltdrfsvlkssvkinvGtlisllkdn 82 
                                       kd++ + + + e +k++ +  ++++i+k   +e+e      +++s v invG l+ +  +n
  gi|298676150|ref|YP_003727899.1| 158 KDLVNNFRIKPEKIKVIHNPYETDKIQKLADYEIEQE-YQDIFESPVIINVGRLVDVKGQN 217
                                       89999**************************999987.789**************988777 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 ?   12.3   0.0   6.7e-05      0.17      98     159 ..     114     176 ..      97     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-05
                   Glyco_trans_4_4  98 plvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeelra.lgvpadrvvvvpn 159
                                        +++++h+   ++ +g ++ + + l ++ +++a ++++vs ++ ++l+  + + ++++ v++n
  gi|298676150|ref|YP_003727899.1| 114 NVIISVHSQISQGLKGLEGKIHKQLIKLFYNHAYLIIAVSKGVKKDLVNnFRIKPEKIKVIHN 176
                                       57888998877777999999999999***********************888**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 2211.66
//
Query:       gi|298676151|ref|YP_003727900.1|  [L=618]
Description: hypothetical protein Metev_2288 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        9.9    6.1   5.8        0.9    9.4   0.3    2.1  2  Tmemb_9   TMEM9


Domain annotation for each model (and alignments):
>> Tmemb_9  TMEM9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.1   1.0         1   1.8e+04      54      68 ..     296     310 ..     292     316 .. 0.58
   2 ?    9.4   0.3     5e-05       0.9      43      86 ..     448     492 ..     444     513 .. 0.77

  Alignments for each domain:
  == domain 1  score: -5.1 bits;  conditional E-value: 1
                           Tmemb_9  54 viivivvislLviYm 68 
                                       v+i+ +v s+ + Y+
  gi|298676151|ref|YP_003727900.1| 296 VLIIFIVFSMWSSYL 310
                                       455555555555555 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 5e-05
                           Tmemb_9  43 esRntttikvvviivivvi.slLviYmlflllldpllnkrkkkas 86 
                                       ++ nt+ i ++++ +i ++ s+L+iY l+l  l   +n++ ++a+
  gi|298676151|ref|YP_003727900.1| 448 KKINTKQISCILLCIILILfSILSIYSLYLSPLTKTVNSQVTEAQ 492
                                       5679999*99998877765379********999999999855554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1245  (0.0694406); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.75u 0.96s 00:00:01.71 Elapsed: 00:00:00.98
# Mc/sec: 1903.90
//
Query:       gi|298676152|ref|YP_003727901.1|  [L=301]
Description: glycosyl transferase family 2 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-41  142.0   0.1    2.4e-41  141.4   0.1    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    1.2e-19   71.1   0.0    1.9e-19   70.5   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    2.6e-19   69.8   2.8    3.4e-19   69.4   2.8    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.014   15.8   0.1      0.035   14.6   0.1    1.7  1  Glyco_tranf_2_4  Glycosyl transferase family 2
      0.039   14.1   0.0      0.082   13.1   0.0    1.6  1  TPR_2            Tetratricopeptide repeat
       0.04   13.5   0.0      0.063   12.8   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
      0.041   13.7   0.0      0.094   12.6   0.0    1.6  1  TPR_1            Tetratricopeptide repeat
      0.088   12.8   0.1       0.23   11.4   0.1    1.8  1  Peptidase_S24    Peptidase S24-like


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 !  141.4   0.1   1.1e-44   2.4e-41       1     164 [.       5     163 ..       5     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 1.1e-44
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       sv+iptyN+++t+ +t++s+l+q +y+dfeii+vDD+S+D+t+ i++++++ d rv++i++++n+G   a+n+g+++
  gi|298676152|ref|YP_003727901.1|   5 SVIIPTYNRSQTVSKTIKSVLNQ-TYQDFEIIIVDDNSSDNTEFIIKSFSHFDSRVKYIKHNKNKGAPEARNTGIKN 80 
                                       8**********************.***************************************************** PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfe 154
                                       ++gdyi++lD+Dde+ p++lek v+ + k+ +d+ l +  + + +++ +        + +l+++ +++ +  ++ ++
  gi|298676152|ref|YP_003727901.1|  81 SKGDYIALLDDDDEWFPQKLEKQVKLFAKESDDIGLIHCGYEKIDENGNILI----PKKKLKETGNMFYELLESNII 153
                                       *****************************87765444443333333333333....234555555555555555555 PP

                                       STCCCEEEEH CS
                   Glycos_transf_2 155 igsaallrre 164
                                        ++  l+r e
  gi|298676152|ref|YP_003727901.1| 154 GSPTNLIRSE 163
                                       5555555555 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 !   70.5   0.0   8.4e-23   1.9e-19       4     208 ..       4     200 ..       2     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 8.4e-23
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       ++v++pt+n+++++ +++ s+l+q+y ++e+++v+d+s++ t   ++ +   + d rv+++   +n   +g+ +a n
  gi|298676152|ref|YP_003727901.1|   4 VSVIIPTYNRSQTVSKTIKSVLNQTYQDFEIIIVDDNSSDNTEFIIKSF-SHF-DSRVKYIKHNKN---KGAPEARN 75 
                                       89***************************************99888874.445.55***9966554...689***** PP

                   Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqff..ltpkvgavg.tpvfllnrstlvsalgalefaerhlrflaarra 154
                                        ++++ k+d+++l+DdD+ + P  l++++ +f  +++++g +  + +  +   + + +  +l+ + + +++l+ ++ 
  gi|298676152|ref|YP_003727901.1|  76 TGIKNSKGDYIALLDDDDEWFPQKLEKQVKLFakESDDIGLIHcGYEKIDENGNILIPKKKLKETGNMFYELLESNI 152
                                       ********************************99999******66678898888888899999999999999999*9 PP

                   Glyco_tranf_2_3 155 lgvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaa 208
                                       +g +t      lir e++k ++  d +     D++l+ r+ ++ +++ y p+ +
  gi|298676152|ref|YP_003727901.1| 153 IGSPT-----NLIRSECFKKIGYCDVQLKSCQDWDLWIRISKH-YKINYIPEIL 200
                                       99997.....9***********9***77777********9987.6777777665 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 !   69.4   2.8   1.5e-22   3.4e-19       1     250 [.       5     236 ..       5     267 .. 0.79

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 1.5e-22
                   Glyco_tranf_2_2   1 svviplraseerhyieerv...lqkakyydeeielivvddgSsekfleevssiidlnllv.ylkdeddkayslaaar 73 
                                       sv+ip ++  ++  +  ++   l+++ +   ++e+i+vdd Ss+++   ++s+ +   +v y+k++  k  +   ar
  gi|298676152|ref|YP_003727901.1|   5 SVIIPTYNRSQT--VSKTIksvLNQTYQ---DFEIIIVDDNSSDNTEFIIKSFSHFDSRVkYIKHN--KNKGAPEAR 74 
                                       89*********9..99999554555555...9****************************888888..6668999** PP

                   Glyco_tranf_2_2  74 NrGaskaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledl 150
                                       N G++++++d++  lD D+ + + k+ek++k    +  +e  d  ++   ++ ++e+ ++l   + l   +++  +l
  gi|298676152|ref|YP_003727901.1|  75 NTGIKNSKGDYIALLDDDDEWFPQKLEKQVK----LFAKESDDIGLIHCGYEKIDENGNILIPKKKLKETGNMFYEL 147
                                       *******************************....5568889999******************99999999999888 PP

                   Glyco_tranf_2_2 151 laakstlvkffapssssilinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellykarakslsnykG 227
                                       l         ++  s + li+ + f ++G  D ++  ++  D+dl +R+ k++k    +     y+ +  s+s  k 
  gi|298676152|ref|YP_003727901.1| 148 LE------SNIIG-SPTNLIRSECFKKIGYCDVQL--KSCQDWDLWIRISKHYKINYIPEILARYNVSDVSIS--KN 213
                                       87......55554.56679****************..9***************97744444445666666666..44 PP

                   Glyco_tranf_2_2 228 frrflealakeaaalglvvfhlY 250
                                         + l+   +    + l++ +  
  gi|298676152|ref|YP_003727901.1| 214 IDSVLSGHKQILDKYFLYICKNN 236
                                       44444444444444444444444 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 ?   14.6   0.1   1.6e-05     0.035      14      81 ..      24      92 ..      11     105 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                   Glyco_tranf_2_4 14 hlalgfd..rilvydndstDgtrailkelpevkllhvdksy...ederrqvellkallaryaeadwvlvvDaD 81
                                       l+  ++  +i+++d++s+D+t  i+k+    ++++++ +y   ++ + + e++++ +++ +++d+++ +D D
  gi|298676152|ref|YP_003727901.1| 24 VLNQTYQdfEIIIVDDNSSDNTEFIIKSF---SHFDSRVKYikhNKNKGAPEARNTGIKN-SKGDYIALLDDD 92
                                      4444443125*****************94...4555554443211223346788887766.589999999977 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.7e-05     0.082       7      33 ..     246     272 ..     243     273 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.7e-05
                             TPR_2   7 lGlayyklgdyeeAleafekAleldPn 33 
                                       +Gl+y+++gdy + l+++  ++ ++P 
  gi|298676152|ref|YP_003727901.1| 246 IGLLYLHKGDYSKSLKYLTLSIHYNPL 272
                                       79*****************99999996 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.8e-05     0.063      25     143 ..       8     125 ..       5     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.8e-05
                                       SEETTETETTHHHHHHHHHTT-SEE.EEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTHHHHTTS CS
                   NTP_transferase  25 vpvlgkerliqatlsrlansgieei.ivvltqehsflveeqlkegskfgvevlialepegkgtAdAvalaaellede 100
                                       +p ++ +  + +t++ ++n+ +++  i+++ ++ s   e  +k+ s+f+ +v+++  +++kg+ +A   +++  + +
  gi|298676152|ref|YP_003727901.1|   8 IPTYNRSQTVSKTIKSVLNQTYQDFeIIIVDDNSSDNTEFIIKSFSHFDSRVKYIKHNKNKGAPEARNTGIKNSKGD 84 
                                       678888899999*******99999735666666778889999************************99998888887 PP

                                       SE..EEEEETTEEEESTTHHHHHHHHHTHSSTT.SEEEEEEESS CS
                   NTP_transferase 101 ksdelvlvLggDhlikdayeeavkkaiekaakg.tvtfgivpve 143
                                       +   ++l   +D ++ +++e+ vk +++++ ++ ++ +g ++ +
  gi|298676152|ref|YP_003727901.1|  85 Y---IALLDDDDEWFPQKLEKQVKLFAKESDDIgLIHCGYEKID 125
                                       7...566667889*******************999999987655 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.2e-05     0.094       7      32 ..     246     271 ..     243     273 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   7 lGnayfklgkydeAleyyekALelnP 32 
                                       +G++y+++g+y + l+y    +  nP
  gi|298676152|ref|YP_003727901.1| 246 IGLLYLHKGDYSKSLKYLTLSIHYNP 271
                                       8****************999988888 PP

>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1    0.0001      0.23       9      57 ..      27     118 ..      22     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                                       CTXXTTXEEEEECTS.....................................---TTSEEEEEETTCE......-EE CS
                     Peptidase_S24   9 ptlldGdlilVdkfs.....................................epkrGdivvfrlpgee......eay 42 
                                        t++d ++i+Vd +s                                     +  +Gd+++  ++++e      e  
  gi|298676152|ref|YP_003727901.1|  27 QTYQDFEIIIVDDNSsdntefiiksfshfdsrvkyikhnknkgapearntgiKNSKGDYIALLDDDDEwfpqklEKQ 103
                                       69**********999999**********************************************99999**999999 PP

                                       EEEEEEETTEEEEE. CS
                     Peptidase_S24  43 iKrviglpgdrvlla 57 
                                       +K + ++ +d+ l++
  gi|298676152|ref|YP_003727901.1| 104 VKLFAKESDDIGLIH 118
                                       99999****998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1768.71
//
Query:       gi|298676153|ref|YP_003727902.1|  [L=417]
Description: glycosyl transferase group 1 [Methanohalobium evestigatum Z-7303]
Scores for complete 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-40  138.4   0.0    3.6e-40  137.3   0.0    1.5  1  Glycos_transf_1  Glycosyl transferases group 1
    2.7e-30  105.5   0.0    4.4e-30  104.9   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.2e-15   57.0   0.0    1.8e-13   50.8   0.0    2.8  2  Glyco_transf_4   Glycosyltransferase Family 4
    4.9e-10   39.6   1.0    2.2e-07   31.0   1.0    2.5  1  Glyco_trans_4_2  Glycosyl transferase 4-like
    1.2e-06   28.8   0.0    3.1e-06   27.5   0.0    1.7  1  Glyco_trans_1_2  Glycosyl transferases group 1
     0.0026   18.2   0.0       0.04   14.4   0.0    2.5  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
      0.051   13.2   0.1        0.1   12.3   0.1    1.5  1  Glyco_transf_5   Starch synthase catalytic domain
      0.085   11.7   0.0       0.18   10.6   0.0    1.5  2  Trp_syntA        Tryptophan synthase alpha chain


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 !  137.3   0.0   1.6e-43   3.6e-40      14     171 ..     229     391 ..     219     392 .. 0.97

  Alignments for each domain:
  == domain 1  score: 137.3 bits;  conditional E-value: 1.6e-43
                                       T-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHH CS
                   Glycos_transf_1  14 kkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleell 90 
                                       k+  +lsvgrl+++Kg++++i+a+ ++ k+  +nv ++i+G+g+  ++l+kl+ +l+++++v++lg ++++ l +++
  gi|298676153|ref|YP_003727902.1| 229 KPIKLLSVGRLVEKKGHEYAIEAMYEVLKR-YQNVEYLIVGDGPLYNYLQKLISKLNIENHVKLLGSIDDKSLFQVY 304
                                       78899***********************98.********************************************** PP

                                       HCESEEEEEESS......BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHH CS
                   Glycos_transf_1  91 knadifvlpsis......EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeel 161
                                       ++++ifv+ps +      Eg G+vl EA a+glpvi++ + g++e v dg +G+lv++++++ala++++ l+e++ l
  gi|298676153|ref|YP_003727902.1| 305 QKSHIFVFPSVTskegdkEGQGLVLQEAQAVGLPVISTFHNGIPEGVIDGISGFLVPEKDVDALADKMEYLIENPFL 381
                                       ***************************************************************************** PP

                                       HHHHHHHHHH CS
                   Glycos_transf_1 162 rerlgenark 171
                                         ++g+n+rk
  gi|298676153|ref|YP_003727902.1| 382 WSHMGYNGRK 391
                                       ********98 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 !  104.9   0.0   1.9e-33   4.4e-30       3     134 .]     232     378 ..     230     378 .. 0.90

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 1.9e-33
                                       EEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHHT..T-T.TEEEE---TH..HHHHHHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleelaa..gleerveftGfved..laellaa 72 
                                       ++l vGrl+e+ kg+++ +ea+ +++k+ + v+ +ivGdgp  +  l++l++  ++e++v+++G ++d  l +++++
  gi|298676153|ref|YP_003727902.1| 232 KLLSVGRLVEK-KGHEYAIEAMYEVLKRyQnVEYLIVGDGPlYN-YLQKLISklNIENHVKLLGSIDDksLFQVYQK 306
                                       6899****665.**********888888636**********775.99998865899999*******5567******* PP

                                       -SEEEE--........---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  73 advfvaPs........egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                       +++fv+Ps        eg gl+l Ea a+glpv++t   gi+e v  g +g+lvp++d++ala++++ L+e+
  gi|298676153|ref|YP_003727902.1| 307 SHIFVFPSvtskegdkEGQGLVLQEAQAVGLPVISTFHNGIPEGVidGISGFLVPEKDVDALADKMEYLIEN 378
                                       **********9987777*******************999**9977799*********************986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   8.1e-17   1.8e-13       5     168 ..      23     215 ..      22     217 .. 0.89
   2 ?    2.3   0.0     0.067   1.5e+02      94     108 ..     334     348 ..     325     383 .. 0.76

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 8.1e-17
                    Glyco_transf_4   5 erhvleLaraLarrGheVtvvtpgddgpleeev.....................................elvvrvp 44 
                                       e+++l+ + +L ++Gh+V +++++++ +   ++                                       v  ++
  gi|298676153|ref|YP_003727902.1|  23 ETFILNQITGLLDNGHDVKIFASSHPNENIVHEdikkynlmsrvhylnlpknfifrflkgitlivfnlykNPVLIIR 99 
                                       899******************98888887777789*******************************99998889999 PP

                    Glyco_transf_4  45 rvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrr.rlgiplVltvHglyekrllkarlkpls 120
                                       + ++++++++ +sl +l    + l ++++D++H+h+ + ++++ ++l+    ++++++++Hg +       ++ p++
  gi|298676153|ref|YP_003727902.1| 100 SLNIFKFGKFALSLKMLYITINFLNKNEFDIIHCHFGPNGILG-VYLKEiGVNAKYITSFHGYD------VNKYPKK 169
                                       999999999******9999****************96666555.5666679*************......4444554 PP

                    Glyco_transf_4 121 rllralerrllrradrviavSeatadelrerygvppekitVipnGvDl 168
                                        +  +++++l+   d +++++e+t++++++ +g++++k++++p G ++
  gi|298676153|ref|YP_003727902.1| 170 -YGCNVYNKLFEEGDLFTVNTEYTKNQVKK-LGCNENKLVTLPVGLNI 215
                                       .4445688899*******************.************99875 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.067
                    Glyco_transf_4  94 rlgiplVltvHglye 108
                                       + g+p++ t+H+  +
  gi|298676153|ref|YP_003727902.1| 334 AVGLPVISTFHNGIP 348
                                       3699********997 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   1.0   9.8e-11   2.2e-07       1     118 [.      10     170 ..      10     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 9.8e-11
                   Glyco_trans_4_2   1 killlanls....svhtlrlakeLakrgyeVhvitpkkgakdeleaegihvhrl.......kvd............. 53 
                                       ki++++n+     +++ l+ + +L ++g++V+++ +  +  ++ + e+i+ ++l       +++             
  gi|298676153|ref|YP_003727902.1|  10 KIAFIVNAFpklsETFILNQITGLLDNGHDVKIFASSHP-NENIVHEDIKKYNLmsrvhylNLPknfifrflkgitl 85 
                                       567777665555599********************9777.5556667777777755455553335577777777777 PP

                   Glyco_trans_4_2  54 ..................rkg.pley.lkafkl.kklikkikPDvvhahyakpygllgslaarlsgvipvvlsvwGl 109
                                                          k+ ++ + lk++ + ++ ++k+++D++h+h   p g+lg  ++ ++   ++++s++G 
  gi|298676153|ref|YP_003727902.1|  86 ivfnlyknpvliirslniFKFgKFALsLKMLYItINFLNKNEFDIIHCHF-GPNGILGVYLKEIGVNAKYITSFHGY 161
                                       777777777999766555444544442467888899*************9.6679********************** PP

                   Glyco_trans_4_2 110 dvlkfpkks 118
                                       dv k pkk 
  gi|298676153|ref|YP_003727902.1| 162 DVNKYPKKY 170
                                       **8888876 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 !   27.5   0.0   1.4e-09   3.1e-06       9      85 ..     323     401 ..     308     407 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.4e-09
                   Glyco_trans_1_2   9 espnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehty 83 
                                       e+  l+l Ea a G +++++   g++e + +g +++l+   d++ la+k++yl++np +++ ++ ++r++v+++++ 
  gi|298676153|ref|YP_003727902.1| 323 EGQGLVLQEAQAVGLPVISTFHNGIPEGVIDGISGFLVPekDVDALADKMEYLIENPFLWSHMGYNGRKFVEKNYDI 399
                                       67788999************88****************************************************987 PP

                   Glyco_trans_1_2  84 dh 85 
                                       ++
  gi|298676153|ref|YP_003727902.1| 400 NK 401
                                       75 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.8e-05      0.04       8     160 .]      27     212 ..      22     212 .. 0.59
   2 ?    0.5   0.0      0.34   7.6e+02      88     107 ..     329     347 ..     323     376 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                   Glyco_trans_4_4   8 aelaraLaarGheVtvltpapapg...........apeleedgvrvhrlpvprr.....pspladlaal........ 60 
                                        + + +L + Gh+V +++++ +++                    rvh l +p +      ++ +    +        
  gi|298676153|ref|YP_003727902.1|  27 LNQITGLLDNGHDVKIFASSHPNEnivhedikkynL------MSRVHYLNLPKNfifrfLKGITL---Ivfnlyknp 94 
                                       556667778888888888655555454433322220......22333333332211000211111...111122222 PP

                   Glyco_trans_4_4  61 .........ralrrl.............lrqrrerpdvvhahsptaglaarlar.rrrgiplvvtlhglllrrgsga 114
                                                + +  +             l   +  +d++h+h  + g++++ ++  + +++++ ++hg +++++   
  gi|298676153|ref|YP_003727902.1|  95 vliirslniFKFGKFalslkmlyitinfL--NKNEFDIIHCHFGPNGILGVYLKeIGVNAKYITSFHGYDVNKY--- 166
                                       22222223322211122222222222225..7999********99*****99997788**********999888... PP

                   Glyco_trans_4_4 115 vrrlyralerrllrradavlvvseaeaeelralgvpadrvvvvpng 160
                                        + +   +   l+   d+++v++e+   ++  lg   +++v++p g
  gi|298676153|ref|YP_003727902.1| 167 PKKYGCNVYNKLFEEGDLFTVNTEYTKNQVKKLGCNENKLVTLPVG 212
                                       334455577899999*******************999999999987 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.34
                   Glyco_trans_4_4  88 arlarrrrgiplvvtlhgll 107
                                          a+ + g+p++ t+h+  
  gi|298676153|ref|YP_003727902.1| 329 LQEAQ-AVGLPVISTFHNGI 347
                                       44455.89*********743 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 ?   12.3   0.1   4.5e-05       0.1     100     171 ..     103     160 ..      31     201 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.5e-05
                    Glyco_transf_5 100 lYgdkgedyednaerfalfsraalellek.l.gwkpdvihahDWhtalvpallkelykerglfkkiktvftiHN 171
                                       ++         +  +fa +s  +l +  + l ++++d+ih+h    ++++++lke+        ++k++ + H 
  gi|298676153|ref|YP_003727902.1| 103 IF---------KFGKFA-LSLKMLYITINfLnKNEFDIIHCHFGPNGILGVYLKEIGV------NAKYITSFHG 160
                                       33.........223333.33333333333243347********************974......4888888875 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.8   4.1e+03      13      40 ..      11      40 ..       7      40 .. 0.74
   2 ?   10.6   0.0   8.1e-05      0.18      84     168 ..     225     312 ..     209     325 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.8
                                      EEEEETTSS-HHHH..HHHHHHHHHCT-SS CS
                         Trp_syntA 13 vpyvtagdpdleqs..leilkalekagadv 40
                                      +++++  +p+l ++  l+ +++l ++g dv
  gi|298676153|ref|YP_003727902.1| 11 IAFIVNAFPKLSETfiLNQITGLLDNGHDV 40
                                      889999999987762357788888888775 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 8.1e-05
                                       HCSSS-EEEEE-CHHHCCC-HHHHCHHHHHC.....TEEEEEETTSBCCCHHHHHHHHHHTT-E.EEEEE-TTS-HH CS
                         Trp_syntA  84 kevevPivlltylnlvlsygeerflaelkea.....gvdglivpDlPleeaeelveaakkkgle.lvflvapttsde 154
                                        +++ Pi ll+   lv ++g+e+ ++++ e+     +v+ liv D Pl   ++l+++++k ++e  v l+   ++d+
  gi|298676153|ref|YP_003727902.1| 225 YDSRKPIKLLSVGRLVEKKGHEYAIEAMYEVlkryqNVEYLIVGDGPLY--NYLQKLISKLNIEnHVKLLGS-IDDK 298
                                       56789***********999999866666554333348**********96..6899********835888776.9*** PP

                                       HHHHHHHH--S-EE CS
                         Trp_syntA 155 rlkevveqaegfvY 168
                                        l +v ++++ fv+
  gi|298676153|ref|YP_003727902.1| 299 SLFQVYQKSHIFVF 312
                                       **********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.90s 00:00:01.47 Elapsed: 00:00:01.06
# Mc/sec: 1192.14
//
Query:       gi|298676154|ref|YP_003727903.1|  [L=483]
Description: multi antimicrobial extrusion protein MatE [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-19   70.3  17.4    1.5e-19   70.3  17.4    2.3  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    2.1e-18   66.7  26.8    2.1e-18   66.7  26.8    3.6  3  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    2.5e-15   56.6  28.8    2.5e-15   56.6  28.8    2.5  3  Polysacc_synt    Polysaccharide biosynthesis protein
    7.3e-09   34.7  43.2    7.3e-09   34.7  43.2    2.9  2  MurJ             Lipid II flippase MurJ
    1.8e-08   34.2   2.1    1.8e-08   34.2   2.1    4.5  4  MatE             MatE


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 !   70.3  17.4   4.2e-23   1.5e-19       7     283 ..      37     320 ..      31     324 .. 0.89
   2 ?   -1.6  11.2      0.33   1.2e+03      50     126 ..     365     433 ..     326     474 .. 0.50

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 4.2e-23
                   Polysacc_synt_3   7 spedFGvvaialvvislanlfvdmGlssal......iqkedlteedlstvftfnlvlgllialvlfllapliasfyn 77 
                                         +d+G+ a +++ ++l+  fv +Gl++a+      i+++++ +e + +   f l+++l i++++++++ +ias++ 
  gi|298676154|ref|YP_003727903.1|  37 PVQDYGIWAQIVITLGLVPEFVMLGLQRAMhrfvpsIKTKENLQELVYSFLIFVLFTSLTISILIYIFSGIIASALF 113
                                       579**************************8555555666666666677777888999*****************665 PP

                   Polysacc_synt_3  78 qpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllsl 154
                                       ++++  ++++l++ +++++l++  ++++r   + k  ++ +++ + + +++ ++ +l   g+   + g l+ss l +
  gi|298676154|ref|YP_003727903.1| 114 DNQI-LIVKILSIIVLIESLNAFLKNYFRATQQVKIHSILQFTKTSLKIFFVVLFVLNNGGIIGAISGLLISSSLVF 189
                                       5443.489*****************************************************************9999 PP

                   Polysacc_synt_3 155 vllwlaskwrprlkf.slkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaeits 230
                                        + +l++ +++++k+ s+ ++k+++++gl l+  +l ++++  +d  liG +l+++ +G+Y+ ++ l +++ +++  
  gi|298676154|ref|YP_003727903.1| 190 FITILTVIYQINIKIpSFINIKKYLKYGLPLIPGSLSKWIIDASDRYLIGFFLGTTFVGYYNPGYALGDIL-KIFFI 265
                                       9999999999999875899************************************************9986.55666 PP

                   Polysacc_synt_3 231 viakVlfPalSrlqddkk..klrelylkvlrlialivlPiavglavvaellvkvl 283
                                       +++ +l  +lS+  d+++  ++++l+  + +    +++P ++gl +++++++++l
  gi|298676154|ref|YP_003727903.1| 266 PLNFMLPMVLSKHYDEHEidEVKNLLSYTSKYFFAVTIPSVFGLSLLSKPILRIL 320
                                       8888888899999988744489999999999999*****************9987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.33
                   Polysacc_synt_3  50 vftfnlvlgllialvlfllapliasfynqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgv 126
                                       ++++  +l l++ ++l+ l  +ia +        ++++l++++ l  +s  +  +l+ +++Fk + k  l+s+++++
  gi|298676154|ref|YP_003727903.1| 365 IWVIAAILNLVLNIILIPLIGIIAAA--------LTTLLSFTISLVIVSYYSLKILKFNMNFKFILKSILASIIMSL 433
                                       34444444444444444444444432........3333333333333333344444445555555555444444443 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   5.7       2.3   8.4e+03      93     136 ..      85     104 ..       6     118 .. 0.56
   2 !   14.2  11.6   9.7e-06     0.035       2      97 ..     120     216 ..     119     250 .. 0.81
   3 !   66.7  26.8     6e-22   2.1e-18       4     142 ..     335     465 ..     332     466 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.3
                   Polysacc_synt_C  93 kpllaalvmgivvylllllllgllllaalalllavlvgalvYll 136
                                         l++                        +l+ ++ + +l+Y++
  gi|298676154|ref|YP_003727903.1|  85 SFLIF------------------------VLFTSLTISILIYIF 104
                                       11111........................222222233333322 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 9.7e-06
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli.plfgivGaaiatvlallvvavlnlyal 77 
                                       + il++++++ sl+ +l +++ ++ ++ki  +  +    +k+ + +l++    gi+Ga+ + +++  +v+++ +  +
  gi|298676154|ref|YP_003727903.1| 120 VKILSIIVLIESLNAFLKNYFRATQQVKIHSILQFTKTSLKIFFVVLFVlNNGGIIGAISGLLISSSLVFFITILTV 196
                                       689**********************************************55668**********************9 PP

                   Polysacc_synt_C  78 rrllgikl.ellrrllkplla 97 
                                         +++ik+ + + ++ k+l  
  gi|298676154|ref|YP_003727903.1| 197 IYQINIKIpS-FINIKKYLKY 216
                                       999*999953.4444344433 PP

  == domain 3  score: 66.7 bits;  conditional E-value: 6e-22
                   Polysacc_synt_C   4 ilalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrl 80 
                                       ++alsi++++ + ++  ++   +++ki +k+ vi+a+++l+ln++lipl+gi+ aa+ t+l++++++v+  y+  ++
  gi|298676154|ref|YP_003727903.1| 335 FVALSILLYGTFEIFKKVILLEKKTKIDAKIWVIAAILNLVLNIILIPLIGIIAAALTTLLSFTISLVIVSYYSLKI 411
                                       679************************************************************************** PP

                   Polysacc_synt_C  81 lgiklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllllr 142
                                       l++++  ++ +lk +la+++m+++   ++ l+++ +l    +l++ ++v+a+ Y+++l+ll+
  gi|298676154|ref|YP_003727903.1| 412 LKFNM-NFKFILKSILASIIMSLL---IFILNPSGIL----NLIFTICVCAISYFVILILLN 465
                                       *****.6*****************...8888887665....99****************986 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6  28.8   6.9e-19   2.5e-15       5     261 ..      11     267 ..       7     274 .. 0.85
   2 ?   -1.0  23.6      0.26   9.5e+02      53     218 ..     268     439 ..     258     460 .. 0.76
   3 ?   -1.0   0.1      0.26   9.2e+02      77     107 ..     442     472 ..     438     475 .. 0.79

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 6.9e-19
                     Polysacc_synt   5 vivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrek...kelvslil 78 
                                       +    l +l++   +++ l++l+  ++  ++G+ a+++ +++l   ++ lGl  a  r++   ++k   +elv ++l
  gi|298676154|ref|YP_003727903.1|  11 IGLVGLTNLLVSFSGIILLPILTKNIPVQDYGIWAQIVITLGLVPEFVMLGLQRAMHRFVPSIKTKenlQELVYSFL 87 
                                       566678888889999**********************************************9999966777777776 PP

                     Polysacc_synt  79 lnvllv.llvlvllfllllliaa.flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrv 153
                                       + vl++ l++++l+++++  ia  ++++++  +++ il++++l + + ++f  ++f++ +  k  ++ q+ +    +
  gi|298676154|ref|YP_003727903.1|  88 IFVLFTsLTISILIYIFSGIIASaLFDNQI--LIVKILSIIVL-IESLNAFLKNYFRATQQVKIHSILQFTKTSLKI 161
                                       666554145777777777777544444444..34555555555.99*************************999999 PP

                     Polysacc_synt 154 ilvliavflfldivaavlgavlaalvggivslavlrkkfrprfvilslklvrellsfsapltisslaillytyidsi 230
                                        +v+++v+  + i +a+ g+++++ +   +++++l++++  + +i+s  ++++ l++++pl+ +sl+  ++  +d++
  gi|298676154|ref|YP_003727903.1| 162 FFVVLFVLNNGGIIGAISGLLISSSLV--FFITILTVIYQINIKIPSFINIKKYLKYGLPLIPGSLSKWIIDASDRY 236
                                       999999999999**********99776..66666666699999999999**************************** PP

                     Polysacc_synt 231 llglllgaeavGiYnaayqllvaisgllapi 261
                                       l+g++lg++ vG+Yn +y l  ++ ++++p 
  gi|298676154|ref|YP_003727903.1| 237 LIGFFLGTTFVGYYNPGYALGDILKIFFIPL 267
                                       ***********************99999886 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.26
                     Polysacc_synt  53 dlGlnaalvreiakyrek..kelvslillnvllvllv.lvllfllllliaaflglpelavlylil....almllllv 122
                                       ++ l+  l+++ ++++ +  k+l s++ +  + v++  ++ l ll+ +i ++l+ p+ a+   i+    al++ll  
  gi|298676154|ref|YP_003727903.1| 268 NFMLPMVLSKHYDEHEIDevKNLLSYTSKYFFAVTIPsVFGLSLLSKPILRILSTPDIASQAYIItpfvALSILLYG 344
                                       666788899999999987654444444444444444434568899999999***99998765554222278888999 PP

                     Polysacc_synt 123 gvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaavlgavlaalvggivslavlrkkfr..prfv 197
                                       ++ +f   ++ +++    a +++++  l  v l +i++ l++ i aa+l+++l+  +++++  +++ k+++   +f+
  gi|298676154|ref|YP_003727903.1| 345 TFEIFKKVILLEKKTKIDAKIWVIAAILNLV-LNIILIPLIG-IIAAALTTLLSFTISLVIVSYYSLKILKfnMNFK 419
                                       9999999999999999999999999999988.999*******.9999999999999999999999998996236666 PP

                     Polysacc_synt 198 ilslklvrellsfsapltiss 218
                                       ++ lk +  ++ +s+ ++i  
  gi|298676154|ref|YP_003727903.1| 420 FI-LKSILASIIMSLLIFILN 439
                                       66.99**99999999998854 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.26
                     Polysacc_synt  77 illnvllvllvlvllfllllliaaflglpel 107
                                       ++ln++++++v+++ ++++l +   ++++el
  gi|298676154|ref|YP_003727903.1| 442 GILNLIFTICVCAISYFVILILLNGFDKKEL 472
                                       6789999999999999999888777777666 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.8  16.3       2.1   7.4e+03     125     301 ..       9     178 ..       6     183 .. 0.74
   2 !   34.7  43.2     2e-12   7.3e-09      50     431 ..      77     436 ..      68     465 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.8 bits;  conditional E-value: 2.1
                              MurJ 125 kkFfapafsPvllNvsvIltllllanklgeeail..aLaiGvliGgvlqllvqlpalkkaglllkprfafrdeglkk 199
                                       k+ ++++++ +l+++s I+ l +l +++   +++  +  i++++G+v ++++     +++ +  +  ++ ++e+l++
  gi|298676154|ref|YP_003727903.1|   9 KRIGLVGLTNLLVSFSGIILLPILTKNIP-VQDYgiWAQIVITLGLVPEFVMLGLQRAMHRFVPS--IK-TKENLQE 81 
                                       56678999*******************99.777755689**********9987777677766644..45.4566777 PP

                              MurJ 200 flklllptllgvs..vsqlnllvdtalAsflaegsvsilayadrilqlPlglfgvsistvlLPrlSrsakekdedev 274
                                       ++  +l  +l+ s  +s+l  + + ++As       ++  +  +i+++   +  +  ++++L +  r+ ++    ++
  gi|298676154|ref|YP_003727903.1|  82 LVYSFLIFVLFTSltISILIYIFSGIIAS-------ALFDNQILIVKILSIIVLIESLNAFLKNYFRATQQVKIHSI 151
                                       77777766665541245555666667777.......66777777777888888888888888888888888888888 PP

                              MurJ 275 rdllsqairltllllipvsfgllvlsk 301
                                        + +++++++ +++l+++  g ++ ++
  gi|298676154|ref|YP_003727903.1| 152 LQFTKTSLKIFFVVLFVLNNGGIIGAI 178
                                       888888888888888888777777765 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 2e-12
                              MurJ  50 ekaaefvrkvltllilvlllvtligilaapllirllatgfdeetlelavsllrillpylllvslsavfgavLnarkk 126
                                       e+ +e+v ++l+++  + l + ++  +++ ++++ l   +        + +++il   +l+ sl a++     a ++
  gi|298676154|ref|YP_003727903.1|  77 ENLQELVYSFLIFVLFTSLTISILIYIFSGIIASALFDNQ--------ILIVKILSIIVLIESLNAFLKNYFRATQQ 145
                                       4667788888888888888888887888888877776666........78899999999999999999999999999 PP

                              MurJ 127 FfapafsPvllNvsvIltllllanklgeeailaLaiGvliGgvlqllvq.lpalkkaglllkprfafrdeglkkflk 202
                                         + ++ +       I++++l+  + g   i++   G+li   l + ++ l  ++++ ++  p       ++kk lk
  gi|298676154|ref|YP_003727903.1| 146 VKIHSILQFTKTSLKIFFVVLFVLNNG--GIIGAISGLLISSSLVFFITiLTVIYQINIKI-P----SFINIKKYLK 215
                                       888888887777677777777766666..46665556666654444444034445555553.3....3345999*** PP

                              MurJ 203 lllptllgvsvsqlnllvdtalAsflaegsvsilayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdlls 279
                                         lp + g++++ + ++ d  l  f+  +++  +++    l   l +f + +  +l   lS++++e + dev++lls
  gi|298676154|ref|YP_003727903.1| 216 YGLPLIPGSLSKWIIDASDRYLIGFFLGTTFVGYYNPGYALGDILKIFFIPLNFMLPMVLSKHYDEHEIDEVKNLLS 292
                                       **************************************************988877779****************** PP

                              MurJ 280 qairltllllipvsfgllvlskpivsllferGnFseedveataevLaay.algLipyalvklllrvfYAredtktPv 355
                                        + +  ++++ip++fgl +lskpi+++l       + d++  a+++  + al+++ y  ++++++v   ++ tk  +
  gi|298676154|ref|YP_003727903.1| 293 YTSKYFFAVTIPSVFGLSLLSKPILRILS------TPDIASQAYIITPFvALSILLYGTFEIFKKVILLEKKTKIDA 363
                                       ***************************96......999********998789************************* PP

                              MurJ 356 kislislvlnillsllllpplgvvglalatslsaliglvllyvllrkrlklteargiktflaklvvllalaavvil 431
                                       ki +i+++ln++l+++l+p +g ++ al t ls++i+lv++ ++  k lk+     +k+ l++ +++ ++++  i 
  gi|298676154|ref|YP_003727903.1| 364 KIWVIAAILNLVLNIILIPLIGIIAAALTTLLSFTISLVIVSYYSLKILKF--NMNFKFILKS-ILASIIMSLLIF 436
                                       ****************************************99999998663..3333344444.222333333322 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1  10.0   6.3e-05      0.23      63     158 ..      74     163 ..      14     166 .. 0.79
   2 ?   -1.3   1.6      0.42   1.5e+03      77     124 ..     174     223 ..     167     270 .. 0.62
   3 !   34.2   2.1   5.1e-12   1.8e-08       1     161 []     219     379 ..     219     379 .. 0.94
   4 ?   -8.2  10.3         5   1.8e+04     117     133 ..     420     436 ..     380     465 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.3e-05
                              MatE  63 knfkrakealrqglilllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgag 139
                                       k +++++e ++  li++l+ sl i++l+++fs +i+s + +++    l+ ++l+i++l +   +l+  l++++r+++
  gi|298676154|ref|YP_003727903.1|  74 KTKENLQELVYSFLIFVLFTSLTISILIYIFSGIIASALFDNQI---LIVKILSIIVLIE---SLNAFLKNYFRATQ 144
                                       56789999*******************************99995...6667777777665...55588999999999 PP

                              MatE 140 ktkvplyislislllnipl 158
                                        +k+  ++ +  + l i +
  gi|298676154|ref|YP_003727903.1| 145 QVKIHSILQFTKTSLKIFF 163
                                       9999999988888888776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.42
                              MatE  77 illlllsliiallvllfseqilslftqdee..vlelakrylrililgipa 124
                                       i++++ +l+i+  +++f+ ++  +++ + +      +k+yl++ ++ ip+
  gi|298676154|ref|YP_003727903.1| 174 IIGAISGLLISSSLVFFITILTVIYQINIKipSFINIKKYLKYGLPLIPG 223
                                       56666666666666666666555555554422222334444444444444 PP

  == domain 3  score: 34.2 bits;  conditional E-value: 5.1e-12
                              MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgl 76 
                                       P++  +l  +++ + d +l+g + g++ ++ ++ +  +  +l +f++ l+  l  + ++ + ++  +++k+ l ++ 
  gi|298676154|ref|YP_003727903.1| 219 PLIPGSLSKWIIDASDRYLIGFFlGTTFVGYYNPGYALGDILKIFFIPLNFMLPMVLSKHYDEHEIDEVKNLLSYTS 295
                                       6666777888899999999999999999999999999999999999999999************************* PP

                              MatE  77 illlllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisll 153
                                       +  +++ ++ ++ + l+s++il+++ ++++++++a  + ++++l+i++++ +++++++    +ktk+ + i +i+++
  gi|298676154|ref|YP_003727903.1| 296 KYFFAVTIPSVFGLSLLSKPILRIL-STPDIASQAYIITPFVALSILLYGTFEIFKKVILLEKKTKIDAKIWVIAAI 371
                                       *************************.5666*********************************************** PP

                              MatE 154 lniplnyl 161
                                       ln++ln +
  gi|298676154|ref|YP_003727903.1| 372 LNLVLNII 379
                                       *****976 PP

  == domain 4  score: -8.2 bits;  conditional E-value: 5
                              MatE 117 ililgipalalqlvlsg 133
                                       +++ +i+a ++  +l  
  gi|298676154|ref|YP_003727903.1| 420 FILKSILASIIMSLLIF 436
                                       22222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1318  (0.0735122); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.36s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 2746.20
//
Query:       gi|298676155|ref|YP_003727904.1|  [L=302]
Description: sulfotransferase domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-10   39.8   0.0    3.6e-08   34.1   0.0    2.8  1  Sulfotransfer_3  Sulfotransferase family
  ------ inclusion threshold ------
       0.02   13.4   0.0      0.029   12.9   0.0    1.1  1  Proteasom_PSMB   Proteasome non-ATPase 26S subunit


Domain annotation for each model (and alignments):
>> Sulfotransfer_3  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0     4e-12   3.6e-08       2     215 ..      14     231 ..      14     233 .. 0.58

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 4e-12
                                       EEEE--TTSSHHHHHHHHHTSTTEE--S--.--TT.-SBH..................HHHHHHHTT.-S...TTTH CS
                   Sulfotransfer_3   2 ifivGlpRSGTTlLhrlLaahpdvripeetlfvaprllal..................leawskdgr.elrrlldag 59 
                                       i i+G  RSG+Tl+  +L++hp++++++e++++++++  +                   ++w+++ + + ++  ++ 
  gi|298676155|ref|YP_003727904.1|  14 IYILGSGRSGSTLIDIVLGNHPEIESKGELYDIIKKYENNelcscdtpsqicpfwidvINRWKEQTKiDDLAFYEN- 89 
                                       78******************************99988877666666666665554444222222211012221122. PP

                                       HHHHHHHHH.....T--HHHHHHHHHHHHHTT-B.HHHHHHHHHHHTTTSEEEE..EESSGGG-HHHHHHHBSSEEE CS
                   Sulfotransfer_3  60 ltqeeaelp.....hledaeepeedlqllraala.svilealarvpsyarwlvd..KsPshlfrldlllelfPdAkf 128
                                       l+++  +l+           ++++  ++ ++ +  ++++++   + s+++ +vd  K Ps + ++  +  +  d ++
  gi|298676155|ref|YP_003727904.1|  90 LQKKVESLKglsllL-----KNKNNSNINDYIFYtQALYHS-ISTVSGKNIIVDssKKPSRALAISMMPNV--DLCL 158
                                       333333333443321.....222222222222220222333.23336666677677887766655444444..6789 PP

                                       EEEE--H.HHHHHHHHHTT----------..-.HHHHHHHHHHHHHHHHHHHHHHS-TTSEEEEEHHHHHH-HHHHH CS
                   Sulfotransfer_3 129 ihlvRdpvdtvlssyvslfgkkresysedsld.eledaleewarayerllaararlppdrfldvrYedLvadpegtl 204
                                       ihlvRd++  ++s +++     ++s     l+ +l+++++    ++        +++ ++  ++rYed+v+ p++tl
  gi|298676155|ref|YP_003727904.1| 159 IHLVRDGRGVTYSGMKEG----KKS-----LRfPLGWMYNNLLSEIV-----FYTIG-SNKAQIRYEDFVNYPVKTL 220
                                       *******77777766655....233.....33345533333333332.....23354.56789************** PP

                                       HHHHHHHT--- CS
                   Sulfotransfer_3 205 rriyeflglpw 215
                                       + i e  g+ +
  gi|298676155|ref|YP_003727904.1| 221 KLIGEVAGINL 231
                                       ***99999876 PP

>> Proteasom_PSMB  Proteasome non-ATPase 26S subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.2e-06     0.029     350     402 ..      93     145 ..      81     152 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-06
                    Proteasom_PSMB 350 kkrlLdalsslfelkteqateelleiaeswYellaekalenvildivkkPFpe 402
                                       k+ +L+ ls+l+++k +++ ++ +  ++ +Y++++    +n+i+d +kkP   
  gi|298676155|ref|YP_003727904.1|  93 KVESLKGLSLLLKNKNNSNINDYIFYTQALYHSISTVSGKNIIVDSSKKPSRA 145
                                       7789**********************************************665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1785.43
//
Query:       gi|298676156|ref|YP_003727905.1|  [L=246]
Description: nucleotidyl transferase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-43  146.7   0.0    9.8e-43  146.5   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    4.3e-15   56.4   0.0    5.6e-15   56.1   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    9.9e-08   32.0   0.1    5.8e-07   29.5   0.1    2.1  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
     0.0037   17.1   0.2     0.0062   16.4   0.2    1.4  1  Glycos_transf_2  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.5   0.0   2.2e-46   9.8e-43       1     247 [.       2     239 ..       2     240 .. 0.92

  Alignments for each domain:
  == domain 1  score: 146.5 bits;  conditional E-value: 2.2e-46
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       k++I a GsGtRL P t++++k l+pv++k  +i+++++  +++gi++ i+++ + +++ + +++++g++fgv++++
  gi|298676156|ref|YP_003727905.1|   2 KGLIPAAGSGTRLGPFTHAMPKELLPVGDK-AVIEHVVESFVKAGIDD-IIIVVSPNKHGLSDYFGSGERFGVDITY 76 
                                       57899*************************.*****************.777777999******************* PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       ++++ + g+A+Ava ++ +++ +     ++vLg++ +  d++ + +k++ e+++  ++t+g+++v + t+ G+i++d
  gi|298676156|ref|YP_003727905.1|  77 VVQDDRLGLANAVAAGEHVVNGSPV---AVVLGDNFFSPDTILQDLKQFHEDNN-ADATVGVMEVLDVTRHGIIQTD 149
                                       *********************9995...***********966666666555555.49******************** PP

                                       TTSBEEEEECS-SSHSH.CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EE CS
                   NTP_transferase 155 eegrverfvEKPkeaka.selassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWs 230
                                       ++ ++ +++EKP+  +a s+l  +G Yvf++e+++ + +d ++  + e ++td ++ ++e+gk+ ++    +     
  gi|298676156|ref|YP_003727905.1| 150 GN-NIVDLIEKPEVGEApSKLGIAGMYVFEPEIFDAI-SDTKPGYKDEYQLTDSIKVMVEQGKNVVYREIGGI--HI 222
                                       95.899*******99986888899*************.67**************************9888885..5* PP

                                       EXSSHHHHHHHHHHHHH CS
                   NTP_transferase 231 DvGtldslleaneklae 247
                                       DvGt+++l++ane +++
  gi|298676156|ref|YP_003727905.1| 223 DVGTPEDLMKANEYYLK 239
                                       ************98765 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0   1.2e-18   5.6e-15       2     121 ..       4     133 ..       3     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 1.2e-18
                                       EEEEESS-TTTT..T...THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTCTS-E..EE-T CS
                      NTP_transf_3   2 viLAGGrSsRmg..g...dKallplggkpllervldalraagvdevvvvggd..eevlaal...arlgvrv..vede 66 
                                       +i A+G ++R+g  +   +K llp+g+k ++e+v++++ +ag+d++++v+ +  + + +++   +r+gv++  v+++
  gi|298676156|ref|YP_003727905.1|   4 LIPAAGSGTRLGpfThamPKELLPVGDKAVIEHVVESFVKAGIDDIIIVVSPnkHGLSDYFgsgERFGVDItyVVQD 80 
                                       677*********651578*****************************998773344444334446667665115554 PP

                                       TSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEE CS
                      NTP_transf_3  67 dpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvp 121
                                           g + ++aa+ + + + ++v+v+++D  + +  +++ l + +++++ad++v 
  gi|298676156|ref|YP_003727905.1|  81 -DRLGLANAVAAGEHVV-NGSPVAVVLGDNFFSPDTILQDLKQFHEDNNADATVG 133
                                       .479**********998.8***********9888888888888888888888775 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 !   29.5   0.1   1.3e-10   5.8e-07       4     100 ..       4     108 ..       1     240 [. 0.56

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.3e-10
                                       EEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG....CCEEEEE- CS
                              IspD   4 vipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld....ksiqlvaG 73 
                                       +ipAAGsG+R++     +pK +l + +++++eh v+++ +   +d i++vvs+++ +    + +      +i+ v+ 
  gi|298676156|ref|YP_003727905.1|   4 LIPAAGSGTRLGpftHAMPKELLPVGDKAVIEHVVESFVK-AGIDDIIIVVSPNKHGLSDYFGSGerfgVDITYVVQ 79 
                                       8*********96443789********************99.88**********997666555554566545665555 PP

                                       -SSH..HHHHHHHHHTTSSTTSEEEE--T CS
                              IspD  74 GdeR..aesVlnglkalegeakfVLvHDa 100
                                        d    a++V +g ++++g+   V++ D 
  gi|298676156|ref|YP_003727905.1|  80 DDRLglANAVAAGEHVVNGSPVAVVLGDN 108
                                       44323367777777777777655555443 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   1.4e-06    0.0062      27     133 ..      45     163 ..      30     216 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-06
                                       CEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TT.HHHHHHH CS
                   Glycos_transf_2  27 pdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgdyilflDaDdepdpd.wleklve 102
                                         ++ii+v    + ++ +   +  + + +++++ ++ + G+a+a+ ag   ++g  ++++  D  ++pd  l++l +
  gi|298676156|ref|YP_003727905.1|  45 GIDDIIIVVSPNKHGLSDYFGSGERFGVDITYVVQDDRLGLANAVAAGEHVVNGSPVAVVLGDNFFSPDtILQDLKQ 121
                                       55556666666666666666666667889**************************999999********88899999 PP

                                       HHHH.TTCEEEEEEEEEECCCCCCCHC-SS...........E CS
                   Glycos_transf_2 103 alekdgadvvlgqrprifgetdeiernkrv...........g 133
                                       + e+++ad+ +g   + ++ ++ i ++ ++           g
  gi|298676156|ref|YP_003727905.1| 122 FHEDNNADATVGVMEVLDVTRHGIIQTDGNnivdliekpevG 163
                                       999999999999988888877777777665555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1508.40
//
Query:       gi|298676157|ref|YP_003727906.1|  [L=186]
Description: hypothetical protein Metev_2294 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   15.6   0.0      0.069   13.7   0.0    1.8  1  DUF2408   Protein of unknown function (DUF2408)


Domain annotation for each model (and alignments):
>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.8e-06     0.069      39     120 ..      71     180 ..       6     185 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-06
                           DUF2408  39 e......................vkeelkelkeeLkkieskrde....egkFkseegke......vvekgqavlngL 83 
                                                               + e +++k++L++i++  d+     + F  e++++       v +++  ++  
  gi|298676157|ref|YP_003727906.1|  71 MeiglteenkeiitsdvgeirifYDPETDSWKKDLHDIQKALDSikplGNDFWDEKTDDngditePVIENKGSVEFV 147
                                       05555555555666666677777444555556666666665555555533354444433445555777889999*** PP

                           DUF2408  84 lddcfdlvedlkaqdgeekkvasslqpiYdrLleikt 120
                                       +ddc + + d++++    ++ ++ ++ i++ L ++k 
  gi|298676157|ref|YP_003727906.1| 148 YDDCDECCLDVEQR----RRAEEFFNAIFRYLWDLKD 180
                                       ************99....4789999*******99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 1091.79
//
Query:       gi|298676158|ref|YP_003727907.1|  [L=396]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-22   77.6   0.0    1.7e-21   76.6   0.0    1.5  1  OrfB_IS605      Probable transposase
      8e-12   44.9   0.0    1.7e-11   43.9   0.0    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0001   21.7   0.1    0.00018   20.9   0.1    1.4  1  Glyco_hydro_97  Glycoside hydrolase 97
  ------ inclusion threshold ------
      0.067   12.5   0.0       0.11   11.7   0.0    1.4  1  EAP30           EAP30/Vps36 family
       0.15   12.4   0.0        0.3   11.5   0.0    1.5  1  RuvX            Holliday junction resolvase
       0.16   12.4   1.7       0.23   11.8   0.7    1.8  2  HEPN_Swt1       Swt1-like HEPN


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.0   5.8e-25   1.7e-21       2     117 ..     164     278 ..     163     281 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 5.8e-25
                        OrfB_IS605   2 ipvevevelpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkksknykkasrkl 77 
                                       i++e + e+p  ++++ a+iDlGinn++t+v++ g+  +++kg  +ks ++ ++k+  +l s+++k +   k s+kl
  gi|298676158|ref|YP_003727907.1| 164 IVYEKDLETPDLNEENIASIDLGINNIVTMVNNIGEKpIVIKGGVAKSINQFYNKKSGKLKSIYDKLG--IKNSKKL 238
                                       78999999****************************99*****************************9..9****** PP

                        OrfB_IS605  78 arlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       ++l++k + ++++++hk+++++++ + + +++tL++g+  
  gi|298676158|ref|YP_003727907.1| 239 KKLYHKYKMKINDFFHKASKRIVDFCVKHNIGTLVIGYNE 278
                                       *************************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   5.6e-15   1.7e-11       1      69 []     299     373 ..     299     373 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 5.6e-15
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l eql+yka++ G kv+e +++yTSk +   g+ +++      ++ +r +  ++ g+ +++Dvn+a+Ni+k+
  gi|298676158|ref|YP_003727907.1| 299 FHRLLEQLKYKAEDVGLKVIEQEESYTSKCSFLDGEPVERrtsylgKRIKRGLFQSSNGTIINADVNGAYNIMKK 373
                                       899**************************999******999****9777777777779***************96 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1     6e-08   0.00018      34     106 ..     254     325 ..     215     348 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 6e-08
                    Glyco_hydro_97  34 tetvkryiDfAaengleyvlvegwdegWee..kkkkekefdftkpypdfdleelvaYakekgvgvelwlhsetsg 106
                                        +  kr +Df+ ++++ ++++ g++egW++  ++ k ++++ ++++p  +l e ++Y k+ +vg++++ ++e ++
  gi|298676158|ref|YP_003727907.1| 254 HKASKRIVDFCVKHNIGTLVI-GYNEGWKQevDMGK-RNNQKFTQIPFHRLLEQLKY-KAEDVGLKVIEQEESYT 325
                                       56789****************.*******9865554.45555667788888888888.44566788887777655 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.8e-05      0.11      63     124 ..     223     281 ..     207     351 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.8e-05
                             EAP30  63 ftkmcaslGvdplsskkseslgfl...ellglgdfyyeLavqivevclatraengglisleelya 124
                                        +++ ++lG+     k+s++l++l     ++++df+ + +++iv++c + +     +i   e ++
  gi|298676158|ref|YP_003727907.1| 223 LKSIYDKLGI-----KNSKKLKKLyhkYKMKINDFFHKASKRIVDFCVKHN-IGTLVIGYNEGWK 281
                                       4458899999.....3344555666666777****************9543.2225555555555 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0001       0.3      14     100 ..     231     327 ..     227     340 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                                       EEEEE-S--SS---EEEEE---HHHHHHHHHHHHHHTT--EEEEE--......----SSS---SSTT..HHHHHHHH CS
                              RuvX  14 GvAvsdplgilaspletierkskekdleelkelvkeeeveeiVvGlP......lnldgsegesakkv..rkfaeeLa 82 
                                       G+  s++l++l +++++  ++  +k+ +++ +++ ++++ ++V+G+       +++ ++++++  ++  +++ e+L+
  gi|298676158|ref|YP_003727907.1| 231 GIKNSKKLKKLYHKYKMKINDFFHKASKRIVDFCVKHNIGTLVIGYNegwkqeVDMGKRNNQKFTQIpfHRLLEQLK 307
                                       555666666666666666666568999********************999888555444444444433488888888 PP

                                       HT....T-EEEEE--S---- CS
                              RuvX  83 krl..kklpvelvDErlttv 100
                                        +    +l+v+  +E++t++
  gi|298676158|ref|YP_003727907.1| 308 YKAedVGLKVIEQEESYTSK 327
                                       887444569*********98 PP

>> HEPN_Swt1  Swt1-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   7.8e-05      0.23      10      70 ..      26      85 ..      18      97 .. 0.67
   2 ?   -2.8   0.0       2.6   7.6e+03      41      64 ..     287     310 ..     269     327 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.8e-05
                         HEPN_Swt1 10 Lrpfverelskayged.wweeveaslekdeeekkesekeiskldvqdllrvitenWkevFkk 70
                                      L++  + +++++++++  w ++e+ l +++ ++ e+ + +  +++q+ l+++++nWk++F++
  gi|298676158|ref|YP_003727907.1| 26 LYNQANFIVKQSLNDEgGWVRYEE-L-NKQLKGTENYSVLPTQTAQQTLKLMDKNWKSFFQS 85
                                      555555566666666664444444.2.444444455666677889999**********7775 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.6
                         HEPN_Swt1  41 kkesekeiskldvqdllrvitenW 64 
                                       +k+++++  ++ +++ll+ ++ + 
  gi|298676158|ref|YP_003727907.1| 287 GKRNNQKFTQIPFHRLLEQLKYKA 310
                                       334455566666666666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1103  (0.0615204); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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: 0.60u 0.44s 00:00:01.04 Elapsed: 00:00:00.99
# Mc/sec: 1209.70
//
Query:       gi|298676159|ref|YP_003727908.1|  [L=373]
Description: restriction endonuclease [Methanohalobium evestigatum Z-7303]
Scores for 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-27   93.4   0.1    6.4e-25   87.4   0.2    2.4  2  Mrr_cat        Restriction endonuclease
    1.1e-06   28.6   0.3    1.1e-06   28.6   0.3    2.0  3  Mrr_cat_2      Restriction endonuclease
    0.00015   21.7   0.8        0.5   10.4   0.1    3.5  3  CARD           Caspase recruitment domain
     0.0049   16.5   0.8     0.0093   15.6   0.4    1.7  2  FAD_binding_1  FAD binding domain
  ------ inclusion threshold ------
       0.17   11.8   3.5       0.47   10.4   1.0    2.6  2  Ferritin       Ferritin-like domain
        0.2   12.4   0.1         63    4.7   0.0    3.2  3  HEAT_PBS       PBS lyase HEAT-like repeat


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.023        69      48      77 ..      51      82 ..      35      95 .. 0.79
   2 !   87.4   0.2   2.1e-28   6.4e-25       2     115 .]     251     362 ..     250     362 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.023
                                      EEEEEEEE--..TS-B-HHHHHHHHHHCTTS. CS
                           Mrr_cat 48 erilvqaKry..knkvgvkeVqeligalkkrg 77
                                      e  ++q+K    +++ +++ ++e+++ l+++ 
  gi|298676159|ref|YP_003727908.1| 51 EPAVIQVKEEirNDENSEELIREFLSILENND 82
                                      689*******8447899999*****9999874 PP

  == domain 2  score: 87.4 bits;  conditional E-value: 2.1e-28
                                       TTT-TTCHHHHHHHHHHHHSSSEEE---B-T..TSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHHHHCTTS CS
                           Mrr_cat   2 dkmspkeFeklvaellealGykeveltgrsg..DggiDliakkdplgserilvqaKryknkvgvkeVqeligalkkr 76 
                                       dk++pke+e+ v ++++ +Gy    +t++++  D+g+D+i++k  lgs+ri+vq+K++++kvg  +Vqe+++++ ++
  gi|298676159|ref|YP_003727908.1| 251 DKLTPKELEQAVCKIYRDKGYY-ASRTKKTNdkDQGADVILTK--LGSKRIAVQVKQSSSKVGNSAVQEVVASMRYY 324
                                       689******************9.7777776633789*****98..999***************************** PP

                                       ..SEEEEEESS-B-HHHHHHHHTT--EEEE-HHHHHHHH CS
                           Mrr_cat  77 gadkgifvttsdftkaAreeaeelnkieLldgdeLaell 115
                                        ++ +++vt++++t++A + a++ n ++L++++eL +l+
  gi|298676159|ref|YP_003727908.1| 325 LCNSAMVVTNNYYTSEAVDLAKA-NDVKLINREELRNLI 362
                                       ***********************.***********9985 PP

>> Mrr_cat_2  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.89   2.6e+03      46      84 ..      54     111 ..      46     127 .. 0.62
   2 ?   -3.4   0.1       2.8   8.4e+03       3      23 ..     182     202 ..     180     210 .. 0.75
   3 !   28.6   0.3   3.6e-10   1.1e-06      22     124 ..     274     372 ..     253     373 .] 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.89
                         Mrr_cat_2  46 AIQcKfYaedekiqkedidsFlsasgkk...................kftkrliisTt 84 
                                        IQ+K    + + ++e i++Fls+ +++                   ++ +r+ i T 
  gi|298676159|ref|YP_003727908.1|  54 VIQVKEEIRNDENSEELIREFLSILENNdsavpfvlhelrnklprpeTIHHRIKIFTY 111
                                       5777766666666677788888877776555555555555555555555555555555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.8
                         Mrr_cat_2   3 dpayaeefkeVwlwkewpeek 23 
                                       dp+ +e +++  + ++++++ 
  gi|298676159|ref|YP_003727908.1| 182 DPETRELLEDMLKDEDFEDRL 202
                                       899999999999999998873 PP

  == domain 3  score: 28.6 bits;  conditional E-value: 3.6e-10
                         Mrr_cat_2  22 e..krlgkkDtGIDlVakerkegeywAIQcKfYaedekiqkedidsFlsasgkkkftkrliisTtdkwsknaeealk 96 
                                       +  k+++ kD+G D++ ++   ++ +A+Q+K  ++++k+ ++ +++ +++  +    ++ +++T +  +++a +  k
  gi|298676159|ref|YP_003727908.1| 274 SrtKKTNDKDQGADVILTK-LGSKRIAVQVK--QSSSKVGNSAVQEVVAS-MRYYLCNSAMVVTNNYYTSEAVDLAK 346
                                       3347889**********99.889999*****..899**********7765.566677777777***********955 PP

                         Mrr_cat_2  97 nqkipvkridledLeeseidwsklslgk 124
                                       +   +vk+i+ e+L+++ i  +kl++++
  gi|298676159|ref|YP_003727908.1| 347 A--NDVKLINREELRNLIISHHKLFKKE 372
                                       5..56**************999998876 PP

>> CARD  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.011        32      57      78 ..      19      40 ..      16      43 .. 0.89
   2 ?    3.1   0.1     0.033        99      36      67 ..      58      88 ..      39      99 .. 0.75
   3 !   10.4   0.1   0.00017       0.5      30      83 ..     129     190 ..     113     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.011
                                      HTSCHHHHHHHHHHHHHHSHHH CS
                              CARD 57 qkkgekacqaflealkegqpdl 78
                                       ++geka + ++++lke++p +
  gi|298676159|ref|YP_003727908.1| 19 VNHGEKAVEPLINCLKETYPNS 40
                                      579***************9975 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.033
                                      HHHHHTSSSHHHHHHHHHHHHHTSCHHHHHHH CS
                              CARD 36 eekikakttrlskareLldlvqkkgekacqaf 67
                                       e+i+++ ++++  re+l++++  ++ a    
  gi|298676159|ref|YP_003727908.1| 58 KEEIRNDENSEELIREFLSILE-NNDSAVPFV 88
                                      478******************9.555555555 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00017
                                       SS-HHHHHHHHTSSS.......HHHHHHHHHHHHHTSCHHHHHHHHHHHHH.HSHHHHHHHH CS
                              CARD  30 VLteeeeekikaktt.......rlskareLldlvqkkgekacqaflealke.gqpdlaslle 83 
                                        L  ee e+ik+++t       +++  + L+++ q+  ++a + +++al e ++p+  +lle
  gi|298676159|ref|YP_003727908.1| 129 YLRHEEREMIKELSTlvyfresVEDEREILIEIFQELEPEAIDPIINALNEnWDPETRELLE 190
                                       57778888888877777777779999999**********************9***9999887 PP

>> FAD_binding_1  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   3.1e-06    0.0093      53     161 ..      65     164 ..      63     180 .. 0.84
   2 ?   -1.9   0.0       0.7   2.1e+03     125     146 ..     182     204 ..     156     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.1e-06
                                       ---HHHHHHHHHHHT--T..T-EEEEEESSTT..S--SSSSSEEHHHHHHHTB--SS---HHHHHHHGGG-SSHHHH CS
                     FAD_binding_1  53 sNneelVeellellgldpkadevvelkaldeesaekeprleptTlrqalkyylditgppskqlleaLaefaseeeek 129
                                       +N+eel+ e+l++l+ ++    ++ l++l     +k pr+e++  r  +  y  i++  sk   + ++ +    ee+
  gi|298676159|ref|YP_003727908.1|  65 ENSEELIREFLSILENND-SAVPFVLHELR----NKLPRPETIHHRIKIFTYKSILNRHSKYTANLIIDYLRH-EER 135
                                       69***************9.88899999999....489999999999999999******************876.578 PP

                                       HHHHHHHH-HHHHHTTTTT--HHHHHHHHHTT CS
                     FAD_binding_1 130 qkLekLssdegakeykelklneartllevlee 161
                                       + ++ Ls+      + e + +e++ l+e+++e
  gi|298676159|ref|YP_003727908.1| 136 EMIKELSTL---VYFRESVEDEREILIEIFQE 164
                                       999999995...55555555556777777665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.7
                                       SHHHHHHHHHHHH-.HHHHHTTT CS
                     FAD_binding_1 125 eeeekqkLekLssd.egakeyke 146
                                       ++e+++ Le++ +d  ++++++e
  gi|298676159|ref|YP_003727908.1| 182 DPETRELLEDMLKDeDFEDRLQE 204
                                       78899999999998666666655 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.31   9.1e+02     113     134 ..     121     143 ..     112     149 .. 0.68
   2 ?   10.4   1.0   0.00016      0.47      97     139 ..     168     209 ..     154     212 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHH.HHHHHHHHHH CS
                          Ferritin 113 atadfledflee.qeehewelea 134
                                        ta+++ d+l+  + e ++el++
  gi|298676159|ref|YP_003727908.1| 121 YTANLIIDYLRHeEREMIKELST 143
                                       58888888887624444555554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  97 eslrelielaeeegDpatadfledfleeqeeheweleallekl 139
                                       e++  +i+  +e+ Dp t+++led+l++ e+ e+ l+++l+++
  gi|298676159|ref|YP_003727908.1| 168 EAIDPIINALNENWDPETRELLEDMLKD-EDFEDRLQEYLKET 209
                                       568889999*******************.8999******9876 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.033        99      15      26 ..      23      34 ..      13      35 .. 0.79
   2 ?   -3.1   0.0         6   1.8e+04       9      19 ..      46      56 ..      45      57 .. 0.83
   3 ?    4.7   0.0     0.021        63      15      26 ..     167     178 ..     147     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.033
                                      GGGHHHHHHHCT CS
                          HEAT_PBS 15 eeaipaLleaLq 26
                                      e a+++L+++L+
  gi|298676159|ref|YP_003727908.1| 23 EKAVEPLINCLK 34
                                      59*********8 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6
                                      HHHCTSGGGHH CS
                          HEAT_PBS  9 Lgqlgdeeaip 19
                                      L+ ++ +++i+
  gi|298676159|ref|YP_003727908.1| 46 LADIREPAVIQ 56
                                      89999999987 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.021
                                       GGGHHHHHHHCT CS
                          HEAT_PBS  15 eeaipaLleaLq 26 
                                       +eai+++++aL+
  gi|298676159|ref|YP_003727908.1| 167 PEAIDPIINALN 178
                                       8*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1052  (0.0586759); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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: 0.64u 0.37s 00:00:01.01 Elapsed: 00:00:00.58
# Mc/sec: 1952.38
//
Query:       gi|298676160|ref|YP_003727909.1|  [L=243]
Description: restriction endonuclease [Methanohalobium evestigatum Z-7303]
Scores for complete 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-23   82.7   0.2    3.7e-23   81.7   0.2    1.5  1  Mrr_cat    Restriction endonuclease
    5.6e-06   26.3   0.4    1.2e-05   25.2   0.2    1.7  1  Mrr_cat_2  Restriction endonuclease
  ------ inclusion threshold ------
      0.019   15.2   1.3       0.48   10.7   0.1    2.9  2  BTB        BTB/POZ domain
      0.081   12.4   1.1       0.11   11.9   1.1    1.3  1  HECT       HECT-domain (ubiquitin-transferase)


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.2   8.3e-27   3.7e-23       1     114 [.     130     240 ..     130     241 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 8.3e-27
                                       HTTT-TTCHHHHHHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEEEEEEEEE--T..S-B-HHHHHHHHHHCTT CS
                           Mrr_cat   1 ldkmspkeFeklvaellealGykeveltgrsgDggiDliakkdplgserilvqaKryk..nkvgvkeVqeligalkk 75 
                                       ld+ms+keFe++++++++ +Gy  ve+tg  +D g+D+++++ +   er++v +K+ +  +kv +++Vqe+++a  +
  gi|298676160|ref|YP_003727909.1| 130 LDEMSWKEFEDFIESMYRDKGYL-VERTG-IKDMGADFVITEYG--VERTAVLIKHLNpgQKVTRNAVQEIVAAKSY 202
                                       689*******************9.****8.9**********965..678888888885549**************** PP

                                       S..SEEEEEESS-B-HHHHHHHHTT--EEEE-HHHHHHH CS
                           Mrr_cat  76 rgadkgifvttsdftkaAreeaeelnkieLldgdeLael 114
                                       ++++ +i+v+++dft++A + ae+ n++ L+++++L e+
  gi|298676160|ref|YP_003727909.1| 203 YHCNSAIVVSNQDFTQKAVKLAES-NNVSLINREQLEEM 240
                                       ************************.***********998 PP

>> Mrr_cat_2  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.2   2.8e-09   1.2e-05      23     113 ..     154     240 ..     131     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.8e-09
                         Mrr_cat_2  23 krlgkkDtGIDlVakerkegeywAIQcKfYaedekiqkedidsFlsasgkkkftkrliisTtdkwsknaeealknqk 99 
                                       +r+g kD+G D V++e    e +A+  K  ++ +k++++ +++ ++a++  +   ++++s  d ++++a +   +++
  gi|298676160|ref|YP_003727909.1| 154 ERTGIKDMGADFVITE-YGVERTAVLIKHLNPGQKVTRNAVQEIVAAKSYYHCNSAIVVSNQD-FTQKAVKL--AES 226
                                       567889**********.888999**************************99999999997776.99999999..677 PP

                         Mrr_cat_2 100 ipvkridledLees 113
                                        +v++i+ e+Lee 
  gi|298676160|ref|YP_003727909.1| 227 NNVSLINREQLEEM 240
                                       79*******99985 PP

>> BTB  BTB/POZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.065   2.9e+02      63     102 ..      13      51 ..       5      65 .. 0.59
   2 ?   10.7   0.1   0.00011      0.48      47      78 ..     121     152 ..     108     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.065
                                       HHHHHHHHHHHSEEEC-CGGGHHHHHHHHHHHT-HHHHHH CS
                               BTB  63 afealLefiYtgeleitseenleelLaaadllqiprlkka 102
                                       a+e++Le++ +     t ++++e+ L   ++l  + ++++
  gi|298676160|ref|YP_003727909.1|  13 AVESMLEVMLSTDSHCT-KKEIEDCLIRMEHLAADTIIEH 51 
                                       55566666655555554.5556655555555555555444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00011
                                       TTCCCEEEEETTSGHHHHHHHHHHHHHSEEEC CS
                               BTB  47 eessvseielddvepeafealLefiYtgelei 78 
                                       + +s+++ +ld+++ ++fe ++e +Y+++  +
  gi|298676160|ref|YP_003727909.1| 121 TGNSQQNNNLDEMSWKEFEDFIESMYRDKGYL 152
                                       3445556789*****************98765 PP

>> HECT  HECT-domain (ubiquitin-transferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.1   2.5e-05      0.11      73     187 ..     131     241 ..      88     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                                       .---TCHHHHH-HHHHHHHHHHH..HS-GGG...GT-BSEEEEETTEEEEEESSTT.GGGSB--TTTHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                              HECT  73 ekitledleeidpelakslkellslesnteevedlaLtFtipenagasatieLipn.GanipVtnenkkeYiklyvn 148
                                       ++++++++e++ +++++   +l     + + ++d++ +F+i+e +g ++t  Li+      +Vt + ++e + +   
  gi|298676160|ref|YP_003727909.1| 131 DEMSWKEFEDFIESMYRDKGYLV----ERTGIKDMGADFVITE-YGVERTAVLIKHlNPGQKVTRNAVQEIVAAKSY 202
                                       34556667777777777777776....333499*******997.588887888888555578*************** PP

                                       HHHTGGGHHHHHHHHHHHHTTS-HHHHTTS-HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              HECT 149 yllkksvekqleaflkGfsevipskalklfdaeelelli 187
                                       y+ +  +    + f++   ++ +s+ ++l++ e+le+++
  gi|298676160|ref|YP_003727909.1| 203 YHCNSAIVVSNQDFTQKAVKLAESNNVSLINREQLEEMV 241
                                       ************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1628  (0.0908026); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1464.15
//
Query:       gi|298676161|ref|YP_003727910.1|  [L=110]
Description: hypothetical protein Metev_2299 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.8e-11   43.3   0.0    4.2e-11   43.2   0.0    1.0  1  PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antit
  ------ inclusion threshold ------
      0.046   13.6   0.0      0.053   13.4   0.0    1.2  1  FliW        FliW protein


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 !   43.2   0.0   4.7e-15   4.2e-11       2     110 ..       6     107 ..       5     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 4.7e-15
                                       TTEEEEEEE-S--TTS--SEEEEEE-S-HHHHCHSEEEEEEEESSSTSSGCSTTEEEE-HHHCSS.SSSSSSEEEEC CS
                        PemK_toxin   2 rGeIvlvdldpsrgseqgkrRpvvVvsndafnekntvivvpltskdkdkkklpfhveleseildl.ngldkdswvkl 77 
                                       +G++v  ++ p +     k+Rp++V+ n +++    +i +++ts    k++  + ++l+ + + +   l+k+s ++ 
  gi|298676161|ref|YP_003727910.1|   6 KGDVVVLPF-PFSDMSNSKKRPALVLANLQGE---DIILCMITSAV--KID-NYSITLNDN-DFEyGTLRKNSNIRP 74 
                                       69*******.95555558**********9877...7*********9..666.999999877.44434455******* PP

                                       CCEEEEEGGGEEEEEEE--HHHHHHHHHHHHHH CS
                        PemK_toxin  78 dqirtvdkarlrkkigklsredlaevqralakl 110
                                         i+t dk+ +  k+g l++++ +ev+++l  +
  gi|298676161|ref|YP_003727910.1|  75 NRIFTADKSLILYKVGYLKNDKTDEVEKKLVNI 107
                                       *********9999***************99765 PP

>> FliW  FliW protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     6e-06     0.053      21      80 ..      21      80 ..      14     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6e-06
                                      .STTS-EEEEEESS-TT-EEEEE-GGGT-TT------HHHHHHTT--SGGGEEEEEEEE- CS
                              FliW 21 eeeespflwLqsleeeelafvvidPflffpdYelelsdeelelleleseedvlvlvivtv 80
                                      ++++ p l+L  l+ e++ + +i  ++  ++Y+++l+d++ e   l++++++    i t+
  gi|298676161|ref|YP_003727910.1| 21 NSKKRPALVLANLQGEDIILCMITSAVKIDNYSITLNDNDFEYGTLRKNSNIRPNRIFTA 80
                                      4556999***********************************999999998876666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.32s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 654.41
//
Query:       gi|298676162|ref|YP_003727911.1|  [L=82]
Description: AbrB family transcriptional regulator [Methanohalobium evestigatum Z-7303]
Scores for complete 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-09   36.0   0.1      6e-09   35.6   0.1    1.3  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0038   17.6   0.1     0.0055   17.1   0.1    1.5  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
  ------ inclusion threshold ------
      0.091   12.8   0.0       0.12   12.4   0.0    1.3  1  MraZ            MraZ protein, putative antitoxin-like
        0.2   11.6   0.0       0.21   11.5   0.0    1.1  1  Phage_T4_gp36   Phage T4 tail fibre


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.1   1.3e-12     6e-09       2      40 ..      10      48 ..       9      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.3e-12
                                      EETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCC CS
                    MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgdkiilrp 40
                                      k++++g+++iPke+r+  +++eG+++++   +d+i lr 
  gi|298676162|ref|YP_003727911.1| 10 KITKKGQISIPKEIRELENFKEGSKIVILAYDDRIELRS 48
                                      899******************************998875 PP

>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.2e-06    0.0055       2      36 ..       9      42 ..       8      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-06
                    PrlF_antitoxin  2 stltergqttiPasvRkaLklkkgrdkiaytildd 36
                                      +++t++gq  iP+ +R+  + k+g+ ki+    dd
  gi|298676162|ref|YP_003727911.1|  9 AKITKKGQISIPKEIRELENFKEGS-KIVILAYDD 42
                                      69********************987.666544443 PP

>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.6e-05      0.12      12      54 ..      13      57 ..       7      75 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.6e-05
                                      TTSEEE--CHHHH..HTTSCSEEEEEECCSEEEEEEHHHHHHHHH CS
                              MraZ 12 akGRlllPaklre..eaklekevvviGvsncLeiwpraeWekyee 54
                                      +kG +++P++ re   +k+   +v+ ++++++e++++++ ++ ++
  gi|298676162|ref|YP_003727911.1| 13 KKGQISIPKEIREleNFKEGSKIVILAYDDRIELRSMDQLDEKIS 57
                                      89********99643899999***************998754444 PP

>> Phage_T4_gp36  Phage T4 tail fibre
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.8e-05      0.21      66     109 ..       3      61 ..       1      79 [. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.8e-05
                     Phage_T4_gp36  66 vfdtRsgnintkGkvgigtrvpa...............dkkltvkGkvd.llnvkltvsa 109
                                        +d Rs+ i+ kG+++i ++++                d  +  + ++d l++ + t  a
  gi|298676162|ref|YP_003727911.1|   3 LIDFRSAKITKKGQISIPKEIRElenfkegskivilayDDRIELR-SMDqLDEKISTALA 61 
                                       589*******************98888888888877777777777.55545555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.99s 00:00:01.53 Elapsed: 00:00:00.72
# Mc/sec: 343.31
//
Query:       gi|298676163|ref|YP_003727912.1|  [L=2251]
Description: S-layer-related duplication domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.5e-154  511.8  32.1    5.1e-78  261.7  13.5    3.1  2  S-layer          S-layer protein
    6.8e-48  163.4   8.4    6.8e-48  163.4   8.4    3.7  2  Peptidase_S8     Subtilase family
    7.8e-08   32.1   2.6    7.8e-08   32.1   2.6    5.7  5  Big_2            Bacterial Ig-like domain (group 2)
    0.00021   21.1   0.1    0.00021   21.1   0.1    6.4  7  FlgD_ig          FlgD Ig-like domain
    0.00052   19.7   0.6      0.024   14.3   0.1    3.3  3  DUF2271          Predicted periplasmic protein (DUF2271)
     0.0074   16.5  20.4       0.35   11.1   0.6    6.7  6  DUF4625          Domain of unknown function (DUF4625)
  ------ inclusion threshold ------
      0.058   13.9   3.1       0.55   10.7   0.1    3.6  2  DUF4179          Domain of unknown function (DUF4179)
       0.31   11.1   2.2       0.66   10.0   2.2    1.4  1  Peptidase_S49_N  Peptidase family S49 N-terminal
        2.4    8.5   6.9        8.3    6.8   0.0    5.0  4  RGI_lyase        Rhamnogalacturonan I lyases beta-sheet domai


Domain annotation for each model (and alignments):
>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.7  13.5   2.5e-81   5.1e-78       2     258 .]     837    1092 ..     836    1092 .. 0.97
   2 !  254.7  10.6   3.6e-79   7.2e-76       4     258 .]    1116    1364 ..    1113    1364 .. 0.95

  Alignments for each domain:
  == domain 1  score: 261.7 bits;  conditional E-value: 2.5e-81
                           S-layer    2 eneeeseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigfla 76  
                                        +n++ s ++ wt++++sg+y ++ ++ ssEs+ ++l++ksdr+i+e++++Ys++pve++f++ee+g+Y+ igfla
  gi|298676163|ref|YP_003727912.1|  837 ANKDLSLNYLWTSDSYSGLYRNLGSENSSESIKIHLDDKSDRNINEDDFEYSAKPVETAFKYEEFGTYKEIGFLA 911 
                                        5677889999***************************************************************** PP

                           S-layer   77 ekYfagydnsa.etsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgee 150 
                                        + Yfagy+ns+ +ts++ ++l+ ++L+kv+++++e++ +++gs+++L++gY++++kqiD+dg+kvw+eL+kdg++
  gi|298676163|ref|YP_003727912.1|  912 KPYFAGYSNSTnFTSNSSNMLAGDQLTKVVLNDNESRYVSVGSKISLKNGYTITPKQIDTDGNKVWFELSKDGNF 986 
                                        *******666559************************************************************** PP

                           S-layer  151 vdskvissskadstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksv 225 
                                        vd+k+++ +++++ +vy+kdlg++ +v +ia  v ++++++e+  v ++gifqis+d + ++ g+++ k++ +sv
  gi|298676163|ref|YP_003727912.1|  987 VDDKIVDINDDSDYFVYSKDLGSVSNVSVIALDVGDIYKSNET--VLVKGIFQISEDLIGLDIGNTYSKLQLESV 1059
                                        ********999*****************************998..899*************************** PP

                           S-layer  226 seneiemenddsitLsrdktieimddlkfkvaD 258 
                                        s+n++ m+n+dsi+L+r++t++++dd+ ++ aD
  gi|298676163|ref|YP_003727912.1| 1060 SSNKLLMKNSDSISLDRGTTTDVADDIIIRAAD 1092
                                        ******************************998 PP

  == domain 2  score: 254.7 bits;  conditional E-value: 3.6e-79
                           S-layer    4 eeeseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaek 78  
                                        ++e e++ w + nF g+yy++d+gl sEs+ + ++  +dr+i+eg+l+Y++ ++e++fe+ +wg+Ye +gf++ek
  gi|298676163|ref|YP_003727912.1| 1116 VAEGENCGWFPINFDGLYYNLDNGLMSESFNVVYD--NDRSIDEGNLEYNSCAIETDFEYPDWGKYESMGFMGEK 1188
                                        66788999***********************9965..7************************************* PP

                           S-layer   79 Yfagydnsa.etsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevd 152 
                                        Y+ gy +s+ + +++++l+s++ L+kvlid+++ kt+k +s l L++gY l ++qiD+dg+kvw++L+kdg++vd
  gi|298676163|ref|YP_003727912.1| 1189 YVSGYTSSTkFAENNTNLVSNNRLTKVLIDNNNVKTIKLDSALFLKNGYVLVPEQIDTDGNKVWFSLYKDGSFVD 1263
                                        *****5555499*************************************************************** PP

                           S-layer  153 skvissskadstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvse 227 
                                        +kv+++   ++++vy  d+g    v+iiavh++++ ++++   +  +g+fq+s+++ +i++gd fg+m+ ++vs 
  gi|298676163|ref|YP_003727912.1| 1264 DKVVTV---NDNFVYRIDMGTISHVPIIAVHISDIDKQSQ--EIEADGTFQVSENYESIHTGDMFGNMQLDTVSA 1333
                                        ******...**************************55544..4788***************************** PP

                           S-layer  228 neiemenddsitLsrdktieimddlkfkvaD 258 
                                        ++i+me+++sitL +++t+++mdd+kfkvaD
  gi|298676163|ref|YP_003727912.1| 1334 SQITMESNSSITLGKGETVYFMDDFKFKVAD 1364
                                        ******************************9 PP

>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.4   8.4   3.4e-51   6.8e-48       1     298 []     257     530 ..     257     530 .. 0.90
   2 ?  -30.2  35.4         9   1.8e+04      23     130 ..    1405    1526 ..    1394    1945 .. 0.59

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 3.4e-51
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaan.a 76 
                                       g+g ++a++DtG+d++  d s +                  + +ds t++++ ++ ++ +   HGthvAG +++  +
  gi|298676163|ref|YP_003727912.1| 257 GSGQTIAIADTGIDTGVDDSSMH-----------------PDLQDSLTGIREYEDAEDYSG--HGTHVAGSVVGDgK 314
                                       789***********999997722.................667788888877777777644..************99 PP

                                       .SSSSSB-SSTTSEEEEEE-SSTTSB-HH...HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  77 peegekngvapgakilsvkvldtsggsmetg.teliraieeaaedkvdvinmslgestslpktgrsiealainravn 152
                                       +++g+  g ap+ +++ ++ l++++++       l++ +++a ++++ ++++s+g   + +++g++++   ++++++
  gi|298676163|ref|YP_003727912.1| 315 KSSGKYRGTAPNTDLY-FQSLSPKDSKYLYPpNPLTELFKDAYNNGASIHSNSWG---HSGNYGSQSS--SVDEFMW 385
                                       999*************.7777777777776679**********************...99****9999..9****** PP

                                       CC.T-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES..TTSSB-TT--B-TT.......-EEEE-S-CCC CS
                                       xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 153 kk.gvlvviSaGNngktgsslqagspvgtpstsknvitvgayt..tegkiapfSsrGpssdgklkpdivapGgnivs 226
                                       ++ ++l+ ++aGN+g       + +++ +p+++kn +tvga +  +++++a+fSsrGp+ dg++kpd+vapG+ i s
  gi|298676163|ref|YP_003727912.1| 386 NHkDMLILFAAGNSG------ANQETIISPGNAKNCLTVGASEssDPKDVASFSSRGPTEDGRVKPDVVAPGTYINS 456
                                       ***************......8999*****************988999**************************888 PP

                                       CCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT....--HHHHHHHHHCCS-EE......SSSSSSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 227 twsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpk....ltpetvraallntAqdlgkadniesfaqGaG 298
                                       t s  ++++ g+  y+ + GTSmA+P+ agaaA +++++ +     t+  ++++l+n A d++ +dn  ++aqG+G
  gi|298676163|ref|YP_003727912.1| 457 TRSSYDSDGSGY--YTEKHGTSMATPLTAGAAASIRQYYVEnsiqPTASLIKTTLINGAHDISSNDNRPNYAQGWG 530
                                       777777666666..9**********************6655585555555*************************9 PP

  == domain 2  score: -30.2 bits;  conditional E-value: 9
                                        GEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B..........SSSSSB-SSTTS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxx RF
                      Peptidase_S8   23 ttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaan........apeegekngvapga 89  
                                        +++++ ++++ id + +++++++s +t   +++++ +       +v  ia ++        +++ +++  +ap++
  gi|298676163|ref|YP_003727912.1| 1405 NIHNTGNITWNIDGNTQKTDTQTSSSTYKVSYDTNGM------FNVTAIASYSnfteqyewSWNVSYNDTIAPNV 1473
                                        5555556666666555555555544444444444322......35555555555556666666666666666666 PP

                                        EEE...............EEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EE CS
                                        xxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   90 kil...............svkvldtsggsmetgteliraieeaaedkvdvinmslg 130 
                                        +++               sv + d+  ++    + li+ i++++  +  + +   g
  gi|298676163|ref|YP_003727912.1| 1474 SLTadtvellsvnnpasiSVSITDKYPNNT---EFLIKDISDEIMLEKNITSHVNG 1526
                                        666666666666666644444444444332...56666666666655555444444 PP

>> Big_2  Bacterial Ig-like domain (group 2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   2.6   3.9e-11   7.8e-08       2      65 ..     659     724 ..     658     738 .. 0.92
   2 ?   -1.5   0.7       1.2   2.4e+03      18      67 ..    1398    1447 ..    1390    1456 .. 0.56
   3 ?   -0.9   1.1      0.79   1.6e+03      20      61 ..    1565    1608 ..    1561    1608 .. 0.78
   4 ?    0.7   1.2      0.25     5e+02      26      49 ..    1777    1801 ..    1763    1807 .. 0.81
   5 ?   -2.6   5.3       2.6   5.3e+03       8      78 ..    1911    1995 ..    1909    1996 .. 0.67

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 3.9e-11
                                       -SEEEEEEC-CEEETT-EEEEEEEEESTT-S-..--EEEEECC-SSEEEETCCEECCCSSEEEEEE CS
                             Big_2   2 vtsvtvsptevtvkkgatqqltvevtpssasd..kkvtwtssngsvAtVsatGlVtavaaGkatit 65 
                                       v ++++ p++vt  +++t+ + + v+ ++ +     v wt++n++v++V+ tGl ta+  G++ti+
  gi|298676163|ref|YP_003727912.1| 659 VSNIEINPENVTAYEDETLSFNADVYDQDGNEveLPVNWTITNTTVGVVNETGLFTAKNIGSTTIE 724
                                       889**************************9998889*****************************8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                                        -EEEEEEEEESTT-S---EEEEECC-SSEEEE.....TCCEECCCSSEEEEEEEE CS
                             Big_2   18 atqqltvevtpssasdkkvtwtssngsvAtVs.....atGlVtavaaGkatitat 67  
                                         tq ++  +  +    + +tw++++++   ++     +t +V+  + G  ++ta+
  gi|298676163|ref|YP_003727912.1| 1398 HTQEFSINIHNT----GNITWNIDGNTQ-KTDtqtssSTYKVSYDTNGMFNVTAI 1447
                                        555555444433....458999955432.22223445666666666666666665 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.79
                                        EEEEEEEESTT-S-..--EEEEECC-SSEEEETCCEECCCSSEE CS
                             Big_2   20 qqltvevtpssasd..kkvtwtssngsvAtVsatGlVtavaaGk 61  
                                        +  +v+v+ ++ +   k++t t s+g+++ +++t++++a+a G+
  gi|298676163|ref|YP_003727912.1| 1565 KNISVTVDNEKPTIdiKDITGTHSAGDKVYTNSTLTINASASGT 1608
                                        555666666665556699999999****************9995 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.25
                                        EESTT-S-.--EEEEECC-SSEEEE CS
                             Big_2   26 vtpssasd.kkvtwtssngsvAtVs 49  
                                        + +s+ ++  ++t+++s+++++tV+
  gi|298676163|ref|YP_003727912.1| 1777 GKMSNEKTgTSITFNTSDNTKGTVT 1801
                                        566777777899**********998 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 2.6
                                        EEC-CEEETT-EEEEEEEEESTT-S-......--EEEEECC-SSEEEE......TCCEECCCSSEEE..EEEEEE CS
                             Big_2    8 sptevtvkkgatqqltvevtpssasd......kkvtwtssngsvAtVs......atGlVtavaaGka..titats 68  
                                         p+e +++ + t +++v + +s+ ++       +++++s+++++   +      at + t +++Gk   t+t+ +
  gi|298676163|ref|YP_003727912.1| 1911 YPAEGSILDSSTSKVKVKFSYSDGQSgintskTTIKFESDDKTTSDNTtitseyATYNSTELSVGKYnsTVTVYD 1985
                                        566677777777778888777777777777555666777666554222334788888889999998533788888 PP

                                        TTTSSEEEEE CS
                             Big_2   69 kdgndkatlt 78  
                                        + gn+k++ t
  gi|298676163|ref|YP_003727912.1| 1986 NAGNSKTYTT 1995
                                        8888888766 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.3   4.6e+03      67      77 ..     628     638 ..     625     640 .. 0.86
   2 ?   -0.7   0.1      0.69   1.4e+03      23      64 ..     650     691 ..     641     693 .. 0.79
   3 ?   -2.2   0.1         2   3.9e+03      61      76 ..     794     809 ..     791     811 .. 0.84
   4 ?    0.4   0.1       0.3   5.9e+02      25      47 ..     990    1012 ..     967    1019 .. 0.77
   5 !   21.1   0.1     1e-07   0.00021      23      77 ..    1501    1557 ..    1478    1559 .. 0.76
   6 ?   -3.6   0.0       5.4   1.1e+04      66      77 ..    1656    1667 ..    1655    1668 .. 0.86
   7 ?   -0.2   0.2      0.47   9.4e+02      12      39 ..    1966    1992 ..    1955    1996 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.3
                                       EEEEEEEEEET CS
                           FlgD_ig  67 GaYtvkvtats 77 
                                       G+Ytvkv+ ++
  gi|298676163|ref|YP_003727912.1| 628 GRYTVKVKGSN 638
                                       9******9875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.69
                                       EEEEEEEE-SS--EEEEEEEEESSSEEEEEEE-SB-TTS-B- CS
                           FlgD_ig  23 devtvtikDasGevVrtidlgaqsaGvvsftWdGtdndGnkl 64 
                                       ++++++  D s+ +++  +++a +  + sf+ d +d+dGn +
  gi|298676163|ref|YP_003727912.1| 650 TSGSIKTVDVSNIEINPENVTAYEDETLSFNADVYDQDGNEV 691
                                       567777788888888888888888888888888888888876 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2
                                       S-B--SEEEEEEEEEE CS
                           FlgD_ig  61 GnkladGaYtvkvtat 76 
                                        n +  G Y++++ta+
  gi|298676163|ref|YP_003727912.1| 794 NNTADVGVYNITATAE 809
                                       678899********96 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.3
                                        EEEEEE-SS--EEEEEEEEESSS CS
                           FlgD_ig   25 vtvtikDasGevVrtidlgaqsa 47  
                                          v i+D+s   V++ dlg++s 
  gi|298676163|ref|YP_003727912.1|  990 KIVDINDDSDYFVYSKDLGSVSN 1012
                                        4699***************9875 PP

  == domain 5  score: 21.1 bits;  conditional E-value: 1e-07
                                        EEEEEEEE-SS--EEEEEEEEESSSE..EEEEEE-SB-TTS-B--SEEEEEEEEEET CS
                           FlgD_ig   23 devtvtikDasGevVrtidlgaqsaG..vvsftWdGtdndGnkladGaYtvkvtats 77  
                                         ++++ ikD s e+    + +++  G  +++ftW+ t+++ +++a+G+Y + v++t+
  gi|298676163|ref|YP_003727912.1| 1501 NNTEFLIKDISDEIMLEKNITSHVNGenQYNFTWNATNSSNEPVANGKYYLVVNSTD 1557
                                        45588899999999966666666666115789*********************9996 PP

  == domain 6  score: -3.6 bits;  conditional E-value: 5.4
                                        SEEEEEEEEEET CS
                           FlgD_ig   66 dGaYtvkvtats 77  
                                        dG+Y+v v+a++
  gi|298676163|ref|YP_003727912.1| 1656 DGRYNVIVEAAD 1667
                                        8*******9975 PP

  == domain 7  score: -0.2 bits;  conditional E-value: 0.47
                                        EEEEEE.ESSSEEEEEEEE-SS--EEEE CS
                           FlgD_ig   12 aplgvelpeaadevtvtikDasGevVrt 39  
                                        ++ + el+ +  + tvt++D +G+  +t
  gi|298676163|ref|YP_003727912.1| 1966 TYNSTELSVGKYNSTVTVYDNAGNS-KT 1992
                                        455555777777889******9997.55 PP

>> DUF2271  Predicted periplasmic protein (DUF2271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   1.2e-05     0.024      72     123 ..    1525    1575 ..    1511    1588 .. 0.86
   2 ?    1.3   0.0      0.13   2.5e+02      92     118 ..    1655    1681 ..    1634    1690 .. 0.80
   3 ?   -2.7   0.1       2.2   4.3e+03      89     126 ..    1970    2008 ..    1957    2022 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                           DUF2271   72 rapGkyklkvdekddklkklkaGkYklvvEaaredggrelvrveielttkaa 123 
                                         ++ +y+++++ ++++ +++++GkY lvv ++   g++  +++ ++++++ +
  gi|298676163|ref|YP_003727912.1| 1525 NGENQYNFTWNATNSSNEPVANGKYYLVVNSTDDAGNTASKNISVTVDNE-K 1575
                                        55558999***************************************999.3 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.13
                           DUF2271   92 kaGkYklvvEaaredggrelvrveiel 118 
                                        ++G Y++ vEaa   ++ + ++  i+l
  gi|298676163|ref|YP_003727912.1| 1655 DDGRYNVIVEAADSANNSNSSKSGIDL 1681
                                        68**********999998888776665 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.2
                           DUF2271   89 kklkaGkYklvvEaaredggrelvrveielttk.aakka 126 
                                         +l  GkY+  v +    g+ ++++  +e+ ++ + +++
  gi|298676163|ref|YP_003727912.1| 1970 TELSVGKYNSTVTVYDNAGNSKTYTTSFEIAEQkTDENV 2008
                                        466667777777777777777777777777666333333 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.54   1.1e+03      17      48 ..     657     687 ..     651     693 .. 0.76
   2 ?   -0.7   0.4      0.78   1.6e+03      49      88 ..    1398    1441 ..    1374    1458 .. 0.68
   3 !    9.0   0.8   0.00078       1.6      51     130 ..    1489    1570 ..    1477    1572 .. 0.74
   4 ?    4.8   0.1     0.016        31      10      43 ..    1571    1604 ..    1565    1609 .. 0.90
   5 ?   -1.5   0.0       1.4   2.7e+03     105     130 ..    1655    1680 ..    1626    1682 .. 0.85
   6 !   11.1   0.6   0.00017      0.35      74     131 ..    1942    1999 ..    1893    2000 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.54
                           DUF4625  17 idllevsaepeeeevlkiGetlhfeaklsdne 48 
                                       +d+++++ +p e+ +++ +etl+f+a++ d++
  gi|298676163|ref|YP_003727912.1| 657 VDVSNIEINP-ENVTAYEDETLSFNADVYDQD 687
                                       4555555544.556788999********9986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.78
                           DUF4625   49 alasykvdihn......nfDhhshsseakegekewsfeksydlsgs 88  
                                        + ++++++ihn      n D+++++++++  +++ +++ syd++g 
  gi|298676163|ref|YP_003727912.1| 1398 HTQEFSINIHNtgnitwNIDGNTQKTDTQ--TSSSTYKVSYDTNGM 1441
                                        44566677766444444568887777776..777788888877664 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00078
                           DUF4625   51 asykvdihnnfDhhshsseakegekewsfeksy.dlsgskkeyelheeieiPad..aeaGdYhlvirvtDasGne 122 
                                        as++v+i   + +++     k+   e   ek++ +  +++++y+++ + +  ++  +++G+Y lv+  tD +Gn+
  gi|298676163|ref|YP_003727912.1| 1489 ASISVSITDKYPNNTEFLI-KDISDEIMLEKNItSHVNGENQYNFTWNATNSSNepVANGKYYLVVNSTDDAGNT 1562
                                        5666677444444444443.34577888888886677788888888888777777799***************** PP

                           DUF4625  123 teesreik 130 
                                          ++++++
  gi|298676163|ref|YP_003727912.1| 1563 ASKNISVT 1570
                                        99998876 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.016
                           DUF4625   10 edtekPvidllevsaepeeeevlkiGetlhfeak 43  
                                         d+ekP+id+  ++ +++ ++++++ +tl+++a 
  gi|298676163|ref|YP_003727912.1| 1571 VDNEKPTIDIKDITGTHSAGDKVYTNSTLTINAS 1604
                                        599***************************9986 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 1.4
                           DUF4625  105 eaGdYhlvirvtDasGneteesreik 130 
                                        ++G Y++++ + D + n++  +  i+
  gi|298676163|ref|YP_003727912.1| 1655 DDGRYNVIVEAADSANNSNSSKSGID 1680
                                        57*************99999887776 PP

  == domain 6  score: 11.1 bits;  conditional E-value: 0.00017
                           DUF4625   74 ekewsfeksydlsgskkeyelheeieiPadaeaGdYhlvirvtDasGneteesreiki 131 
                                        ++  +fe + +++  +++ + +      ++   G+Y+ +++v D++Gn++ + ++++i
  gi|298676163|ref|YP_003727912.1| 1942 KTTIKFESDDKTTSDNTTITSEYATYNSTELSVGKYNSTVTVYDNAGNSKTYTTSFEI 1999
                                        45666777666666655555555555567799*********************99998 PP

>> DUF4179  Domain of unknown function (DUF4179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00028      0.55      24      82 ..     909     977 ..     907     981 .. 0.73
   2 ?    0.7   0.4      0.37   7.4e+02      25      84 ..    1194    1254 ..    1186    1256 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00028
                                       XXXXXXXXXXX..--SS-HHHHT--SS-.........HHHHSEEEEEEEEETTEEEEEEEEEE-SSEEE CS
                           DUF4179  24 rllspalAsaln.pvigslfeklsdskg.........eqeyvkpvnksaednGitvtvnevvaDgnkli 82 
                                        l+ p +A + n + + s  +++  +++         e+ yv++  k   +nG+t+t +++ +Dgnk++
  gi|298676163|ref|YP_003727912.1| 909 FLAKPYFAGYSNsTNFTSNSSNMLAGDQltkvvlndnESRYVSVGSKISLKNGYTITPKQIDTDGNKVW 977
                                       5677888877754444444444444333667777777888888889999******************97 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.37
                                        XXXXXXXXXX.--SS-HHHHT--SS-..HHHHSEEEEEEE...EETTEEEEEEEEEE-SSEEEEE CS
                           DUF4179   25 llspalAsalnpvigslfeklsdskg..eqeyvkpvnksa...ednGitvtvnevvaDgnklivs 84  
                                        ++s+ +A++      +l+++ + +k    ++ vk +        +nG+ +  +++ +Dgnk+++s
  gi|298676163|ref|YP_003727912.1| 1194 TSSTKFAENN----TNLVSNNRLTKVliDNNNVKTIKLDSalfLKNGYVLVPEQIDTDGNKVWFS 1254
                                        5566677666....3444444444446677777777555456799****************9986 PP

>> Peptidase_S49_N  Peptidase family S49 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.2   0.00033      0.66      52     117 ..      25     115 ..       5     134 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00033
                   Peptidase_S49_N  52 elkeeleealldeeelkaaekkekkeekeekkaekkkake...........................eeekkrvfvl 101
                                       ++++++++   +  ++ +++k e+ke k++++++kk+ ++                            ++k++++++
  gi|298676163|ref|YP_003727912.1|  25 KVSTNVSDDNSS--NQLEFKKYEEKELKTNNNEKKKSINKnkiylkqgaietnksnlttqskpkqfyPDSKEKIYLI 99 
                                       333333322221..1222233333333333333333333234455566666788888888889999999******** PP

                   Peptidase_S49_N 102 dFkGdikAsevesLre 117
                                       +Fk  ik + ++sL+ 
  gi|298676163|ref|YP_003727912.1| 100 QFKDVIKDEWIQSLKS 115
                                       ****999999999975 PP

>> RGI_lyase  Rhamnogalacturonan I lyases beta-sheet domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       8.5   1.7e+04      38      59 ..     356     377 ..     354     381 .. 0.84
   2 ?   -0.5   0.1       0.8   1.6e+03      15      48 ..     958     991 ..     954    1014 .. 0.78
   3 ?    6.8   0.0    0.0041       8.3      26      56 ..    1244    1274 ..    1230    1300 .. 0.87
   4 ?   -0.2   0.5      0.62   1.2e+03      47      74 ..    1414    1440 ..    1396    1448 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 8.5
                                       EETTEE-CSSSB-SSSEEEETT CS
                         RGI_lyase  38 YrdgkkinsapitdstnylDak 59 
                                       Y +g+ i+s++  +s ny  ++
  gi|298676163|ref|YP_003727912.1| 356 YNNGASIHSNSWGHSGNYGSQS 377
                                       99********999999997665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.8
                                       ETTEEEEE--B-TTS-TT-EEEEEETTEE-CSSS CS
                         RGI_lyase  15 teegvfvsWRllgteeeevaFnvYrdgkkinsap 48 
                                        ++g  ++ + + t+ ++v F++ +dg+ + ++ 
  gi|298676163|ref|YP_003727912.1| 958 LKNGYTITPKQIDTDGNKVWFELSKDGNFVDDKI 991
                                       5677777778888999999999999999886654 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0041
                                        -TTS-TT-EEEEEETTEE-CSSSB-SSSEEE CS
                         RGI_lyase   26 lgteeeevaFnvYrdgkkinsapitdstnyl 56  
                                        + t+ ++v F +Y+dg+ + ++ +t + n++
  gi|298676163|ref|YP_003727912.1| 1244 IDTDGNKVWFSLYKDGSFVDDKVVTVNDNFV 1274
                                        5689999*****************9999997 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.62
                                        SSB-SSSEEEETT--TT-EEEEEEEETT CS
                         RGI_lyase   47 apitdstnylDakgtasskYtvkavvng 74  
                                         +i  +t+ +D++ t+ss+Y+v+  +ng
  gi|298676163|ref|YP_003727912.1| 1414 WNIDGNTQKTDTQ-TSSSTYKVSYDTNG 1440
                                        5788899999999.5599****988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1178  (0.0657036); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.98u 0.38s 00:00:01.36 Elapsed: 00:00:00.54
# Mc/sec: 12644.86
//
Query:       gi|298676164|ref|YP_003727913.1|  [L=609]
Description: hypothetical protein Metev_2305 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.33s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 3442.48
//
Query:       gi|298676165|ref|YP_003727914.1|  [L=568]
Description: hypothetical protein Metev_2306 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score 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   0.8       0.21   11.9   0.8    1.7  1  KxDL      Uncharacterized conserved protein


Domain annotation for each model (and alignments):
>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.8   1.2e-05      0.21      20      84 ..     227     293 ..     220     295 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.2e-05
                              KxDL  20 qtsgrlnkknreLlelnalsqerl..aklrarfkqgtkllkevkkdLesifkkirslkaklakkyPe 84 
                                        + ++ln++++ L+++n+l+++    +  ++ fk+  +++    ++L+++  +i++++a+l k+ P+
  gi|298676165|ref|YP_003727914.1| 227 TIEAHLNSTKENLKNVNHLVNKSNdaEVKNEYFKEMLNVITLSVNQLQTSGYNIEQIRANLDKRLPN 293
                                       56789***************87642145566789999**************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.32s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3387.48
//
Query:       gi|298676166|ref|YP_003727915.1|  [L=486]
Description: hypothetical protein Metev_2307 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.053   13.6   0.2       0.15   12.1   0.2    1.7  1  TaqI_C    TaqI-like C-terminal specificity domain


Domain annotation for each model (and alignments):
>> TaqI_C  TaqI-like C-terminal specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   8.3e-06      0.15       8      71 ..     315     380 ..     310     397 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.3e-06
                            TaqI_C   8 dikrysieikgnYldlikkklkneka....kelfeekpKilv.rdiskkldaaydekayyvlntlylli 71 
                                       +i+   i+++g+Yl+ i++ +k+ ++    +++f+   Ki++  d +++l + +d + y+ + +l++  
  gi|298676166|ref|YP_003727915.1| 315 NISLQTIDYPGEYLKQIPDAIKGTSElitkDRYFQ---KIFFnVDSANTLIFLIDIERYFNKDKLNISD 380
                                       788899*******************8888577777...***9567888*************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.38s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 2614.98
//
Query:       gi|298676167|ref|YP_003727916.1|  [L=1066]
Description: hypothetical protein Metev_2308 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.1e-09   36.5   0.0    3.1e-09   36.5   0.0    2.4  2  Tubulin_2  Tubulin like
    4.4e-07   30.3   0.0    4.4e-07   30.3   0.0    4.1  4  Tubulin    Tubulin/FtsZ family, GTPase domain
  ------ inclusion threshold ------
      0.024   14.7   0.9       0.23   11.6   0.2    3.1  2  DUF1563    Protein of unknown function (DUF1563)


Domain annotation for each model (and alignments):
>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   5.2e-13   3.1e-09     100     227 ..     124     237 ..      10     343 .. 0.67
   2 ?   -3.9   1.1      0.98   5.8e+03      49      79 ..     534     564 ..     493     606 .. 0.54

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 5.2e-13
                         Tubulin_2 100 WlppeleelrkapeseGAGqiRtvGRlalfanleeirealrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDv 176
                                       W  +++ ++ ++   +G   +R +G+++ ++ + e  + ++++++  +++       +v +v++L GGTGSG+++D+
  gi|298676167|ref|YP_003727916.1| 124 WWIKSEYINENLDFATGVIRKRGLGKALYYKAYAE-DDDISNVVDLPENG-------KVALVVGLGGGTGSGLMIDM 192
                                       44455555555544455555666666544444443.66777777777774.......9******************* PP

                         Tubulin_2 177 ayllrkilkeekqkvkiiglvllPdvfplnkeggervkaNayaaLkELna...l 227
                                       a  l+   + +    +i+++ +lP+       +g + ++Naya+L EL++   +
  gi|298676167|ref|YP_003727916.1| 193 ARHLKRQQPTT----EITLFGVLPNQ-----VEGVKENTNAYATLSELEYlnlI 237
                                       98777655554....59********7.....33567789***********5441 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.98
                         Tubulin_2  49 kdatdetaekageslksrekealsissaevd 79 
                                       +++ +e ++k ++ +++ +k + s  +++v+
  gi|298676167|ref|YP_003727916.1| 534 QQKVREFVQKIQTPVQQYQKIQDSNLETDVT 564
                                       2223333333333333333333333333333 PP

>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   7.3e-11   4.4e-07     106     178 ..     162     232 ..     146     239 .. 0.88
   2 ?    2.0   0.4     0.034   2.1e+02      25     115 ..     332     412 ..     320     424 .. 0.62
   3 ?   -3.6   1.5       1.8   1.1e+04      58     114 ..     494     545 ..     459     553 .. 0.65
   4 ?   -1.7   0.1      0.47   2.8e+03     172     192 ..     621     641 ..     608     678 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 7.3e-11
                                       HHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE--GG.G-HHHHHHHHHHHHHHH CS
                           Tubulin 106 irkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPsefsevvvepynailalkeli 178
                                       i + v+  ++  ++ ++ +lgGGTGSGl   +++ lk++ p + ++ + vlP++  e+v e+ na  +l+el 
  gi|298676167|ref|YP_003727916.1| 162 ISNVVDLPEN-GKVALVVGLGGGTGSGLMIDMARHLKRQQPTTEITLFGVLPNQV-EGVKENTNAYATLSELE 232
                                       5555555555.568999**************************************.**************996 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.034
                                       HHCH....HHHT......TTEEEEE....EEESBHHHHHTS-GS......EEEE--CCCCTTC--TT-HHHHHHHHH CS
                           Tubulin  25 ehgiqsdgdslesfFse.sgkveyiprsvaidtdpqvlneikagselfnpnklllgkegagnngaggypevgkeaae 100
                                       +++++ ++d  +s+F+  ++ ++y p  + + + +q++ne+++    f++ + ll      n++ + ++    +   
  gi|298676167|ref|YP_003727916.1| 332 QQSLEAENDLYSSIFRYlENIEKYHPDKLQVQLKEQDINELQER---FSNINSLLNL----NLFKKLNY----QSLS 397
                                       3444444466666665556667888****************999...5555555532....23322222....2444 PP

                                       HTHHHHHHHHTT-SE CS
                           Tubulin 101 eileeirkevekcds 115
                                          ++i++++e+cds
  gi|298676167|ref|YP_003727916.1| 398 VYTDIIKNAAEQCDS 412
                                       445555555555555 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.8
                                       HHHHHTS-GS......EEEE--CCC.CTTC--TT-HHHHHHHHHHTHHHHHHHHTT-S CS
                           Tubulin  58 pqvlneikagselfnpnklllgkeg.agnngaggypevgkeaaeeileeirkevekcd 114
                                        q l+++ ++   f+++k  l+ke   ++ ++++ +e   +  +e+++++r+ v+k +
  gi|298676167|ref|YP_003727916.1| 494 LQRLQSSYNN---FKERKERLKKEFkEKEDYIQSLQE---KENDENQQKVREFVQKIQ 545
                                       3344444444...777777776665566666666666...556777777777777655 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.47
                                       HHHHHHHHT-SEEEEEEHHHH CS
                           Tubulin 172 lalkelieesdavividNdaL 192
                                       ++lk+l++   a ++i+N++ 
  gi|298676167|ref|YP_003727916.1| 621 ESLKKLKQAKKAFLLIHNENV 641
                                       677777777777777777765 PP

>> DUF1563  Protein of unknown function (DUF1563)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.2   7.4e+03      11      22 ..     789     800 ..     787     815 .. 0.72
   2 ?   11.6   0.2   3.9e-05      0.23      24      40 ..     960     976 ..     938     978 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.2
                           DUF1563  11 LETLENLYaTYV 22 
                                          L NL +T+ 
  gi|298676167|ref|YP_003727916.1| 789 FKNLQNLRTTFT 800
                                       567899999975 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.9e-05
                           DUF1563  24 ysLKQiFLDkiQKisKa 40 
                                        ++  iFLD+iQKi Ka
  gi|298676167|ref|YP_003727916.1| 960 VFITGIFLDNIQKIVKA 976
                                       46788***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1066 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3161  (0.176307); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 1.02u 0.35s 00:00:01.37 Elapsed: 00:00:00.56
# Mc/sec: 5743.65
//
Query:       gi|298676168|ref|YP_003727917.1|  [L=313]
Description: flagellin [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-31  109.6   7.0    1.7e-31  109.6   7.0    2.1  2  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.034   13.8   0.1       0.11   12.2   0.1    1.7  1  VanW            VanW like protein


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   7.0   1.9e-35   1.7e-31       1     137 [.      21     176 ..      21     197 .. 0.89
   2 ?    3.0   2.9     0.012     1e+02     103     164 .]     213     297 ..     192     297 .. 0.62

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 1.9e-35
                                       X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE.EEE-SSSSSE....EEEE CS
                    Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg.dsatngtine....itiy 72 
                                       ++vgigtlI+fIAm+lVAAvaa vli+t+g lqqkaq+tgee+t+qv+s+l++  + g  ++t+gt++       i 
  gi|298676168|ref|YP_003727917.1|  21 AQVGIGTLIIFIAMILVAAVAAAVLIQTSGNLQQKAQTTGEEATSQVASNLNVRTIEGlRGSTSGTLEPtvdqFLIR 97 
                                       79********************************************************8455555544466567777 PP

                                       EE--TTS--EEGGG-EEEEEESS--EE--E................................T-EE-TT-EEEEEEE CS
                    Arch_flagellin  73 vklnaGsspidlnkttisvtddgqetlltad..............efgivvisdtdgsltngdevlekgekvelevn 135
                                          +aG++++dl++ +++v+d ++ ++l ++               f+  +i d+d+s++++++v++kg++++l + 
  gi|298676168|ref|YP_003727917.1|  98 TSISAGGNRMDLSQLIVTVSDLNKTNTLEYNysekeaflfnksksYFTAKAIRDEDQSFSSDSPVMNKGDLIALSIS 174
                                       7777*******************999999999********************************************9 PP

                                       -- CS
                    Arch_flagellin 136 vn 137
                                       + 
  gi|298676168|ref|YP_003727917.1| 175 TL 176
                                       74 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.012
                                       ..........................T-EE-TT-EEEEEEE--..................TTT---TT-EEEEEEE CS
                    Arch_flagellin 103 d.......efgivvisdtdgsltng.devlekgekvelevnvn..................eddgitagdevsvevv 153
                                       d       ++++++ sd  +++++g + v e ++++el    n                   d +++++++ +++++
  gi|298676168|ref|YP_003727917.1| 213 DhygvdnsSTTLYNASD--DTVDSGnYTVFESNNTIELDGH-NlsdneytltygysenwnsSDLKLKPRTDLKITLT 286
                                       23334422222222222..2222223466666666666644.257888888888999999978889*********** PP

                                       -SSS--EEEEE CS
                    Arch_flagellin 154 penGasttief 164
                                       pe+G s ++ef
  gi|298676168|ref|YP_003727917.1| 287 PETGTSKILEF 297
                                       *****999887 PP

>> VanW  VanW like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.2e-05      0.11      41     122 ..     200     291 ..     187     297 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.2e-05
                              VanW  41 eakvivngklvkgvGGGvcqvsttlynaall....agleiverh......pHslpvsyvplglDAtvaygslDlkfk 107
                                       +++ i+++++ k    Gv + sttlyna        ++++ e +       H+l ++ ++l  +   +++s Dlk+k
  gi|298676168|ref|YP_003727917.1| 200 DGTYISSNQTYKLDHYGVDNSSTTLYNASDDtvdsGNYTVFESNntieldGHNLSDNEYTLTYGYSENWNSSDLKLK 276
                                       678889999999999************976533322455555543333337888888888888888899999***99 PP

                              VanW 108 Nntdypilieasvsd 122
                                         td +i +  ++ +
  gi|298676168|ref|YP_003727917.1| 277 PRTDLKITLTPETGT 291
                                       999999988776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.37s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 1734.89
//
Query:       gi|298676169|ref|YP_003727918.1|  [L=68]
Description: hypothetical protein Metev_2310 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.045   14.0   0.2      0.062   13.5   0.2    1.2  1  Clr5      Clr5 domain
       0.14   12.5   0.0       0.16   12.3   0.0    1.1  1  SF1-HH    Splicing factor 1 helix-hairpin domain


Domain annotation for each model (and alignments):
>> Clr5  Clr5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   6.9e-06     0.062       3      33 ..      28      57 ..      27      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.9e-06
                              Clr5  3 edWeahkatIrrLYleenrsLkdvmeiMeee 33
                                       dW+++ + I +LY +e+  ++++++ ++ e
  gi|298676169|ref|YP_003727918.1| 28 IDWDDLTEKILDLY-TEGFDIDEIIQKLKSE 57
                                      79************.9**********99875 PP

>> SF1-HH  Splicing factor 1 helix-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.8e-05      0.16      27      53 ..      29      58 ..      12      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                            SF1-HH 27 n...ltqeqleayllqlrieeitrkLrtgd 53
                                      +   lt++ l+ y   + i+ei +kL++++
  gi|298676169|ref|YP_003727918.1| 29 DwddLTEKILDLYTEGFDIDEIIQKLKSEE 58
                                      33359**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.51
# Mc/sec: 404.03
//
Query:       gi|298676170|ref|YP_003727919.1|  [L=59]
Description: hypothetical protein Metev_2311 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.016   14.9   0.1      0.018   14.8   0.1    1.0  1  TraT       Enterobacterial TraT complement resistance protein
      0.049   13.2   0.1      0.056   13.0   0.1    1.2  1  AHJR-like  REase_AHJR-like


Domain annotation for each model (and alignments):
>> TraT  Enterobacterial TraT complement resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1     2e-06     0.018      18      56 ..       9      47 ..       5      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-06
                              TraT 18 akekrtiyvqirntSdkqeldleqkiiskLeakGYkvvn 56
                                      +++++t  + ++n+ + +e +l++kii+k +++GY++ +
  gi|298676170|ref|YP_003727919.1|  9 GPNQKTSNLTLKNADKLSESELKKKIIEKYKENGYTIKQ 47
                                      57899999****************************965 PP

>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   6.2e-06     0.056       5      33 ..      22      51 ..      11      58 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.2e-06
                         AHJR-like  5 tsel.ererleslaeqyrekGyevllhPnr 33
                                      + +l e e  ++++e+y+e+Gy++ + P +
  gi|298676170|ref|YP_003727919.1| 22 ADKLsESELKKKIIEKYKENGYTIKQLPIS 51
                                      4444055555789***********999943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1091  (0.0608511); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.34s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 341.68
//
Query:       gi|298676171|ref|YP_003727920.1|  [L=414]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for 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-26   90.6   0.8    2.2e-25   89.2   0.0    2.0  2  OrfB_IS605      Probable transposase
    8.9e-12   44.8   0.3    2.4e-11   43.4   0.1    1.9  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.018   15.5   0.0      0.037   14.4   0.0    1.5  1  RuvX            Holliday junction resolvase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2      0.45   2.7e+03      71      86 ..      16      31 ..       4      64 .. 0.66
   2 !   89.2   0.0   3.7e-29   2.2e-25      15     119 ..     190     292 ..     176     293 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.45
                        OrfB_IS605 71 kkasrklarlhrkrsr 86
                                       ++ +++++l++++++
  gi|298676171|ref|YP_003727920.1| 16 YEVLKRITKLSKNLYN 31
                                      3444444444444444 PP

  == domain 2  score: 89.2 bits;  conditional E-value: 3.7e-29
                        OrfB_IS605  15 gnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrkhl 91 
                                        nk+++iDlG+nn+at+v+++gt+f+++gr lks +++++k +  lqs ++k++   k  +kl  l++kr+++++++
  gi|298676171|ref|YP_003727920.1| 190 YNKHLSIDLGVNNFATCVDTNGTAFIIEGRGLKSYNRWWNKVKSGLQSVYDKQG--IKSGQKLNWLFEKRKNKLNDF 264
                                       699**************************************************9..9******************** PP

                        OrfB_IS605  92 lhklathliktlkevgvetLnvgnmkdi 119
                                       +++ +++++k++ +++++++++g++kdi
  gi|298676171|ref|YP_003727920.1| 265 MNQSVNYIVKHCIDNNIGNIIIGELKDI 292
                                       *************************998 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.4   1.4e+04       9      22 ..     167     180 ..     167     181 .. 0.81
   2 !   43.4   0.1     4e-15   2.4e-11       1      69 []     311     385 ..     311     385 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.4
                    OrfB_Zn_ribbon   9 eykakeyGikveev 22 
                                       +y  +++ i++++ 
  gi|298676171|ref|YP_003727920.1| 167 KYNGQWFEIEYVYR 180
                                       68899999999885 PP

  == domain 2  score: 43.4 bits;  conditional E-value: 4e-15
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f+k+k++l+ k++ yGi+ +ev++ayTSkt +   +  ++      ++ +r +  ++ g  +++Dvn+a+Nil++
  gi|298676171|ref|YP_003727920.1| 311 FGKFKQKLRSKCEYYGINCIEVDEAYTSKTDALALEPIEKhqkymgKRVKRGLFQSSTGKLLNADVNGALNILRK 385
                                       89****************************887776666666688977788888888***************986 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   6.1e-06     0.037      36     107 ..     263     346 ..     241     362 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.1e-06
                                       H..HHHHHHHHHHHHHTT--EEEEE--......---..-SSS---SSTTHHHHHHHHHT....T-EEEEE--S---- CS
                              RuvX  36 k..ekdleelkelvkeeeveeiVvGlP......lnl..dgsegesakkvrkfaeeLakrl..kklpvelvDErlttv 100
                                       +  +++++ + + + ++++ +i++G         n+  +++++ ++  + kf ++L++++  ++++ + vDE +t++
  gi|298676171|ref|YP_003727920.1| 263 DfmNQSVNYIVKHCIDNNIGNIIIGELkdikqnSNMgkKNNQTFQTIPFGKFKQKLRSKCeyYGINCIEVDEAYTSK 339
                                       14479999*****************88677777444114455555556699*******9977899***********9 PP

                                       XXXXXXX CS
                              RuvX 101 eaerilr 107
                                       + + +l+
  gi|298676171|ref|YP_003727920.1| 340 TDALALE 346
                                       8776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1095  (0.0610742); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 3130.12
//
Query:       gi|298676172|ref|YP_003727921.1|  [L=835]
Description: hypothetical protein Metev_2313 [Methanohalobium evestigatum Z-7303]
Scores for 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  123.5   0.2    1.1e-35  121.6   0.1    2.1  2  MTES_1575        REase_MTES_1575
    1.8e-14   53.8   3.5      3e-13   49.9   1.7    2.8  2  AAA_12           AAA domain
    1.5e-09   38.1   0.1    3.1e-09   37.0   0.1    1.6  1  AAA_11           AAA domain
    0.00027   20.7   0.0    0.00079   19.3   0.0    1.8  1  DUF559           Protein of unknown function (DUF559)
     0.0014   18.6   0.5     0.0053   16.8   0.1    2.3  3  RAP              RAP domain
     0.0021   18.4   0.0     0.0043   17.4   0.0    1.7  1  AAA_19           AAA domain
      0.004   16.9   0.0      0.009   15.7   0.0    1.5  1  AAA_30           AAA domain
     0.0091   15.6   1.5      0.021   14.4   1.5    1.7  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.035   13.9   0.0    1.5  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> MTES_1575  REase_MTES_1575
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.1   8.3e+03      11      42 ..     542     572 ..     536     585 .. 0.79
   2 !  121.6   0.1   5.8e-39   1.1e-35       1      95 []     722     819 ..     722     819 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.1
                         MTES_1575  11 ergykvkpqvgvggfriDlvvedpgkyllaIe 42 
                                       + g ++k+  +v++  ++++ ++p ++ l++ 
  gi|298676172|ref|YP_003727921.1| 542 KGGTNIKEAQRVAEAAVEFMQTNP-EQSLGVV 572
                                       568889999999999999999999.7777775 PP

  == domain 2  score: 121.6 bits;  conditional E-value: 5.8e-39
                         MTES_1575   1 FeeeVaeaLrergykvkpqvgvggfriDlvvedp...gkyllaIecdgdkyhsskeardrdierqevLerlGWkilR 74 
                                       Fe++V e+L++rg++v  qvgv+g+ iDl+v +p   ++yl++Iecdg++yhs+k+ardrd++rqe+Le+lGW+i+R
  gi|298676172|ref|YP_003727921.1| 722 FERHVKEHLEKRGFDVDCQVGVSGYFIDLAVSHPafsDGYLAGIECDGATYHSAKSARDRDRLRQEILENLGWDIYR 798
                                       9**************************************************************************** PP

                         MTES_1575  75 iwssdwyrnpeeeleklveal 95 
                                       +ws+dw+ np++e++kl++++
  gi|298676172|ref|YP_003727921.1| 799 VWSTDWFANPKKETDKLEQYI 819
                                       *****************9987 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.6   3.2e+03     119     134 ..     185     200 ..     165     256 .. 0.63
   2 !   49.9   1.7   1.5e-16     3e-13       3     195 ..     476     674 ..     474     678 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.6
                            AAA_12 119 pYraqvellkkklkek 134
                                        Y++q+++l+k+ ++ 
  gi|298676172|ref|YP_003727921.1| 185 DYKSQKDYLSKMAANI 200
                                       6889999998888752 PP

  == domain 2  score: 49.9 bits;  conditional E-value: 1.5e-16
                            AAA_12   3 rSlferllkkekekvvlLdtqYRm.hpeIsrfpsklfYkgkLkdaesvkkreleaqealeepleplvfidvekseee 78 
                                       +S++e  +++  +++  L   YR+ h+++ +f++k+fY+++L   +s  +++ +            + +++e    +
  gi|298676172|ref|YP_003727921.1| 476 ESILEMAMRCW-QPYRRLLWHYRSrHESLIDFSNKKFYNDQLIVFPSPVTNHPS------------YGVHMEYVGGT 539
                                       69999999999.9999999****86899*************9987754444333............33333333333 PP

                            AAA_12  79 kekkeksyiNeeEaelvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeekseke............. 142
                                        +   k  +N +Ea+ v++   +++++ +e+   ++gv+++ + q +l+++++++  +e+++               
  gi|298676172|ref|YP_003727921.1| 540 CR---KGGTNIKEAQRVAEAAVEFMQTNPEQ---SLGVVAMNKVQTDLIEDEVSRLLTENTAAYnyiehwdkinggl 610
                                       33...4578*****************99999...9*******************98877766558999999999**9 PP

                            AAA_12 143 ..ievntvdgfQGrekdviilslVRsn......ekkeig...flkderrlNValTRAkskliiv 195
                                         + v+  +++QG e+dvi++s+           ++++g       +rrlNV +TRAk+++ ++
  gi|298676172|ref|YP_003727921.1| 611 esFFVKNLENVQGDERDVIFISTTYGPdsesgkVHQRFGpinSNVGYRRLNVLFTRAKEQVQLF 674
                                       99**********************99533333333355530033458************98776 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.1   1.6e-12   3.1e-09     209     258 ..     407     455 ..     312     458 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.6e-12
                            AAA_11 209 klleklakkfdvviIDEAaqavEpstliPlrlgakkvvLvGDpkQLpatv 258
                                       + l+  + +fd+v+IDEA+q     +l +l +  k++v vGDpkQLp+t 
  gi|298676172|ref|YP_003727921.1| 407 QYLKPGTSEFDLVVIDEASQMKPEDSLGALARS-KQIVVVGDPKQLPPTS 455
                                       556666679************999999999999.**************96 PP

>> DUF559  Protein of unknown function (DUF559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0     4e-07   0.00079      31     105 ..     733     816 ..     713     820 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4e-07
                                       TT--EEEEEEETTEEEEEEETTTTEE......EEEE---.----..----HHHHHHHHHTT-EEEEEEHHHHHH-HH CS
                            DUF559  31 sglkfrRqkpigsYivDfvclkakli......velDGaq.hdee..eeyDaeRtelLeslGftvlRfkndevlknie 98 
                                        g+    q+ +  Y++D +  +          +e DGa  h+ +  +++D  R+e+Le+lG+ + R +  +  +n++
  gi|298676172|ref|YP_003727921.1| 733 RGFDVDCQVGVSGYFIDLAVSHPAFSdgylagIECDGATyHSAKsaRDRDRLRQEILENLGWDIYRVWSTDWFANPK 809
                                       467788899999999999877655422222359****862655566889999****************999999988 PP

                                       HHHHHHH CS
                            DUF559  99 evleeil 105
                                       + ++++ 
  gi|298676172|ref|YP_003727921.1| 810 KETDKLE 816
                                       8777665 PP

>> RAP  RAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       6.6   1.3e+04      46      58 .]     184     196 ..     173     196 .. 0.72
   2 ?   -2.9   0.0       3.9   7.8e+03      24      34 ..     727     737 ..     727     737 .. 0.87
   3 !   16.8   0.1   2.6e-06    0.0053       1      56 [.     765     820 ..     765     822 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6.6
                               RAP  46 knkedkveylkkk 58 
                                       k+ + +++yl k+
  gi|298676172|ref|YP_003727921.1| 184 KDYKSQKDYLSKM 196
                                       6777788888775 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.9
                               RAP  24 kriLsklGykv 34 
                                       k++L+k G+ v
  gi|298676172|ref|YP_003727921.1| 727 KEHLEKRGFDV 737
                                       579******87 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 2.6e-06
                               RAP   1 IevdGpshyykns.knltgktklKkriLsklGykvinIpyfeWnql.knkedkve.ylk 56 
                                       Ie+dG + +  +s +      +l+++iL++lG+ + ++   +W    k++ dk+e y+ 
  gi|298676172|ref|YP_003727921.1| 765 IECDGATYHSAKSaR---DRDRLRQEILENLGWDIYRVWSTDWFANpKKETDKLEqYIH 820
                                       899999998888833...4689*********************9988888888887876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.2e-06    0.0043      99     143 ..     411     453 ..     156     456 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.2e-06
                            AAA_19  99 klqeee.llivDEfqdvdelqyrLlkallgekkklllvGDpdQliy 143
                                       + ++e+ l+++DE++++++     l al+ ++k++++vGDp+Ql++
  gi|298676172|ref|YP_003727921.1| 411 PGTSEFdLVVIDEASQMKPEDS--LGALA-RSKQIVVVGDPKQLPP 453
                                       33455669**********7654..89999.6677**********97 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   4.5e-06     0.009      89     130 ..     415     453 ..     385     456 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.5e-06
                            AAA_30  89 g.tllivDEagmvdtkqlaallkaaekagakvilvGDerQlas 130
                                       + +l+++DEa+ +  ++    l++      ++++vGD++Ql++
  gi|298676172|ref|YP_003727921.1| 415 EfDLVVIDEASQMKPEDSLGALARS----KQIVVVGDPKQLPP 453
                                       449********99777654444333....67**********97 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.5     1e-05     0.021     168     294 ..     215     450 ..      52     451 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
                                       H.........................................HHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSS CS
                     UvrD-helicase 168 k.........................................keelslskskaeelrelvskakekqlspkelkkaf 203
                                       k                                         k+  + +k +   ++ +++++ +++l  ++l+   
  gi|298676172|ref|YP_003727921.1| 215 KdiahidfedffkgdsekleiqylidtivraennpeelqnwsKFIDTVEKASEAGISPVIDTYLSGDLYFENLDT-T 290
                                       133333333333333333333333333333333333333333555555555555555555555555555555555.3 PP

                                       TSCSHHHHHHHHHHHHHHHHHHHHTC................................................... CS
                     UvrD-helicase 204 ekasdlqkkiaeflkeyqeqkkeena................................................... 229
                                       +++  +++ +  ++++y e  +++ +                                                   
  gi|298676172|ref|YP_003727921.1| 291 YEQVLYRNLAHIAYEKYPELNRFSGLkqeearerfrktdrelidlerkylraklakapitrrnseglprdktelgli 367
                                       45555555555666666666666666777777777777777777777777777777777888888888888888888 PP

                                       ..........EEHHHHHHHHHHHHHH...........CHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTT CS
                     UvrD-helicase 230 ..........lDfsdllhallellee...........neelaealrerykeiliDEyQDTnkiQyrilkllasghee 285
                                                 + f dl++++ ++ +e            ++ ++   ++++ + iDE+ +  +  ++ l  la+++ +
  gi|298676172|ref|YP_003727921.1| 368 nherskkrkhISFRDLMNRAGKAIQElkpcfmmsplsVSQYLKPGTSEFDLVVIDEASQMKP--EDSLGALARSK-Q 441
                                       8888888888************9999999***99999899999999**********987776..78899***998.7 PP

                                       EEEEE-GGG CS
                     UvrD-helicase 286 lfmvGDpkQ 294
                                       +++vGDpkQ
  gi|298676172|ref|YP_003727921.1| 442 IVVVGDPKQ 450
                                       ********* PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.7e-05     0.035      50     103 ..     405     454 ..     400     459 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
                   Viral_helicase1  50 vdsflmalvkstkgkililDEylllhaGyill.laalskaklvilfGDplQipfh 103
                                       v ++l++ + +  ++++++DE+ ++++   +  l al+++k+++++GDp+Q p  
  gi|298676172|ref|YP_003727921.1| 405 VSQYLKPGTSE--FDLVVIDEASQMKP---EDsLGALARSKQIVVVGDPKQLPPT 454
                                       56777777765..9***********96...5559*****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (835 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.81u 0.37s 00:00:01.18 Elapsed: 00:00:00.58
# Mc/sec: 4341.83
//
Query:       gi|298676173|ref|YP_003727922.1|  [L=449]
Description: putative PAS/PAC sensor protein [Methanohalobium evestigatum Z-7303]
Scores for complete 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-45  153.7   0.9      1e-20   73.8   0.3    3.7  4  PAS_3     PAS fold
    3.9e-32  110.6   6.2      4e-13   49.5   0.0    4.1  4  PAS_9     PAS domain
    2.7e-25   88.6   0.1      4e-15   55.8   0.0    4.1  4  PAS       PAS fold
      4e-25   88.2   0.0    2.1e-10   40.8   0.0    4.2  4  PAS_4     PAS fold
    7.1e-09   35.8   0.0    5.3e-06   26.5   0.0    2.7  2  PAS_11    PAS domain
    4.4e-06   26.6   0.0       0.73    9.9   0.0    4.3  4  PAS_8     PAS domain
  ------ inclusion threshold ------
      0.018   15.2   0.5          2    8.6   0.0    3.9  4  PAS_7     PAS fold


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00048       1.2       4      87 ..      31     112 ..      29     114 .. 0.91
   2 !   66.7   0.0   6.5e-22   1.7e-18       2      86 ..     155     237 ..     154     239 .. 0.96
   3 !   73.8   0.3     4e-24     1e-20       3      89 .]     282     371 ..     280     371 .. 0.95
   4 ?   -2.5   0.0       2.6   6.6e+03      45      64 ..     397     417 ..     385     434 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00048
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdeng 80 
                                       ++++  + lG++++e+++   +++++   +  ++++++ ++++k++e++++   +++ +G  r ++ + ++  d+ +
  gi|298676173|ref|YP_003727922.1|  31 ANKAHADFLGLDKNEFENV--NIYNVFTRDVADYCFKENEKIFKENEKIHTRRWFKNSNGVSRLLSITKTPKLDSFN 105
                                       6888999************..****************************999999999**99999999999888888 PP

                             PAS_3  81 kpvrvig 87 
                                       ++ ++i+
  gi|298676173|ref|YP_003727922.1| 106 NVEYIIC 112
                                       8888876 PP

  == domain 2  score: 66.7 bits;  conditional E-value: 6.5e-22
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +y+ ++++  lGy+pe l+gk  s+ ++vhp+D++r++++++ +l++  p + eyR++++dG+y w+e++++ i+d+
  gi|298676173|ref|YP_003727922.1| 155 VYAGPSYKSNLGYDPENLIGK--SVFNFVHPDDLDRIKSEFNSLLETLIPRKSEYRCLHADGHYLWLETYGNFIYDD 229
                                       799999***************..****************************************************** PP

                             PAS_3  79 ngkpvrvi 86 
                                        g++ +++
  gi|298676173|ref|YP_003727922.1| 230 VGNIKKIV 237
                                       **999887 PP

  == domain 3  score: 73.8 bits;  conditional E-value: 4e-24
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyege...yRirrkdGeyrwveararvir 76 
                                       yvs++v +i+Gy+ + + g + s++d++hp+D+ervr++++++ ++  +++++   yRi++k G++rwv++r+++ir
  gi|298676173|ref|YP_003727922.1| 282 YVSNNVVDIFGYTVDYFSGGKLSYADIIHPDDLERVRSEVETYSDDPDRFKFQhkpYRIITKTGDIRWVDDRTTIIR 358
                                       9*******************************************999977666678********************* PP

                             PAS_3  77 dengkpvrvigva 89 
                                       ++ g++++++gv+
  gi|298676173|ref|YP_003727922.1| 359 NDFGEITHYQGVI 371
                                       ***********96 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 2.6
                             PAS_3  45 alkkge.pyegeyRirrkdGe 64 
                                       ++++g   +++e+ ++r++ +
  gi|298676173|ref|YP_003727922.1| 397 SIQDGIsIIDTEFNVLRANSK 417
                                       455555355888777777643 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.7   4.7e-10   1.2e-06       5     104 .]      21     119 ..      17     119 .. 0.92
   2 !   49.5   0.0   1.6e-16     4e-13       2     104 .]     143     245 ..     142     245 .. 0.88
   3 !   24.1   0.1   1.2e-08   3.2e-05       7     104 .]     273     376 ..     265     376 .. 0.86
   4 !    8.7   0.0   0.00076         2       2      41 ..     400     440 ..     399     448 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 4.7e-10
                             PAS_9   5 lidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvl 79 
                                       +++ ++ +   aN+a +++lG +++e+ + +i ++f  + +++  ++ ++++++ +    +    + ++ng   +  
  gi|298676173|ref|YP_003727922.1|  21 IFI-DEQTYYLANKAHADFLGLDKNEFENVNIYNVFtrDVADYCFKENEKIFKENE--KIHTRRWFKNSNGVSRLLS 94 
                                       334.4555789*************************99999999999999999999..******************* PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDite 104
                                       +t +p  d+ +++  ii+  +Dite
  gi|298676173|ref|YP_003727922.1|  95 ITKTPKLDSFNNVEYIICSAEDITE 119
                                       ************************8 PP

  == domain 2  score: 49.5 bits;  conditional E-value: 1.6e-16
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirkngetf 76 
                                       ++i++++++g+ +ya ++ +  lGy+pe ++gks+++++  +p++ +r++  ++++ +  ++r  e+ + + +g ++
  gi|298676173|ref|YP_003727922.1| 143 EMICLTDKNGNFVYAGPSYKSNLGYDPENLIGKSVFNFV--HPDDLDRIKSEFNSLLEtlIPRKSEYRCLHADGHYL 217
                                       6789999********************************..44444444444444444488**************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       w +     ++dd g+++ i+++ rDit+
  gi|298676173|ref|YP_003727922.1| 218 WLETYGNFIYDDVGNIKKIVFTGRDITK 245
                                       **************************95 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 1.2e-08
                             PAS_9   7 dnpdgril.yaNeaalrllGyspeevlgks..itdlfvtdpeanerlraaleqgrk.....kerevevvlirknget 75 
                                       d ++g  + y+++ + +++Gy+ + + g +  + d++  +p++ er+r  +e+ ++     k++++++ +i+k+g  
  gi|298676173|ref|YP_003727922.1| 273 DKENGWPVeYVSNNVVDIFGYTVDYFSGGKlsYADII--HPDDLERVRSEVETYSDdpdrfKFQHKPYRIITKTGDI 347
                                       567885555*******************998899999..777777777777777768889***************** PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                        wv+ + + +++d ge++++ +++ Dit+
  gi|298676173|ref|YP_003727922.1| 348 RWVDDRTTIIRNDFGEITHYQGVILDITD 376
                                       ***************************96 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.00076
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGys.peevlgksitdlf..v 41 
                                       dgi i+++++++l+aN ++ +++  +    + gk++ +++  +
  gi|298676173|ref|YP_003727922.1| 400 DGISIIDTEFNVLRANSKMGEWY--KvNTPLEGKKCYQVYhnS 440
                                       8999999***************5..5234499******99433 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0054        14      25     113 .]      30     117 ..       9     117 .. 0.73
   2 !   55.8   0.0   1.6e-18     4e-15       2     113 .]     133     243 ..     132     243 .. 0.96
   3 !   18.2   0.0   7.1e-07    0.0018       6     113 .]     259     374 ..     257     374 .. 0.88
   4 ?    3.7   0.0     0.024        61       3      32 ..     391     420 ..     389     422 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0054
                                       EECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC......TTSSEEEEEEEEEE CS
                               PAS  25 yvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl......rdgrpihlevrasp 95 
                                       ++N+a +++lGl+ +e  + +++ ++  +           + +++e+   ++ ++ +       +g  + l ++ +p
  gi|298676173|ref|YP_003727922.1|  30 LANKAHADFLGLDKNEFENVNIYNVFTRD-------VADYCFKENEKIFKENEKIHTrrwfknSNGVSRLLSITKTP 99 
                                       78999999999999999999999988544.......3333333333333333333333344679************* PP

                                       EEETTEEEEEEEEEEEES CS
                               PAS  96 vrdaggeilgflgvlrdi 113
                                        +d   ++ ++++ + di
  gi|298676173|ref|YP_003727922.1| 100 KLDSFNNVEYIICSAEDI 117
                                       *************99997 PP

  == domain 2  score: 55.8 bits;  conditional E-value: 1.6e-18
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                        +r+i e++ ++i+++D++g+++y+ +++ + lG+++e ++gks++ ++h++d +  ++++  lle+  +++++ ++
  gi|298676173|ref|YP_003727922.1| 133 LFREITENMVEMICLTDKNGNFVYAGPSYKSNLGYDPENLIGKSVFNFVHPDDLDRIKSEFNSLLETLIPRKSEYRC 209
                                       6899*************************************************999999999999999999999999 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +   dg + +le+  + ++d  g+i+ +++++rdi
  gi|298676173|ref|YP_003727922.1| 210 LHA-DGHYLWLETYGNFIYDDVGNIKKIVFTGRDI 243
                                       999.******************************8 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 7.1e-07
                                       HHHHSSSEEEEEE...TTSB.EEEECHHHHHHHSSTHHHCT.TSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   6 ileslpdpifvvD...edgr.ilyvNaaaeellGlsreevl.gkslldliheeddaelaelleqlleqgeesragei 77 
                                       i++++++  f++    e+g+ + yv+ +  +++G++ +  + gk  + +i+++dd e+++   + +++  ++  +++
  gi|298676173|ref|YP_003727922.1| 259 IINNSRVVAFLWKndkENGWpVEYVSNNVVDIFGYTVDYFSgGKLSYADIIHPDDLERVRSEVETYSDDPDRFKFQH 335
                                       7777777777776567777745599************66652688899***************************** PP

                                       EEEC...TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfkl...rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +  +   + g +++++ r++ +r+  gei+++ gv+ di
  gi|298676173|ref|YP_003727922.1| 336 KPYRiitKTGDIRWVDDRTTIIRNDFGEITHYQGVILDI 374
                                       8888999*****************************998 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.024
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHH CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaee 32 
                                       l+  +es+ d+i ++D   ++l +N+++ e
  gi|298676173|ref|YP_003727922.1| 391 LDDTFESIQDGISIIDTEFNVLRANSKMGE 420
                                       556689********************9975 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.1e-05     0.028       2     108 ..      13     120 ..      12     122 .. 0.84
   2 !   40.8   0.0   8.1e-14   2.1e-10       2     110 .]     139     248 ..     138     248 .. 0.91
   3 !   15.2   0.0   7.4e-06     0.019      17     109 ..     280     378 ..     275     379 .. 0.97
   4 !   12.3   0.0   5.9e-05      0.15       1      43 [.     395     436 ..     395     444 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pge 77 
                                       d+++  ++++ +++++  aN+a a+ +g++  e+ +   + +++ ++a+      ++  +++e i++    +  +g 
  gi|298676173|ref|YP_003727922.1|  13 DQTNTQIFIFIDEQTYYLANKAHADFLGLDKNEFENVNIYNVFTRDVADYCFKENEKIFKENEKIHTRRWFKNsNGV 89 
                                       566666777777889999**************************987777666677776666666666655556*** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTer 108
                                        r ++++++P +d+   v  +++ + DiTe 
  gi|298676173|ref|YP_003727922.1|  90 SRLLSITKTPKLDSFNNVEYIICSAEDITEK 120
                                       *****************************97 PP

  == domain 2  score: 40.8 bits;  conditional E-value: 8.1e-14
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pge 77 
                                       +++ ++++  d++g+++ya +++ + +g++pe l+Gk+++ ++ ++d +r+ +  + +le+  p +++   l+ +g 
  gi|298676173|ref|YP_003727922.1| 139 ENMVEMICLTDKNGNFVYAGPSYKSNLGYDPENLIGKSVFNFVHPDDLDRIKSEFNSLLETLIPRKSEYRCLHaDGH 215
                                       688899***********************************99999***********************99995555 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                         ++e+  + + d+ G +  +++++rDiT r++
  gi|298676173|ref|YP_003727922.1| 216 YLWLETYGNFIYDDVGNIKKIVFTGRDITKRKE 248
                                       55555555999*******************985 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 7.4e-06
                             PAS_4  17 vlyaNaaaaelfgappeellGktla..ellpeedaarleralrrvlegeepiefleelll....pgeerhyelrllP 87 
                                       v+y++++  ++fg++ + + G +l   ++  ++d +r+++ ++   +  ++ +f++ + +     g+ r+++ r + 
  gi|298676173|ref|YP_003727922.1| 280 VEYVSNNVVDIFGYTVDYFSGGKLSyaDIIHPDDLERVRSEVETYSDDPDRFKFQHKPYRiitkTGDIRWVDDRTTI 356
                                       789999***************999999999999***********************9999***************** PP

                             PAS_4  88 lrdesGevigvlvisrDiTerr 109
                                       +r++ Ge+ ++ +++ DiT+r+
  gi|298676173|ref|YP_003727922.1| 357 IRNDFGEITHYQGVILDITDRK 378
                                       ********************97 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 5.9e-05
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlael 43 
                                       ++s++d++ ++d++++vl+aN  + e++++    l Gk+++++
  gi|298676173|ref|YP_003727922.1| 395 FESIQDGISIIDTEFNVLRANSKMGEWYKVN-TPLEGKKCYQV 436
                                       79************************99875.56777777665 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   2.1e-09   5.3e-06       8      92 ..     148     228 ..     141     239 .. 0.90
   2 !    6.1   0.0    0.0046        12      38      84 ..     303     351 ..     298     367 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.1e-09
                            PAS_11   8 ldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvk 84 
                                        d +g+++   +   + +  lg+  e+l+g+s+++++hp+dl ++ks +   + ++   ++s yR   ++++++++ 
  gi|298676173|ref|YP_003727922.1| 148 TDKNGNFVYAGP---SYKSNLGYDPENLIGKSVFNFVHPDDLDRIKSEFNSLL-ETLIPRKSEYRCLHADGHYLWLE 220
                                       678899999999...99999*********************************.999999***************** PP

                            PAS_11  85 tksklfkn 92 
                                       t + + ++
  gi|298676173|ref|YP_003727922.1| 221 TYGNFIYD 228
                                       *9888765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0046
                            PAS_11  38 rsiydLchpqdlstlkshlrevissngeatssl..yRLrlsqdkfvkvk 84 
                                       +s+ d++hp+dl++++s  +   + +++++ +   yR++++++++ +v 
  gi|298676173|ref|YP_003727922.1| 303 LSYADIIHPDDLERVRSEVETYSDDPDRFKFQHkpYRIITKTGDIRWVD 351
                                       6889**************99888888877655555*****999987665 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.012        31       7      42 ..      12      48 ..       9      73 .. 0.68
   2 ?    4.5   0.0     0.015        37       1      45 [.     132     177 ..     132     201 .. 0.73
   3 ?    1.5   0.0      0.12   3.1e+02       6      52 ..     259     309 ..     251     325 .. 0.69
   4 !    9.9   0.0   0.00028      0.73       7      37 ..     395     425 ..     389     446 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.012
                             PAS_8  7 fesspdgiav.vdlgdrivdvNqaalellGys.adlkg 42
                                      +++ +  i++ +d+++    +N+a +++lG++ +++  
  gi|298676173|ref|YP_003727922.1| 12 LDQTNTQIFIfIDEQT-YYLANKAHADFLGLDkNEFEN 48
                                      5555555665456555.778**********77766655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.015
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgell 45 
                                       e +r + e++ + i+++d +g+ +v++ +++   lGy+ + l+g+ +
  gi|298676173|ref|YP_003727922.1| 132 ELFREITENMVEMICLTDkNGN-FVYAGPSYKSNLGYDpENLIGKSV 177
                                       67999*************8888.*99977777777776555555444 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.12
                             PAS_8   6 lfesspdgiavvdlgdr....ivdvNqaalellGys.adlkgellgqllpvl 52 
                                       ++++s++  +++++++     + +v +   +++Gy+ + ++g +l  + + +
  gi|298676173|ref|YP_003727922.1| 259 IINNSRVVAFLWKNDKEngwpVEYVSNNVVDIFGYTvDYFSGGKLS-YADII 309
                                       567777766667655534677999999999*****98877777774.33333 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.00028
                             PAS_8   7 fesspdgiavvd.lgdrivdvNqaalellGys 37 
                                       fes++dgi ++d +  +++ +N ++ e + ++
  gi|298676173|ref|YP_003727922.1| 395 FESIQDGISIIDtEF-NVLRANSKMGEWYKVN 425
                                       9***********454.5******998777665 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.5   3.9e+03     101     114 ..     111     124 ..     109     125 .. 0.81
   2 ?    1.7   0.0      0.11   2.8e+02       3      41 ..     140     177 ..     138     251 .. 0.53
   3 ?   -2.3   0.0       1.8   4.7e+03      88     114 ..     372     381 ..     337     382 .. 0.70
   4 ?    8.6   0.0   0.00077         2       1      30 [.     395     424 ..     395     434 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.5
                             PAS_7 101 VttytDiTerrrae 114
                                       + + +DiTe+ ++e
  gi|298676173|ref|YP_003727922.1| 111 ICSAEDITEKNQSE 124
                                       56779****99987 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.11
                             PAS_7   3 nmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpl 41 
                                       nm + i++ D++++ v     y + l++ +e + +g+++
  gi|298676173|ref|YP_003727922.1| 140 NMVEMICLTDKNGNFVYAGPSYKSNLGYDPENL-IGKSV 177
                                       666666666666666666666666665555544.34433 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.8
                             PAS_7  88 ievrgnplpdgGfVttytDiTerrrae 114
                                       +                 DiT+r+ ae
  gi|298676173|ref|YP_003727922.1| 372 L-----------------DITDRKLAE 381
                                       3.................666666555 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.00077
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldl 30 
                                       +e++++Gis++D + +++  N+++ e +++
  gi|298676173|ref|YP_003727922.1| 395 FESIQDGISIIDTEFNVLRANSKMGEWYKV 424
                                       589********************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1075  (0.0599587); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2713.10
//
Query:       gi|298676174|ref|YP_003727923.1|  [L=254]
Description: signal transduction histidine kinase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-30  102.6   5.1    9.2e-30  102.6   5.1    2.4  2  HisKA_2          Histidine kinase
    1.7e-07   31.7   0.0    1.7e-06   28.5   0.0    2.4  1  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    4.6e-07   30.4   1.6    1.5e-06   28.8   0.2    2.3  2  HWE_HK           HWE histidine kinase
    0.00049   20.0   0.0     0.0011   18.9   0.0    1.6  1  HATPase_c_2      Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.011   15.6   2.9      0.013   15.4   2.9    1.1  1  Apolipoprotein   Apolipoprotein A1/A4/E domain
      0.011   15.9   1.3      0.018   15.3   1.3    1.4  1  Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3
      0.031   14.1   5.7      0.043   13.7   5.7    1.2  1  PIN_8            PIN like domain
       0.08   12.7   8.1       0.12   12.1   1.6    3.4  4  SPOB_a           Sensor_kinase_SpoOB-type, alpha-helical doma
      0.091   12.8   1.9       0.16   12.0   1.9    1.3  1  Succ_DH_flav_C   Fumarate reductase flavoprotein C-term
       0.23   11.6   6.5       0.36   11.0   6.5    1.4  1  Fib_alpha        Fibrinogen alpha/beta chain family
       0.37   10.4   4.3       0.45   10.1   4.3    1.1  1  DUF572           Family of unknown function (DUF572)
        2.7    7.8   9.9        4.6    7.0   0.3    2.1  2  Spc29            Spindle Pole Component 29


Domain annotation for each model (and alignments):
>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.3       1.1   1.6e+03       1       6 [.      42      47 ..       8      58 .. 0.63
   2 !  102.6   5.1   6.1e-33   9.2e-30       1      76 []      64     139 ..      64     139 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                           HisKA_2  1 EihHRv 6 
                                      E++HRv
  gi|298676174|ref|YP_003727923.1| 42 ELEHRV 47
                                      344444 PP

  == domain 2  score: 102.6 bits;  conditional E-value: 6.1e-33
                           HisKA_2   1 EihHRvkNnLqvisslLslqarkakdeevkealresqnRvlsialiheeLyksedletvdfseylekLvenlfksy 76 
                                       E+hHR+kNnLqvisslL+lq++k++d++v+ea+r++qnRv+s++l+h+++y++++le++++++y+e+L+e+l+++y
  gi|298676174|ref|YP_003727923.1|  64 ELHHRIKNNLQVISSLLNLQSEKFNDDTVNEAFRDTQNRVISMSLVHQKIYHTKGLESINVRDYIEDLIEHLISLY 139
                                       99**********************************************************************9976 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 !   28.5   0.0   1.2e-09   1.7e-06       5     107 ..     162     251 ..     158     253 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.2e-09
                                       HHHHHHHHHHHHHHHHHS...TTTEEEEEEEEEE.TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHH CS
                         HATPase_c   5 rLrqiisnlvdNavkfat...kageieveikase.ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlG 77 
                                        L  +i++lv+N++k+a    k ge+ v    s+ + +++ v+DnG+Gip+ d++     +++          + lG
  gi|298676174|ref|YP_003727923.1| 162 PLGMLINELVSNSLKYAYpedKYGELNVIFYESNpGLYTLIVSDNGKGIPE-DID-----LDN---------PSSLG 223
                                       67789***********5442244444555443336899************8.555.....344.........6679* PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftft 107
                                       + i k+lv +++G++ v+ +   Gttf+++
  gi|298676174|ref|YP_003727923.1| 224 MQIIKSLVGQIDGDLDVDGNN--GTTFIIN 251
                                       ******9999*******7777..***9986 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.97   1.4e+03      24      39 ..      33      48 ..      23      52 .. 0.67
   2 !   28.8   0.2   9.8e-10   1.5e-06       1      69 [.      64     139 ..      64     151 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.97
                                      XS-HHHHHHHHHHHHH CS
                            HWE_HK 24 aesleefaeklsgRLq 39
                                      a++l++++e+l+ R+q
  gi|298676174|ref|YP_003727923.1| 33 ATKLKQMNEELEHRVQ 48
                                      5566666666666654 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 9.8e-10
                                       HHHHHHHHHHHHHHHHHHHHSS..SXS-HHHHHHHHHHHHHHHHHHHHHHHHCTT.S-E....EHHHHHHHHHHHH CS
                            HWE_HK   1 ElnHRvKNlLavvqsiarqtlr..saesleefaeklsgRLqALsaahdllsreew.aga....eLaelleeelapy 69 
                                       El+HR+KN L v++s+ +  ++  + ++++e+ ++ ++R+ ++s +h+ + +++  +++     +++l+e+ ++ y
  gi|298676174|ref|YP_003727923.1|  64 ELHHRIKNNLQVISSLLNLQSEkfNDDTVNEAFRDTQNRVISMSLVHQKIYHTKGlESInvrdYIEDLIEHLISLY 139
                                       9****************9877623467889999999***********98665543133311113455555555555 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 !   18.9   0.0   7.6e-07    0.0011      32     113 ..     163     235 ..     151     251 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.6e-07
                       HATPase_c_2  32 irlaveEactNavehayleapegpvevr.lesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikg 107
                                       + + ++E+++N  ++ay+e++ g+++v  +es+++  t+ v+D+G+g +             + + ++ +G+ +ik+
  gi|298676174|ref|YP_003727923.1| 163 LGMLINELVSNSLKYAYPEDKYGELNVIfYESNPGLYTLIVSDNGKGIPEDI----------DLDNPSSLGMQIIKS 229
                                       66789****************655555549999999***********66643..........667788899999999 PP

                       HATPase_c_2 108 lvDeve 113
                                       lv +++
  gi|298676174|ref|YP_003727923.1| 230 LVGQID 235
                                       987774 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   2.9   8.8e-06     0.013       5      97 ..       8     103 ..       4     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.8e-06
                                       CCCCHHHHHCCHHHCHHCHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHH CS
                    Apolipoprotein   5 sldelkayaeeleeqlaplaq..elrdrlskeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapyt 79 
                                       +++ +++++ ++ e+++   q  + +++l +  eel  r+++++ee +++   ++ e++++++ nl+ + + l+  +
  gi|298676174|ref|YP_003727923.1|   8 KISAVVEFVRDITEKVKTEKQlkKYATKLKQMNEELEHRVQKQTEEIKNAERLRVLELHHRIKNNLQVISSLLNLQS 84 
                                       677888888889999998888866999***************************************99999999999 PP

                                       HHHHH.HHHHCHHCCHHCH CS
                    Apolipoprotein  80 eelre.rlaadaeelqeql 97 
                                       e+ ++  ++++ ++ q+++
  gi|298676174|ref|YP_003727923.1|  85 EKFNDdTVNEAFRDTQNRV 103
                                       9998877888888888876 PP

>> Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   1.3   1.2e-05     0.018      28      87 ..      11      70 ..       3     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                   Gluconate_2-dh3 28 gvaafidrqladaplppeqeayrkglaaldayaraeygksFveldgaqqdalLealekea 87
                                       v++f+  + +++ ++++ + y  +l++++++++++ +k+  e+++a++ ++Le   + +
  gi|298676174|ref|YP_003727923.1| 11 AVVEFVRDITEKVKTEKQLKKYATKLKQMNEELEHRVQKQTEEIKNAERLRVLELHHRIK 70
                                      599**************************************************9877664 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   5.7   2.9e-05     0.043      41     130 ..      12     100 ..       9     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.9e-05
                             PIN_8  41 alEfqrnresviskekkayedlekeleklkkaaekkleealkkwakkkaldteelrkelkkqleelkeelkaeleel 117
                                       + Ef+r  ++ ++  +k++++++++l+++++++e+ +++ +++ ++ ++l++ el++++k++l+ +++ l+ ++e++
  gi|298676174|ref|YP_003727923.1|  12 VVEFVRDITEKVK-TEKQLKKYATKLKQMNEELEHRVQKQTEEIKNAERLRVLELHHRIKNNLQVISSLLNLQSEKF 87 
                                       6799988888777.6677888999*******************************************9994444444 PP

                             PIN_8 118 kksskadkeedpi 130
                                       ++++ +++ +d+ 
  gi|298676174|ref|YP_003727923.1|  88 NDDTVNEAFRDTQ 100
                                       4444444333333 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.098   1.5e+02      36      59 ..       6      29 ..       4      32 .. 0.89
   2 ?   -1.8   0.1       1.7   2.5e+03      40      57 ..      41      58 ..      34      65 .. 0.63
   3 ?   12.1   1.6   7.8e-05      0.12      16      54 ..      63     100 ..      46     108 .. 0.75
   4 ?   -0.6   0.0      0.74   1.1e+03      42      54 ..     124     136 ..     122     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.098
                            SPOB_a 36 Lgkydkaeeyieevvkelkeeski 59
                                      +gk+  ++e++ ++++ +k+e+++
  gi|298676174|ref|YP_003727923.1|  6 TGKISAVVEFVRDITEKVKTEKQL 29
                                      588999***************987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.7
                            SPOB_a 40 dkaeeyieevvkelkees 57
                                      ++ e+ +++ ++e+k+ +
  gi|298676174|ref|YP_003727923.1| 41 EELEHRVQKQTEEIKNAE 58
                                      455555666666666655 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 7.8e-05
                            SPOB_a  16 LrsqRHDflNhLQvIsGylqLgkydkaeeyieevvkelk 54 
                                       L  ++H   N+LQvIs++l L+     ++ ++e+ ++++
  gi|298676174|ref|YP_003727923.1|  63 L-ELHHRIKNNLQVISSLLNLQSEKFNDDTVNEAFRDTQ 100
                                       4.568999*************987777776666666665 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.74
                            SPOB_a  42 aeeyieevvkelk 54 
                                       +++yie+++++l 
  gi|298676174|ref|YP_003727923.1| 124 VRDYIEDLIEHLI 136
                                       7899999999875 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.9   0.00011      0.16      15      70 ..      23      78 ..      14      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                      SB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHH CS
                    Succ_DH_flav_C 15 fRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaks 70
                                      ++te++Lk+  ++lk+++e+l++   ++++++ N e +++lel++ +++  +++ s
  gi|298676174|ref|YP_003727923.1| 23 VKTEKQLKKYATKLKQMNEELEHRVQKQTEEIKNAERLRVLELHHRIKNNLQVISS 78
                                      689*****************9998889999**************999988887766 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 ?   11.0   6.5   0.00024      0.36      49     123 ..       7      81 ..       1     115 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH.HHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  49 nstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe.snirvLqnvlesneqkiqkLeq 123
                                        + + + e v++i+++++ +++ kk   + +k++++ele+++++  e+i++ e  ++ +L   +++n q i+ L +
  gi|298676174|ref|YP_003727923.1|   7 GKISAVVEFVRDITEKVKTEKQLKK-YATKLKQMNEELEHRVQKQTEEIKNAErLRVLELHHRIKNNLQVISSLLN 81 
                                       4556666778888888777777666.7999*******************99998899999********99998855 PP

>> DUF572  Family of unknown function (DUF572)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.3    0.0003      0.45     111     185 ..      21      94 ..       8     149 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0003
                            DUF572 111 eeakreekeke.eeeaedamkklEkrtkdskkemealesLeeLqelnqrqakvdfdanlelrkefreekkereeee 185
                                       e++k e++ k+ +++ +   ++lE+r++++++e++  e+L  L+  ++ + +  +   ++l++   e+ +  + +e
  gi|298676174|ref|YP_003727923.1|  21 EKVKTEKQLKKyATKLKQMNEELEHRVQKQTEEIKNAERLRVLELHHRIKNNLQV--ISSLLNLQSEKFNDDTVNE 94 
                                       4445555554404455666679*********************944444444444..4444433333333333332 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   4.0     0.018        27     114     168 ..       7      61 ..       1      74 [. 0.82
   2 ?    7.0   0.3    0.0031       4.6       3      21 ..      76      94 ..      74     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.018
                             Spc29 114 ssvkkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkrlaale 168
                                        +++ +ve  + + ++  + k+Lk+   + + +n+eL ++v++  ee+k+ + l+
  gi|298676174|ref|YP_003727923.1|   7 GKISAVVEFVRDITEKVKTEKQLKKYATKLKQMNEELEHRVQKQTEEIKNAERLR 61 
                                       56788889999999999999999*999999************9999997655554 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0031
                             Spc29  3 vsqflNsadkklkDDTLnn 21
                                      +s++lN +++k++DDT n+
  gi|298676174|ref|YP_003727923.1| 76 ISSLLNLQSEKFNDDTVNE 94
                                      79**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2968  (0.165542); expected 358.6 (0.02)
Passed bias filter:                     1151  (0.0641977); expected 358.6 (0.02)
Passed Vit filter:                       155  (0.00864521); 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: 0.73u 0.35s 00:00:01.08 Elapsed: 00:00:00.60
# Mc/sec: 1269.30
//
Query:       gi|298676175|ref|YP_003727924.1|  [L=398]
Description: hypothetical protein Metev_2316 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2331.82
//
Query:       gi|298676176|ref|YP_003727925.1|  [L=174]
Description: membrane-bound metal-dependent hydrolase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-15   55.2   3.8    6.5e-15   54.9   3.8    1.1  1  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   3.8   3.7e-19   6.5e-15       1     157 [.       1     153 [.       1     171 [. 0.77

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 3.7e-19
                              YdjM   1 MdgltHallGaalglalaallgaakeavllavavlgAllPD.iD..hpsstlgrklgllskklaklvgHRgftHSll 74 
                                       M  ++H+ ++++++ ++ + l  +k  + + ++++ A+lPD +D  ++ + + +++          +  R   H+l+
  gi|298676176|ref|YP_003727925.1|   1 MFIFAHIGFTIIIFYLVTKILRLDKP-IDYRLVAFVAILPDlVDkgFGILLFPEQV----------GNGRIYAHTLI 66 
                                       7889******************9876.9999999999****999333333333333..........459******** PP

                              YdjM  75 flallalvlllllrlfgrsalrlglllllgvlsHlllDlltkyGvpllwPfskkkvrlsllfiiidplltll..... 146
                                       f++l+ +++ +++r++g +   +  ++ +g++ HlllD +++ +  l+wP+ + +++ +  ++ +d  ++       
  gi|298676176|ref|YP_003727925.1|  67 FAVLFIVAGDYFVRRRGSY---FVSIIGWGFMCHLLLDKMWTIPQTLYWPLLGLNFKADYEVVQTDFSVYIMqvidn 140
                                       *****************99...56669999***********************999999999977765555466666 PP

                              YdjM 147 ...srrglvalelv 157
                                          s+ ++v l + 
  gi|298676176|ref|YP_003727925.1| 141 vftSGLSQV-LIFE 153
                                       655333333.2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1063.23
//
Query:       gi|298676177|ref|YP_003727926.1|  [L=47]
Description: hypothetical protein Metev_2318 [Methanohalobium evestigatum Z-7303]
Scores for complete 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   19.2   0.5     0.0014   19.0   0.5    1.1  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0019   17.7   0.8     0.0027   17.2   0.8    1.3  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0048   16.6   0.3     0.0054   16.5   0.3    1.0  1  FlhC             Flagellar transcriptional activator (FlhC)
  ------ inclusion threshold ------
      0.029   14.4   0.9       0.12   12.4   0.9    2.0  1  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
      0.038   14.1   0.5      0.043   13.9   0.5    1.1  1  Opiods_neuropep  Vertebrate endogenous opioids neuropeptide
      0.049   13.6   1.3      0.074   13.0   1.3    1.4  1  DUF4428          Domain of unknown function (DUF4428)
      0.072   13.2   2.9       0.88    9.7   0.1    2.1  2  DUF1272          Protein of unknown function (DUF1272)
       0.16   12.3   0.6       0.16   12.3   0.6    1.5  1  zinc_ribbon_9    zinc-ribbon
       0.21   11.5   2.6        2.8    7.8   2.6    2.0  1  VATC             Vms1-associating treble clef domain


Domain annotation for each model (and alignments):
>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.5   6.8e-07    0.0014       4      36 ..       6      34 ..       4      46 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.8e-07
                   Lar_restr_allev  4 kpCPfCggravlersqrvvaeigqcvyCad.Cga 36
                                      k CP Cgg+ v+ ++  +       vyC+  C  
  gi|298676177|ref|YP_003727926.1|  6 KSCPICGGKFVVMEDAANE-----AVYCTLeCLS 34
                                      89************98888.....6999555977 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.8   1.4e-06    0.0027       3      23 ..       8      29 ..       7      35 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                                      ETTTTCEE.CHEETSTTCEEES CS
                      TF_Zn_Ribbon  3 CPnCgstn.lveDpergelvCt 23
                                      CP+Cg+++ + eD+++  ++Ct
  gi|298676177|ref|YP_003727926.1|  8 CPICGGKFvVMEDAANEAVYCT 29
                                      ********889999999999*8 PP

>> FlhC  Flagellar transcriptional activator (FlhC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   2.7e-06    0.0054     134     169 ..       5      39 ..       2      43 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.7e-06
                              FlhC 134 lasCkrCkgefvthaedlesefvCglCqlpsRagkt 169
                                       ++sC  C+g+fv+++++ ++++ C+l + +s+a k+
  gi|298676177|ref|YP_003727926.1|   5 MKSCPICGGKFVVMEDAANEAVYCTL-ECLSKAEKS 39 
                                       689*********************99.455666665 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.9   6.3e-05      0.12       2      20 ..       8      28 ..       7      45 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-05
                    DNA_ligase_ZBD  2 CPvCGsavvRee...geaiyRC 20
                                      CP+CG + v  e   +ea+ +C
  gi|298676177|ref|YP_003727926.1|  8 CPICGGKFVVMEdaaNEAV-YC 28
                                      *******996661434555.55 PP

>> Opiods_neuropep  Vertebrate endogenous opioids neuropeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.5   2.2e-05     0.043       4      35 ..       6      38 ..       5      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                   Opiods_neuropep  4 kdCllCayklqdqqksfntlv.ClleCegklss 35
                                      k C  C+ k    +++ n  v C+leC  k+  
  gi|298676177|ref|YP_003727926.1|  6 KSCPICGGKFVVMEDAANEAVyCTLECLSKAEK 38
                                      6899******999999998888*****888766 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.3   3.7e-05     0.074       2      37 ..       8      43 ..       7      47 .] 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                           DUF4428  2 CaiCgkKigllkrlkleDg.yvCk.dClkKlseflsdv 37
                                      C+iCg+K  +++  + +++ + C+ +Cl+K+  ++ +v
  gi|298676177|ref|YP_003727926.1|  8 CPICGGKFVVME--DAANEaVYCTlECLSKAEKSMNKV 43
                                      ***********9..444443455549****94443444 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00044      0.88      40      52 ..       4      16 ..       1      19 [. 0.83
   2 ?    4.8   0.3     0.015        30      17      29 ..      20      32 ..      17      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00044
                           DUF1272 40 lenvCPncgGelv 52
                                      + + CP cgG++v
  gi|298676177|ref|YP_003727926.1|  4 IMKSCPICGGKFV 16
                                      4689*******98 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.015
                           DUF1272 17 pdseearicsyEc 29
                                       +++ea+ c+ Ec
  gi|298676177|ref|YP_003727926.1| 20 DAANEAVYCTLEC 32
                                      567899******9 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.6     8e-05      0.16      23      32 ..       7      16 ..       2      18 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8e-05
                     zinc_ribbon_9 23 lCPhCgggFV 32
                                      +CP Cgg FV
  gi|298676177|ref|YP_003727926.1|  7 SCPICGGKFV 16
                                      6********9 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.6    0.0014       2.8       5      33 ..       7      34 ..       4      42 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0014
                              VATC  5 rCsiCgeslegkvyFekfdfrYCstkClr 33
                                      +C iCg +++  +     + +YC+ +Cl 
  gi|298676177|ref|YP_003727926.1|  7 SCPICGGKFVVME-DAANEAVYCTLECLS 34
                                      6777777777533.2445789******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.42
# Mc/sec: 333.42
//
Query:       gi|298676178|ref|YP_003727927.1|  [L=298]
Description: hypothetical protein Metev_2319 [Methanohalobium evestigatum Z-7303]
Scores for complete 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-113  377.9   0.2   3.8e-113  377.7   0.2    1.0  1  DUF1616   Protein of unknown function (DUF1616)
    2.3e-06   26.8   1.8    3.5e-06   26.2   1.8    1.2  1  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.044   14.1   0.1      0.044   14.1   0.1    2.7  2  DUF4064   Protein of unknown function (DUF4064)
       0.22   11.7   0.9         26    5.0   0.0    2.4  2  DUF872    Eukaryotic protein of unknown function (DUF872)


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 !  377.7   0.2  8.5e-117  3.8e-113       2     293 .]      15     294 ..      14     294 .. 0.96

  Alignments for each domain:
  == domain 1  score: 377.7 bits;  conditional E-value: 8.5e-117
                           DUF1616   2 lvlalllllailvpvlnetplRivlglplvLflPGYaliaaLFPekrdidgieRlaLSfglSiaivpliglvlnvtp 78 
                                       ++l++l+++++lvp+lnetp+Ri+lglp+vLf+PGY liaaLFP+k+d+dgieR+aLSfglSia+vpligl+ln+tp
  gi|298676178|ref|YP_003727927.1|  15 IILVILTIVFVLVPPLNETPIRIILGLPMVLFIPGYSLIAALFPKKDDLDGIERIALSFGLSIAVVPLIGLGLNYTP 91 
                                       789************************************************************************** PP

                           DUF1616  79 wgirlepilvslslftlllalvAivrRsrlpeeerfsvplralieslkeeleek.sesr...ldkalnvlLvvsivl 151
                                       wgirl pi+vsls ft+l++++ i+rRs+l e+e f+vp+++ +es+k+el +  ++s    ldkal+++Lv+si++
  gi|298676178|ref|YP_003727927.1|  92 WGIRLIPIIVSLSTFTILMCVATIIRRSSLDENEVFTVPFKSSLESIKTELLTPpEDSTrpkLDKALSIILVISIIA 168
                                       **************************************************998744433566*************** PP

                           DUF1616 152 avaalgyavvaPkegekfTelyllgedgdelvaenypteltagesqevivgieNhEheevnYtvvvllqevtdeeev 228
                                       ++a+l+y+v++Pk+gekfTe+y+lg++g   +a++yptel+ ge+ +vi+gi+NhE+e+++Yt++++l+++  +   
  gi|298676178|ref|YP_003727927.1| 169 SIATLAYVVTTPKQGEKFTEFYVLGPNG---MADDYPTELEKGEKGTVIIGITNHEYEKTEYTLKMQLENN--T--- 237
                                       ****************************...*************************************983..2... PP

                           DUF1616 229 evlerteldrrevtladnetweqelevepeatgenlrleflLYkdevpeeptteeayrslhlwVn 293
                                             + + +++ l++n+twe++l+++p++tg+n++leflLYkd     ++ +e+yr+lhlwVn
  gi|298676178|ref|YP_003727927.1| 238 ---LPIDNNAKTIALKHNQTWEDTLKFTPHNTGTNMKLEFLLYKD-----NNFTEPYRNLHLWVN 294
                                       ...23567899**********************************.....**************7 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   1.8   7.8e-10   3.5e-06      65     231 ..      14     180 ..       9     195 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 7.8e-10
                             MFS_1  65 lllglllfalglllllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllg 141
                                       +++ ++l+++++l    +++l      r++ Gl + +lf  g++lia++fpk++   +i  ++++f+l++++ pl+g
  gi|298676178|ref|YP_003727927.1|  14 IIILVILTIVFVL----VPPLN-ETPIRIILGLPM-VLFIPGYSLIAALFPKKDDLDGIERIALSFGLSIAVVPLIG 84 
                                       3333333333322....23333.5569*******7.***************************************** PP

                             MFS_1 142 glla.sslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdp.......... 207
                                         l  + +g r++ +i+ + ++  +++++  + ++ +  +++  +      ++++l ++ ++ll++p          
  gi|298676178|ref|YP_003727927.1|  85 LGLNyTPWGIRLIPIIVSLSTFTILMCVATII-RRSSLDENEVFTVP----FKSSLESIKTELLTPPedstrpkldk 156
                                       *****************999999988766666.33333333333333....45555554555555554444432222 PP

                             MFS_1 208 vlw.illialllfffgfsglltllp 231
                                         + i+l++++++++++ ++++++p
  gi|298676178|ref|YP_003727927.1| 157 A-LsIILVISIIASIATLAYVVTTP 180
                                       1.24566666666666666666665 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   4.6       1.5   6.6e+03      66      80 ..      12      26 ..       4      32 .. 0.62
   2 ?   14.1   0.1   9.8e-06     0.044       9      84 ..      95     181 ..      91     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                           DUF4064 66 vialiaivlgivgal 80
                                      +  +i+ +l+iv++l
  gi|298676178|ref|YP_003727927.1| 12 ITIIILVILTIVFVL 26
                                      445555555555554 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 9.8e-06
                           DUF4064   9 glIGgilgillglllllflfllssgefsqeltee...........qalsgedasavleflstllivlgvialiaivl 74 
                                       +lI +i+++  + +l+ ++ ++ +++ +++  ++           ++l +   +++   l + l +++vi++ia+++
  gi|298676178|ref|YP_003727927.1|  95 RLIPIIVSLSTFTILMCVATIIRRSSLDENEVFTvpfksslesikTELLTPPEDSTRPKLDKALSIILVISIIASIA 171
                                       78999**************************999*******9999999999999999******************** PP

                           DUF4064  75 givgalllkk 84 
                                       +++ ++   k
  gi|298676178|ref|YP_003727927.1| 172 TLAYVVTTPK 181
                                       **99987665 PP

>> DUF872  Eukaryotic protein of unknown function (DUF872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.1     0.013        60      56      91 ..      15      50 ..       3      59 .. 0.77
   2 ?    5.0   0.0    0.0058        26      47      83 ..     157     193 ..     132     194 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.013
                            DUF872 56 GlvLlllgvvilvepseGvssavflvlGlllfiPGv 91
                                       ++++l+ v++lv p + +   + l l ++lfiPG 
  gi|298676178|ref|YP_003727927.1| 15 IILVILTIVFVLVPPLNETPIRIILGLPMVLFIPGY 50
                                      345566678899999999999999***********5 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0058
                            DUF872  47 laallLlllGlvLlllgvvilvepseGvssavflvlG 83 
                                       +++++L++  ++ +++ ++++++p++G++ + f+vlG
  gi|298676178|ref|YP_003727927.1| 157 ALSIILVISIIASIATLAYVVTTPKQGEKFTEFYVLG 193
                                       578999999999999999***************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1834.43
//
Query:       gi|298676179|ref|YP_003727928.1|  [L=282]
Description: abortive infection protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-17   63.2   5.4    2.3e-17   63.2   5.4    2.4  2  CPBP      CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
       0.15   12.2   0.4        2.2    8.4   0.1    2.4  2  DUF1419   Protein of unknown function (DUF1419)


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.0     0.093   8.4e+02      60      77 ..      59      76 ..      23     159 .. 0.81
   2 !   63.2   5.4   2.5e-21   2.3e-17       4      91 ..     177     266 ..     172     267 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.093
                                      HHHHHHHHHHHHHHHHTT CS
                              CPBP 60 llaalaGlvlgylylktg 77
                                       l++l+Glvl+ ++++++
  gi|298676179|ref|YP_003727928.1| 59 HLIILIGLVLSTVWIQEK 76
                                      566777888887777665 PP

  == domain 2  score: 63.2 bits;  conditional E-value: 2.5e-21
                                       THHHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG.HHH.HHHHHHHHHHHHHHHHHTT- CS
                              CPBP   4 lllvfllalllapllEEllfRglllqllqergsstlailissilFglaHlpn.gps.vllaalaGlvlgylylktgs 78 
                                       +l + ++++++++l+EEl+fR++l+++l++ ++ +  +li+s+lFg++H ++ +++ +++++laGlv+gy++ kt+s
  gi|298676179|ref|YP_003727928.1| 177 ILELSIVMIFFVGLVEELIFRSILQTRLENSFGLLPGLLITSLLFGMMHSIYgNVYeIFFTSLAGLVIGYMFQKTRS 253
                                       566778999**********************888***************99977778******************** PP

                                       HHHHHHHHHHHHH CS
                              CPBP  79 llaaillHallnl 91 
                                       l +++++H+ +n+
  gi|298676179|ref|YP_003727928.1| 254 LPVVAITHGTVNI 266
                                       ***********97 PP

>> DUF1419  Protein of unknown function (DUF1419)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.042   3.8e+02      63      93 ..      46      76 ..       5      84 .. 0.81
   2 ?    8.4   0.1   0.00024       2.2      50      87 ..     200     237 ..     195     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.042
                           DUF1419 63 Plflrgdmfalrefltgsvtsvffalkidgr 93
                                       l+++++ fa+   l   ++ v+ +++i+++
  gi|298676179|ref|YP_003727928.1| 46 MLYMQKQSFAIGLHLIILIGLVLSTVWIQEK 76
                                      489*********9999999999999999886 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00024
                           DUF1419  50 seaehdymleilPPlflrgdmfalrefltgsvtsvffa 87 
                                        +++ +  + +lP l + + +f++ + + g+v  +ff+
  gi|298676179|ref|YP_003727928.1| 200 LQTRLENSFGLLPGLLITSLLFGMMHSIYGNVYEIFFT 237
                                       5667778899**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1656.48
//
Query:       gi|298676180|ref|YP_003727929.1|  [L=86]
Description: hypothetical protein Metev_2321 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 496.18
//
Query:       gi|298676181|ref|YP_003727930.1|  [L=405]
Description: hypothetical protein Metev_2322 [Methanohalobium evestigatum Z-7303]
Scores for complete 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-06   26.5   1.0    0.00031   20.7   0.0    3.0  3  Y_Y_Y       Y_Y_Y domain
  ------ inclusion threshold ------
      0.028   14.6   0.2         12    6.0   0.0    3.2  4  DUF669      Protein of unknown function (DUF669)
      0.043   13.8   1.1        1.7    8.7   0.7    3.3  4  BsuPI       Intracellular proteinase inhibitor
      0.067   13.4   2.0          9    6.6   0.6    3.6  3  Big_3_5     Bacterial Ig-like domain (group 3)
      0.076   12.0   0.8       0.11   11.4   0.8    1.2  1  Tox-ODYAM1  Toxin in Odyssella and Amoebophilus


Domain annotation for each model (and alignments):
>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       3.8   1.4e+04       3      33 ..     121     128 ..     111     131 .. 0.53
   2 ?    3.2   0.0     0.024        88      25      45 ..     186     207 ..     178     212 .. 0.77
   3 !   20.7   0.0   8.5e-08   0.00031      17      55 ..     324     364 ..     322     375 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.8
                                       TCCTTEEEEEEEETTESSEEEESSTS.EEEE CS
                             Y_Y_Y   3 dnperllYrYrlegidkeWveasdysqeasy 33 
                                       ++ +                       +++y
  gi|298676181|ref|YP_003727930.1| 121 SGKN-----------------------NVTY 128
                                       2333.......................3333 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.024
                                       SSTS..EEEEES--SEEEEEEE CS
                             Y_Y_Y  25 sdysq.easytnlppGdYtlkV 45 
                                       +d++  + ++ nl +G+Y +++
  gi|298676181|ref|YP_003727930.1| 186 DDNGDtNGEFENLDAGEYSVLI 207
                                       444445789*********9865 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 8.5e-08
                                       TESSEEEESSTS...EEEEES--SEEEEEEEEEEETTS-B- CS
                             Y_Y_Y  17 idkeWveasdysq..easytnlppGdYtlkVkakdndgqwn 55 
                                       ++++ ++ +++++  ++s   lppG+Y+l+V+a++ +    
  gi|298676181|ref|YP_003727930.1| 324 LSGKTMTVDSNQTslNISTEGLPPGNYKLLVQASNQNDPIV 364
                                       567888888888899*******************9876555 PP

>> DUF669  Protein of unknown function (DUF669)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0034        12       5      25 ..     188     209 ..     184     231 .. 0.80
   2 ?   -2.5   0.0       1.5   5.2e+03     106     128 ..     238     259 ..     223     268 .. 0.71
   3 ?   -2.6   0.0       1.5   5.5e+03      44      69 ..     271     295 ..     267     308 .. 0.71
   4 ?    4.7   0.0    0.0082        29       2      27 ..     330     358 ..     329     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0034
                            DUF669   5 ssnve.gfealpsGeYevtivs 25 
                                       + +++ +fe+l++GeY v i+ 
  gi|298676181|ref|YP_003727930.1| 188 NGDTNgEFENLDAGEYSVLIIL 209
                                       5566746***********9984 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                            DUF669 106 lnkplkvkVkleedkngkkYpeV 128
                                       ++++lkv+++le+   + +Y  +
  gi|298676181|ref|YP_003727930.1| 238 VGNNLKVDIELEDAP-DTEYTYI 259
                                       467778888877766.5666555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.5
                            DUF669  44 evRsDldgklkgrkikydnlvvikdn 69 
                                       +vR + +g  +g+ ++ +n ++i+ +
  gi|298676181|ref|YP_003727930.1| 271 DVRLETNGHKTGTDLLVNNEYIID-D 295
                                       566677788888888888888884.3 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.0082
                            DUF669   2 tfdssnve.g..fealpsGeYevtivsae 27 
                                       t+ds++++ +  +e lp+G+Y+  +++++
  gi|298676181|ref|YP_003727930.1| 330 TVDSNQTSlNisTEGLPPGNYKLLVQASN 358
                                       7999999874669**********998775 PP

>> BsuPI  Intracellular proteinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.7   0.00047       1.7       8      66 ..      87     143 ..      81     164 .. 0.80
   2 ?   -0.3   0.0      0.31   1.1e+03      79      98 ..     194     212 ..     172     214 .. 0.74
   3 ?   -2.5   0.0       1.5   5.5e+03      68      95 ..     236     262 ..     229     267 .. 0.63
   4 ?    0.1   0.0      0.23   8.1e+02      81      98 ..     341     359 ..     324     361 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00047
                                       EE-SS-EEEEEEEEE-SSS-EEEEESSS--EEEEEE-TT--EEEETTTT-------EEE CS
                             BsuPI   8 easgeavelaltvtNesdeavtlqFssgqkydlvvkdeegeevwrysegrmFtqalsse 66 
                                       ++ +++v+++l v+N +d  ++  F++ q y       ++++ +++   + F+   s++
  gi|298676181|ref|YP_003727930.1|  87 STDSKNVDIKLNVKNYTDYVIEYPFETHQMYTNTS--GKNNVTYQFNGSKYFANKESKV 143
                                       455668***********************997655..7888888888888888765555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.31
                                       EE.S---SEEEEEEEEE--E CS
                             BsuPI  79 twdedlepGeYtleaelvae 98 
                                       ++ e+l +GeY++ ++l++e
  gi|298676181|ref|YP_003727930.1| 194 EF-ENLDAGEYSVLIILNNE 212
                                       34.78999****99998876 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.5
                                       E-TT-EEEEEEEE.S---SEEEEEEEEE CS
                             BsuPI  68 lepgesatyeetwdedlepGeYtleael 95 
                                       +  g+++ ++ ++ ed +  eYt+ a +
  gi|298676181|ref|YP_003727930.1| 236 ITVGNNLKVDIEL-EDAPDTEYTYIAGI 262
                                       4556666666666.67777777776655 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.23
                                       ..S---SEEEEEEEEE--E CS
                             BsuPI  81 d.edlepGeYtleaelvae 98 
                                       + e l+pG+Y+l ++  ++
  gi|298676181|ref|YP_003727930.1| 341 StEGLPPGNYKLLVQASNQ 359
                                       137899****999877665 PP

>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.6    0.0025         9      55      81 ..     118     144 ..      85     148 .. 0.86
   2 ?   -0.0   0.0      0.28     1e+03      38      63 ..     181     205 ..     172     219 .. 0.81
   3 ?    2.7   0.0      0.04   1.4e+02      38      64 ..     326     353 ..     315     361 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0025
                                       -SS-EEEEEEEEEE-TTS---S--EEE CS
                           Big_3_5  55 alaaGthsitAtYsGdanyaastssav 81 
                                       + + G++++t +++G++ +a   s  v
  gi|298676181|ref|YP_003727930.1| 118 TNTSGKNNVTYQFNGSKYFANKESKVV 144
                                       3579*****************999866 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.28
                                       SS-EE--TTSEEEEEEE-SS-EEEEE CS
                           Big_3_5  38 gtavllsanGtAtltvsalaaGthsi 63 
                                        t+  l++nG  +  +++l aG++s+
  gi|298676181|ref|YP_003727930.1| 181 ETKD-LDDNGDTNGEFENLDAGEYSV 205
                                       4444.4559***************98 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.04
                                       SS-EE--.TTSEEEEEEE-SS-EEEEEE CS
                           Big_3_5  38 gtavlls.anGtAtltvsalaaGthsit 64 
                                       g +++++ ++ + ++++++l++G++++ 
  gi|298676181|ref|YP_003727930.1| 326 GKTMTVDsNQTSLNISTEGLPPGNYKLL 353
                                       6677777234567777788******975 PP

>> Tox-ODYAM1  Toxin in Odyssella and Amoebophilus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.8   3.2e-05      0.11      41     112 ..     103     177 ..      87     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.2e-05
                        Tox-ODYAM1  41 dkivldynakycqevtklsrfskakqkf..skafaklakvikdvvlGpeinslkklqqkveaaygs...evlkldrg 112
                                          v++y     q +t+ s  +++  +f  sk fa+  k +k v++  +insl+++ +k +++  +   ++l ld++
  gi|298676181|ref|YP_003727930.1| 103 TDYVIEYPFETHQMYTNTSGKNNVTYQFngSKYFAN--KESKVVLIESDINSLIDILDKFKQGQIDsinDILSLDKV 177
                                       557999**99***********999988743677876..67898899*************999976511145556554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2384.36
//
Query:       gi|298676182|ref|YP_003727931.1|  [L=262]
Description: hypothetical protein Metev_2323 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1524.65
//
Query:       gi|298676183|ref|YP_003727932.1|  [L=181]
Description: hypothetical protein Metev_2324 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-26   93.2   9.9    1.2e-26   92.9   9.4    1.4  1  UPF0228   Uncharacterised protein family (UPF0228)
  ------ inclusion threshold ------
       0.26   11.7   2.9       0.52   10.7   0.4    2.2  2  DUF3221   Protein of unknown function (DUF3221)


Domain annotation for each model (and alignments):
>> UPF0228  Uncharacterised protein family (UPF0228)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   9.4   1.4e-30   1.2e-26       6     120 ..      63     176 ..      58     179 .. 0.96

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 1.4e-30
                           UPF0228   6 tieydsniveekyYivvdkdnitdvrkelekeknwtssipaikkgdeyiievseqaiedeevlaiLekydlqvkkfv 82 
                                       +++y+ n+ +++yY+vv++d+ + +++el k + w+   ++ikkgd+y+i vs+ + +++++l iL+k dlq+kkfv
  gi|298676183|ref|YP_003727932.1|  63 KLDYNINHLHNQYYLVVNQDKKSVLYNELMKANIWIRDEEVIKKGDNYLIVVSKSIANNKDFLDILSKQDLQLKKFV 139
                                       79*************************************************************************** PP

                           UPF0228  83 wCyiefgdgsekywineedairikneLeknekilsvsl 120
                                        Cyi f++ ++++ +  +   +ik+eL +++ki+ v l
  gi|298676183|ref|YP_003727932.1| 140 NCYIYFSKQPKDW-VGYDKGQKIKKELLEKDKIIRVAL 176
                                       ***********65.99999***************9976 PP

>> DUF3221  Protein of unknown function (DUF3221)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.059   5.3e+02      21      61 ..      59      98 ..      46     101 .. 0.62
   2 ?   10.7   0.4   5.8e-05      0.52       4      58 ..     103     162 ..     102     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.059
                           DUF3221 21 eeaenlseeeiekykgeaiwvlidsdkvsnlevGqkVrVwf 61
                                       e+++l+++ i   +++ ++v+++++k   + + +k ++w+
  gi|298676183|ref|YP_003727932.1| 59 REDIKLDYN-INHLHNQYYLVVNQDKKSVLYNELMKANIWI 98
                                      455554444.4666677777766666666666666666666 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 5.8e-05
                           DUF3221   4 vieksdnriLvvse...iekeeaenlseee..iekykgeaiwvlidsdkvsnlevGqkVr 58 
                                       vi+k dn ++vvs+   ++k+  + ls+++  ++k+ +  i+++ + ++  ++ +Gqk++
  gi|298676183|ref|YP_003727932.1| 103 VIKKGDNYLIVVSKsiaNNKDFLDILSKQDlqLKKFVNCYIYFSKQPKDWVGYDKGQKIK 162
                                       899*********9854469999999999999999999999999***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1156.12
//
Query:       gi|298676184|ref|YP_003727933.1|  [L=115]
Description: hypothetical protein Metev_2325 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 785.53
//
Query:       gi|298676185|ref|YP_003727934.1|  [L=494]
Description: hypothetical protein Metev_2326 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.041   13.9   4.3      0.069   13.1   4.3    1.3  1  PGF-CTERM  PGF-CTERM motif
      0.042   14.2   0.1          2    8.8   0.0    2.5  2  TraA       TraA


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   4.3   7.7e-06     0.069       6      23 .]     477     494 .]     477     494 .] 0.95

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.7e-06
                         PGF-CTERM   6 avlAlaGLLaaalLaRRr 23 
                                       +++A++G+L+a+lL++Rr
  gi|298676185|ref|YP_003727934.1| 477 ILIAVIGILGAVLLVKRR 494
                                       689**************9 PP

>> TraA  TraA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00022         2      23      55 ..      11      43 ..       2      80 .. 0.83
   2 ?    2.7   0.0     0.017   1.6e+02      61      84 ..     257     279 ..     244     288 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00022
                              TraA 23 rvftkkkllklakvvlpvavliaffpdlamaat 55
                                        ++k k+++lak+ + ++ +i+f+p +    t
  gi|298676185|ref|YP_003727934.1| 11 NEYNKNKAIHLAKALIFITLIILFIPSVNAEVT 43
                                      469***********************9875554 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.017
                              TraA  61 mksgdatvkatfgkdssvvkwvvl 84 
                                       m+s +  vk+ f k+s  vk++ +
  gi|298676185|ref|YP_003727934.1| 257 MRS-NQLVKSEFNKESNPVKYINI 279
                                       554.778*************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1374  (0.0766356); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 2852.98
//
Query:       gi|298676186|ref|YP_003727935.1|  [L=228]
Description: hypothetical protein Metev_2327 [Methanohalobium evestigatum Z-7303]
Scores for complete 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   22.7   0.1    0.00041   21.2   0.0    1.9  2  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   2.3e-08   0.00041      12      72 ..       1      78 [.       1      88 [. 0.70
   2 ?   -2.8   0.0      0.73   1.3e+04      60      76 ..     138     154 ..     125     158 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.3e-08
                           Pilin_N 12 mvaitvIlaAviaafvlgl.asneekapqasi.............evkidssastgkna.....vslehkgGdsidtkd 71
                                      mvaitvIlaAv++ + +gl    + ++p+ ++                 d s++t++ +     v++ ++ G +id ++
  gi|298676186|ref|YP_003727935.1|  1 MVAITVILAAVLGESLFGLgITSKLTEPKDQLvfdntqvllgveyRS-WDGSGGTEN-NgdidhVYMDYQHGPVIDGQE 77
                                      9******************7567778888777667776666553211.222222322.246778999999999998876 PP

                           Pilin_N 72 l 72
                                      +
  gi|298676186|ref|YP_003727935.1| 78 I 78
                                      6 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.73
                           Pilin_N  60 ehkgGdsidtkdlkivl 76 
                                       + ++G  ++ +d+ +++
  gi|298676186|ref|YP_003727935.1| 138 KGQSGGKTNPEDIGVQY 154
                                       44556666667776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 1697.93
//
Query:       gi|298676187|ref|YP_003727936.1|  [L=243]
Description: hypothetical protein Metev_2328 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1456.63
//
Query:       gi|298676188|ref|YP_003727937.1|  [L=180]
Description: hypothetical protein Metev_2329 [Methanohalobium evestigatum Z-7303]
Scores for 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  139.1   4.1    6.3e-41  139.1   4.1    2.0  2  UPF0228   Uncharacterised protein family (UPF0228)


Domain annotation for each model (and alignments):
>> UPF0228  Uncharacterised protein family (UPF0228)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.4   0.2    0.0074   1.3e+02      53      77 ..      40      63 ..      27      65 .. 0.84
   2 !  139.1   4.1   3.5e-45   6.3e-41       3     124 .]      64     179 ..      62     179 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0074
                           UPF0228 53 yiievseqaiedeevlaiLekydlq 77
                                      y+i+  e  + ++e+ +iL +ydl 
  gi|298676188|ref|YP_003727937.1| 40 YYIAF-EDNVTEQEIESILTNYDLI 63
                                      78887.78888899********996 PP

  == domain 2  score: 139.1 bits;  conditional E-value: 3.5e-45
                           UPF0228   3 vnYtieydsniveekyYivvdkdnitdvrkelekeknwtssipaikkgdeyiievseqaiedeevlaiLekydlqvk 79 
                                       +nYtieyd++++++ yY++vdk+n+t+v++ +  +++w+s++++ k++d+yii++ ++ i+d evl++Le+y+lq+k
  gi|298676188|ref|YP_003727937.1|  64 INYTIEYDEGRRPS-YYTSVDKNNFTSVYYGDLLSRTWASRGMVSKNNDDYIISI-RKPIND-EVLETLESYNLQLK 137
                                       7*********8887.****************************************.9*****.9************* PP

                           UPF0228  80 kfvwCyiefgdgsekywineedairikneLeknekilsvsldyiv 124
                                       kfvwCyi++g+gs+   +n++d+i+ik++Leknekil+v++dyiv
  gi|298676188|ref|YP_003727937.1| 138 KFVWCYIDYGTGSH---VNRKDSIKIKDKLEKNEKILFVRFDYIV 179
                                       **************...9*************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:01.14
# Mc/sec: 478.65
//
Query:       gi|298676189|ref|YP_003727938.1|  [L=75]
Description: hypothetical protein Metev_2330 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.012   15.2   2.3      0.012   15.2   2.3    2.2  3  DUF3149       Protein of unknown function (DUF3149)
        0.6    9.6   1.7       0.67    9.5   1.7    1.1  1  E1-E2_ATPase  E1-E2 ATPase
        1.3    7.7   6.1        1.5    7.5   6.1    1.0  1  DUF2207       Predicted membrane protein (DUF2207)
        3.1    7.9   5.6        3.8    7.6   5.6    1.0  1  DHHC          DHHC palmitoyltransferase


Domain annotation for each model (and alignments):
>> DUF3149  Protein of unknown function (DUF3149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2      0.31   1.4e+03      14      20 ..      14      20 ..      10      26 .. 0.71
   2 ?   -3.5   0.3       1.8   8.2e+03      27      32 ..      36      41 ..      34      42 .. 0.64
   3 ?   15.2   2.3   2.7e-06     0.012      15      33 ..      54      72 ..      53      75 .] 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.31
                           DUF3149 14 liVIvft 20
                                      l+VI++ 
  gi|298676189|ref|YP_003727938.1| 14 LLVILLL 20
                                      6777765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.8
                           DUF3149 27 firyFi 32
                                       +++F 
  gi|298676189|ref|YP_003727938.1| 36 LYSFFR 41
                                      577875 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 2.7e-06
                           DUF3149 15 iVIvftigmgaffiryFir 33
                                      ++I+++ig+++ff+ry ++
  gi|298676189|ref|YP_003727938.1| 54 LGIFVIIGIVGFFLRYLVK 72
                                      68**************876 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.7   0.00015      0.67     115     170 ..       2      61 ..       1      68 [. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHHHHHHHHHHS-STTTSSTT....HHHHHHHHHHHHHS-TTHHHHHHHH CS
                      E1-E2_ATPase 115 ldklgkvlvpvvlliallvflialllgksla....eallralallvaaiPcaLplavpla 170
                                       l+kl + l+ +vll++ll++ ++++l++++     ++++r ++ +++ +  aL+++v + 
  gi|298676189|ref|YP_003727938.1|   2 LQKLNSNLISTVLLVILLLLTLLYYLEEFIHpgalYSFFRYISQFIGGVCYALGIFVIIG 61 
                                       45555666666666666666666666666556666******************9998775 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   6.1   0.00034       1.5     387     437 ..       9      74 ..       2      75 .] 0.70

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00034
                           DUF2207 387 glgliilglilillallllvll..................lvfllilllillliaiivlllfsrllgrr 437
                                       ++  ++l+++l+l +l+    l                  +++ + ++l++++i+ iv +++++l++r+
  gi|298676189|ref|YP_003727938.1|   9 LISTVLLVILLLLTLLYY---LeefihpgalysffryisqFIGGVCYALGIFVIIGIVGFFLRYLVKRF 74 
                                       333333333333333333...13458899********************************99999985 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   5.6   0.00085       3.8      55     118 ..       9      70 ..       7      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00085
                              DHHC  55 llylllllilalvlllialvklveeekkseflavtllkkllsilllvlsllfllllgllllfhl 118
                                       l++++ll+il l++ll++l + ++     +f ++    +++  ++++l +++++ ++ ++l++l
  gi|298676189|ref|YP_003727938.1|   9 LISTVLLVILLLLTLLYYLEEFIHPGALYSFFRYIS--QFIGGVCYALGIFVIIGIVGFFLRYL 70 
                                       789999999999999999999999999998887754..45777777777777777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.52
# Mc/sec: 437.32
//
Query:       gi|298676190|ref|YP_003727939.1|  [L=273]
Description: hypothetical protein Metev_2331 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.083   12.6   0.0       0.65    9.7   0.0    1.9  2  MMADHC    Methylmalonic aciduria and homocystinuria type D pr


Domain annotation for each model (and alignments):
>> MMADHC  Methylmalonic aciduria and homocystinuria type D protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   3.6e-05      0.65     191     220 ..     116     145 ..     112     151 .. 0.89
   2 ?    0.5   0.0     0.024   4.2e+02      16      53 ..     211     251 ..     201     268 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 3.6e-05
                            MMADHC 191 saLqseGyWaDFidPssGraffgsytnatl 220
                                       ++L s GyW DFi    G+  +g +t+++ 
  gi|298676190|ref|YP_003727939.1| 116 DKLSSGGYWDDFIAKKDGKIMMGFKTDNSQ 145
                                       68999*****************99999875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.024
                            MMADHC  16 sdepaiaispanlskrtvwpdeamgpf...gpqdqrfqLpg 53 
                                       +++  i+is + +  rt  pde +g++    ++ +r +L +
  gi|298676190|ref|YP_003727939.1| 211 KTTVDIEISITCYNDRTNRPDEYQGYYecyVENKHRTNLIN 251
                                       5566689999999***********99855545555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 1967.88
//
Query:       gi|298676191|ref|YP_003727940.1|  [L=56]
Description: hypothetical protein Metev_2332 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.084   13.6   0.4      0.092   13.4   0.4    1.0  1  GRP       Glycine rich protein family


Domain annotation for each model (and alignments):
>> GRP  Glycine rich protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   5.1e-06     0.092       1      46 [.       1      48 [.       1      52 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.1e-06
                               GRP  1 Maska.lilLglllaavlLissevaaael.skeeksekeeevkdekyg 46
                                      M++k   +l+ ++l+++ ++s  + +++  +k++ s+k++++  ek g
  gi|298676191|ref|YP_003727940.1|  1 MKAKSsTLLMVMVLISMAFVSAVIGQNNIsNKTQYSDKTDNISLEKAG 48
                                      55554378888999999****999999886677889999999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 344.31
//
Query:       gi|298676192|ref|YP_003727941.1|  [L=400]
Description: carbohydrate-binding and sugar hydrolysis protein [Methanohalobium evestigatum Z-7303]
Scores for complete 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-44  151.4 123.7      2e-19   69.8  35.8    3.1  3  NosD             Periplasmic copper-binding protein (NosD)
    4.7e-36  124.0 133.2    1.2e-17   64.2  39.8    3.4  4  Beta_helix       Right handed beta helix region


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 !   69.8  35.8   2.3e-23     2e-19       5     173 ..      47     228 ..      43     229 .. 0.81
   2 !   62.9  29.0   2.9e-21   2.6e-17      59     172 ..     205     315 ..     203     316 .. 0.97
   3 !   46.3  42.9   3.4e-16   3.1e-12      39     178 ..     229     366 ..     228     379 .. 0.76

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 2.3e-23
                              NosD   5 isgdevlvsa..rgngiqlens............egseisnneisnsrdgilldnssnntitgntienl....ryGi 63 
                                        sgd+++v+   +     +en+            ++ e +  + +++++++   ns++++i+g +i       ++G+
  gi|298676192|ref|YP_003727941.1|  47 NSGDNIVVYPgkY-----VENIvidkevsiesksKNPENTVIQSKTPEKNVIQVNSNKVNISGFKIMGAkntnQSGV 118
                                       5667776664441.....33333222244443332222344555566677788899999999996666556679*** PP

                              NosD  64 hlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssnt 139
                                       +l+  e+++i+++++s+n +G+++ +s+ ntl nNt+++n+n+Gi+l++s+nn + nN +  n+ +Gifl++s +n 
  gi|298676192|ref|YP_003727941.1| 119 YLDRVEKCNISNSIFSKNFNGVSFIKSEWNTLVNNTVKSNKNHGIYLKKSKNNRVINNIVGsNSRYGIFLQRSINNN 195
                                       ************************************************************76*************** PP

                              NosD 140 itgNriesnqkiGilllsssegntiynNyFinns 173
                                       i  N+i+++ + Gil +++s++n + +N F++n+
  gi|298676192|ref|YP_003727941.1| 196 IITNHIQNHSNNGIL-VDHSNNNFLGDNKFFGNE 228
                                       ***************.***************996 PP

  == domain 2  score: 62.9 bits;  conditional E-value: 2.9e-21
                              NosD  59 lryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtisnnnkGiflens 135
                                       +++Gi ++ s++n + dn++++ne+Gi+++ss+ n l+ N+isnn++ Gi    s++n++ nN i++n+ Gifl++ 
  gi|298676192|ref|YP_003727941.1| 205 SNNGILVDHSNNNFLGDNKFFGNEYGIYIHSSQSNKLKVNNISNNKI-GIQGGLSNKNELINNSILKNKVGIFLYKC 280
                                       578********************************************.***************************** PP

                              NosD 136 ssntitgNriesnqkiGilllsssegntiynNyFinn 172
                                       ++n i  N i++n   Gil l++s +n+i nN++ n+
  gi|298676192|ref|YP_003727941.1| 281 NGNDIIANIINENIHKGIL-LQYSVDNKISNNTL-NS 315
                                       *******************.**************.53 PP

  == domain 3  score: 46.3 bits;  conditional E-value: 3.4e-16
                              NosD  39 dgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssn 115
                                       +gi++ +s++n+++ n i+n++ Gi    s++n + +n + +n+ Gi+l++ ++n +  N+i++n  +Gill++s +
  gi|298676192|ref|YP_003727941.1| 229 YGIYIHSSQSNKLKVNNISNNKIGIQGGLSNKNELINNSILKNKVGIFLYKCNGNDIIANIINENIHKGILLQYSVD 305
                                       57888888888888888888888888888888888888888888888888888886668888888888888888888 PP

                              NosD 116 ntisnNtisnnnkGiflens.ssntitgNriesnqkiGilllsssegntiynNyFinnsenvky 178
                                       n+isnNt  +n+ Gi +e+  ++nt+  N++++n    i   ++++ n+i nNy+ nns +  +
  gi|298676192|ref|YP_003727941.1| 306 NKISNNTLNSNGLGIIMEDFsNNNTVHYNSLSKN-RDNIR--ANYSINQIKNNYMNNNSSQNLN 366
                                       8888888888888888888657888888888888.77777..6666888888888665555444 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 ?   -1.1   1.3      0.17   1.6e+03     100     129 ..      34      65 ..      20      86 .. 0.62
   2 !   64.2  39.8   1.3e-21   1.2e-17       3     157 ..      93     245 ..      91     246 .. 0.94
   3 !   51.1  33.4   1.4e-17   1.3e-13      16     144 ..     199     321 ..     199     324 .. 0.96
   4 !   36.2  44.0   5.5e-13   4.9e-09       1     158 []     229     379 ..     229     379 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.17
                                       -S--EEES-EEESTT--SEE---TT..---EE CS
                        Beta_helix 100 ssnntienNiidnnagsGividdss..snvtv 129
                                       ++ ++i++ + d+n+g+ iv+++++   n+++
  gi|298676192|ref|YP_003727941.1|  34 NNYTSIKKAVNDANSGDNIVVYPGKyvENIVI 65 
                                       44466777777778888888888884333333 PP

  == domain 2  score: 64.2 bits;  conditional E-value: 1.3e-21
                                       EEE-SS-E.EEESEEEES-...SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT- CS
                        Beta_helix   3 isingssnvtiknntisns...ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfg 76 
                                       i +n++++ +i++++i+++   +++G+yl+  +++ i+n+ +++ +++G++  +s+ nt+ nnt+  n++ gi+l++
  gi|298676192|ref|YP_003727941.1|  93 IQVNSNKV-NISGFKIMGAkntNQSGVYLDRVEKCNISNSIFSK-NFNGVSFIKSEWNTLVNNTVKSNKNHGIYLKK 167
                                       45555555.*****************************999999.******************************** PP

                                       -S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EE CS
                        Beta_helix  77 asnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtv 153
                                       ++nn + nn +  n+++Gi+l+ s nn i  N+i n +++Gi +d s+ n+   +N++++n  +Gi++ +s+s +++
  gi|298676192|ref|YP_003727941.1| 168 SKNNRVINNIVGSNSRYGIFLQRSINNNIITNHIQNHSNNGILVDHSN-NNFLGDNKFFGNE-YGIYIHSSQS-NKL 241
                                       ************************************************.8889********8.*******999.777 PP

                                       ES-E CS
                        Beta_helix 154 rnNt 157
                                       + N+
  gi|298676192|ref|YP_003727941.1| 242 KVNN 245
                                       7666 PP

  == domain 3  score: 51.1 bits;  conditional E-value: 1.4e-17
                                       EEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS CS
                        Beta_helix  16 ntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdngg 92 
                                       n+i+n +++Gi +++s+n+ + +n++ + +++Giyi++s+ n+++ n+is+n+  gi    +++n + nn i +n+ 
  gi|298676192|ref|YP_003727941.1| 199 NHIQNHSNNGILVDHSNNNFLGDNKFFG-NEYGIYIHSSQSNKLKVNNISNNK-IGIQGGLSNKNELINNSILKNKV 273
                                       789*************************.************************.*********************87 PP

                                       -SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE- CS
                        Beta_helix  93 sGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiav 144
                                        Gi+l+ ++ n+i  Nii++n + Gi +++s  +++++nNt+++n+  Gi +
  gi|298676192|ref|YP_003727941.1| 274 -GIFLYKCNGNDIIANIINENIHKGILLQYSV-DNKISNNTLNSNG-LGI-I 321
                                       .*******************************.************7.777.4 PP

  == domain 4  score: 36.2 bits;  conditional E-value: 5.5e-13
                                       -SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT-- CS
                        Beta_helix   1 sgisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfga 77 
                                       +gi+i +s++ ++k n+isn ++ Gi+ + s+++ + nn i + +  Gi ++++++n i  n i++n + gi l+++
  gi|298676192|ref|YP_003727941.1| 229 YGIYIHSSQSNKLKVNNISN-NKIGIQGGLSNKNELINNSILK-NKVGIFLYKCNGNDIIANIINENIHKGILLQYS 303
                                       68999999999999999999.5999999999999999999999.999999999999999999999999999999999 PP

                                       S--EEES-EEES-SS-SEE-TT.-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EE CS
                        Beta_helix  78 snnlienneitdnggsGiylny.ssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtv 153
                                         n i+nn+ + ng  Gi +++ s+nnt+++N ++ n+ + i  ++s   + ++nN ++nn+  + +++++s+++ +
  gi|298676192|ref|YP_003727941.1| 304 VDNKISNNTLNSNGL-GIIMEDfSNNNTVHYNSLSKNR-DNIRANYSI--NQIKNNYMNNNS--SQNLNSDSHEIPF 374
                                       999999999999988.9999987889999999999999.999999999..666999999998..5556777777888 PP

                                       ES-E. CS
                        Beta_helix 154 rnNti 158
                                        n t+
  gi|298676192|ref|YP_003727941.1| 375 INSTF 379
                                       88776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1239  (0.0691059); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 2890.71
//
Query:       gi|298676193|ref|YP_003727942.1|  [L=46]
Description: hypothetical protein Metev_2334 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.26u 0.19s 00:00:00.45 Elapsed: 00:00:00.34
# Mc/sec: 406.41
//
Query:       gi|298676194|ref|YP_003727943.1|  [L=1594]
Description: hypothetical protein Metev_2335 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-10   40.0  49.9     0.0035   17.5   1.9    7.7  7  FixG_C          IG-like fold at C-terminal of FixG, putative 
    0.00011   22.0   0.4    0.00017   21.4   0.4    1.3  1  PGF-CTERM       PGF-CTERM motif
     0.0015   18.7  57.0      0.011   16.0   1.6    6.9  7  DUF11           Domain of unknown function DUF11
     0.0021   17.8   2.5       0.92    9.2   0.4    3.1  2  Ail_Lom         Enterobacterial Ail/Lom protein
  ------ inclusion threshold ------
      0.057   13.5   0.0         19    5.4   0.0    4.3  3  Fn3-like        Fibronectin type III-like domain
      0.088   13.0   0.1       0.38   10.9   0.1    2.1  1  Pentapeptide_4  Pentapeptide repeats (9 copies)
        1.2    9.2  26.1        3.2    7.8   0.8    8.2 10  BsuPI           Intracellular proteinase inhibitor
        2.4    8.4  33.7       0.76   10.0   0.8    6.8  7  ASH             Abnormal spindle-like microcephaly-assoc'd, A


Domain annotation for each model (and alignments):
>> FixG_C  IG-like fold at C-terminal of FixG, putative oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   1.3    0.0046        10      34     102 ..     388     452 ..     370     470 .. 0.74
   2 !   17.5   1.9   1.6e-06    0.0035      34      89 ..     490     543 ..     478     575 .. 0.83
   3 !   16.0   0.5   4.8e-06     0.011      34      88 ..     598     652 ..     595     670 .. 0.86
   4 ?    4.4   0.6     0.019        42      34      89 ..     701     754 ..     683     793 .. 0.84
   5 !   10.4   1.3   0.00026      0.58      34     101 ..     806     868 ..     779     883 .. 0.79
   6 !   13.5   1.3   2.8e-05     0.064      34     111 ..     905     982 ..     890     990 .. 0.70
   7 ?    1.7   1.9      0.13   2.9e+02      34     109 ..    1016    1090 ..    1003    1104 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0046
                                       EEEEEEEE-SSS-EEEEEEEES-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEE CS
                            FixG_C  34 sYtlkilNktekprrytlsveglpglelagraekeitvapgekrkvpvfvrvpaealkkkstpitfkvt 102
                                        Y lki N   k+ +++l+ +   g+   + +e++i+v p+e++ +++ v+  +     k+ p+ +k++
  gi|298676194|ref|YP_003727943.1| 388 IYDLKIKNIGLKKETINLTKTKVRGVNA-EFNESQISVMPDETKIIKLKVSSSQIG---KNYPVIVKAS 452
                                       49*****************998876666.43679*********9999999886644...3346666665 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.6e-06
                                       EEEEEEEE-SSS-EEEEEEEES-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG CS
                            FixG_C  34 sYtlkilNktekprrytlsveglpglelagraekeitvapgekrkvpvfvrvpaea 89 
                                       +Yt++++N+ ++++++++s ++  ++ +   ++++it++ g++ +v  +v   ++ 
  gi|298676194|ref|YP_003727943.1| 490 TYTFTVTNTGNQEHTFNISSTNPSDIGI-L-KNDSITLKGGQSDTVEYVVNSSSKG 543
                                       7********************9999*99.5.47*************9999887665 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 4.8e-06
                                       EEEEEEEE-SSS-EEEEEEEES-S..S-EE.E.S--EEEE-TT-EEEEEEEEEE-GG CS
                            FixG_C  34 sYtlkilNktekprrytlsveglp..glelagraekeitvapgekrkvpvfvrvpae 88 
                                       +Y+++i+N+ +++ +y+l+v +    +++l  +++k++++ pgek+  ++ v++p +
  gi|298676194|ref|YP_003727943.1| 598 TYNITITNTGNQKDTYDLTVISPRtnNTSL--NNSKPVNLNPGEKTFRKLNVSAPVS 652
                                       7********************843347777..467***********99999999865 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.019
                                       EEEEEEEE-SSS-EEEEEEEES.-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG CS
                            FixG_C  34 sYtlkilNktekprrytlsveg.lpglelagraekeitvapgekrkvpvfvrvpaea 89 
                                        Yt+ + N+ + +  ++l+ +   +++e+   ++   +v+pg+++++ v ++ p + 
  gi|298676194|ref|YP_003727943.1| 701 NYTVNVKNTGNVEDDFKLTNKTnIDSIEM---PSVIKNVKPGKTESFDVAISNPDSG 754
                                       4******************9975789999...4578899**********99988766 PP

  == domain 5  score: 10.4 bits;  conditional E-value: 0.00026
                                       EEEEEEEE-SSS-EEEEEEEES-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEE CS
                            FixG_C  34 sYtlkilNktekprrytlsveglpglelagraekeitvapgekrkvpvfvrvpaealkkkstpitfkv 101
                                       +Y l i N+ + + +y++s e l ++ +  +  +++t+ pge+++++v v+   ++ +  s+p+++k 
  gi|298676194|ref|YP_003727943.1| 806 TYILNIKNTGNIKDTYEISSE-LTDANI-VD--NKTTLYPGESTSITVNVSGFNDS-NIYSIPVKVKS 868
                                       6********************.89****.55..8999*************986665.33344555554 PP

  == domain 6  score: 13.5 bits;  conditional E-value: 2.8e-05
                                       EEEEEEEE-SSS-EEEEEEEES-S...S-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEE.EGGG CS
                            FixG_C  34 sYtlkilNktekprrytlsveglp...glelagraekeitvapgekrkvpvfvrvpaealkkkstpitfkvt.ddde 106
                                       sYt+k++N+  ++++y+l+v ++    ++ la   ++  ++ pge+++v ++   +++  +  +++  +k++ ++++
  gi|298676194|ref|YP_003727943.1| 905 SYTIKVTNTGVHTHTYDLKVADNSsntTANLAI--NSIPDLNPGESTTVDFTFNNTQDTDR--RIEAVIKAEvQNNP 977
                                       7********************854444444433..467789********999888777734..44555555543433 PP

                                       TEEEE CS
                            FixG_C 107 ketve 111
                                       +++++
  gi|298676194|ref|YP_003727943.1| 978 EKSAT 982
                                       33332 PP

  == domain 7  score: 1.7 bits;  conditional E-value: 0.13
                                        EEEEEEEE-SSS-EEEEEEEES.-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEE..EGG CS
                            FixG_C   34 sYtlkilNktekprrytlsveg.lpglelagraekeitvapgekrkvpvfvrvpaealkkkstpitfkvt..ddd 105 
                                        +Y l++ N  +++ +++l++ + +++ +  +  +k++++ + ++ + + ++++++  +  +++++++ ++  +  
  gi|298676194|ref|YP_003727943.1| 1016 TYFLELKNLGNTNNSFNLEIVEgKEKYTTFK--KKSVDLNASGTNNDTEIIKLTHYPEGVGEHTVKINANssN-- 1086
                                        6999999999999999999874366666634..4888888888888777777777776678888888886321.. PP

                                        GTEE CS
                            FixG_C  106 eket 109 
                                        ++ t
  gi|298676194|ref|YP_003727943.1| 1087 SNDT 1090
                                        2222 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.4   7.7e-08   0.00017       1      22 [.    1571    1592 ..    1571    1593 .. 0.97

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7.7e-08
                         PGF-CTERM    1 tPGFGavlAlaGLLaaalLaRR 22  
                                        +PGF a ++l+G+  +a+L+RR
  gi|298676194|ref|YP_003727943.1| 1571 IPGFKATFTLVGMVTIAYLIRR 1592
                                        6********************9 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   6.3    0.0018       4.1      10      79 ..     483     570 ..     475     577 .. 0.69
   2 !    9.6   4.9   0.00047       1.1       6      83 ..     587     654 ..     582     661 .. 0.76
   3 !   16.0   1.6   5.1e-06     0.011       7      40 ..     691     751 ..     676     804 .. 0.62
   4 ?    0.6   1.4      0.32   7.1e+02      11      28 ..     800     817 ..     787     858 .. 0.74
   5 !   14.1   3.5   1.9e-05     0.042      15      83 ..     903     962 ..     866     969 .. 0.76
   6 ?   -2.8   0.2       3.5   7.9e+03      15      29 ..    1014    1028 ..    1002    1033 .. 0.78
   7 ?   -2.8   0.4       3.6   8.1e+03      61      90 ..    1108    1139 ..    1077    1140 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0018
                             DUF11  10 vrpGdtvtytltvtNtgpasangvvvtDtl..................Paglayvsvsasqgtasaltsv.gsLeag 67 
                                        +   + tyt tvtNtg++   +  ++ t                      ++yv +s+s+g++  + +v +s +  
  gi|298676194|ref|YP_003727943.1| 483 TATNTNATYTFTVTNTGNQEH-TFNISSTNpsdigilkndsitlkggqSDTVEYVVNSSSKGVYVSDITVnESTNHN 558
                                       4445579************99.6666666633666666666666666668999999999988888887776666666 PP

                             DUF11  68 esatlsftvrvt 79 
                                        + tl +  +v+
  gi|298676194|ref|YP_003727943.1| 559 ITETLFVITNVK 570
                                       666666655555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00047
                             DUF11   6 dksevrpGdtvtytltvtNtgpasangvvvtDtlP..aglayvsvsasqgtasaltsvgsLeagesatlsftvrvtr 80 
                                       +k++v+   + ty++t tNtg+++  ++ +t + P   ++++  ++             +L++ge++  ++ v++++
  gi|298676194|ref|YP_003727943.1| 587 TKPPVDVNKNATYNITITNTGNQKD-TYDLTVISPrtNNTSLNNSKPV-----------NLNPGEKTFRKLNVSAPV 651
                                       466899999*************999.5555555553255555555555...........999999999999998888 PP

                             DUF11  81 taa 83 
                                       +++
  gi|298676194|ref|YP_003727943.1| 652 SGD 654
                                       887 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 5.1e-06
                             DUF11   7 ksevrpGdtvtytltvtNtgpasangvvvtDtl............................P 40 
                                       +++++pG tv+yt+ v+Ntg++   + ++t                               P
  gi|298676194|ref|YP_003727943.1| 691 SATANPGNTVNYTVNVKNTGNVED-DFKLTNKTnidsiempsviknvkpgktesfdvaisnP 751
                                       458******************998.8888876666777776666666644444444444443 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.32
                             DUF11  11 rpGdtvtytltvtNtgpa 28 
                                          ++vty+l  +Ntg+ 
  gi|298676194|ref|YP_003727943.1| 800 ENNENVTYILNIKNTGNI 817
                                       566899999999999975 PP

  == domain 5  score: 14.1 bits;  conditional E-value: 1.9e-05
                             DUF11  15 tvtytltvtNtgpasa.ngvvvtDtlPaglayvsvsasqgtasaltsv.gsLeagesatlsftvrvtrtaa 83 
                                       + +yt+ vtNtg  +  ++++v D     +           a+ + ++ ++L++ges+t+ ft + t+ ++
  gi|298676194|ref|YP_003727943.1| 903 ASSYTIKVTNTGVHTHtYDLKVADNSSNTT-----------ANLAINSiPDLNPGESTTVDFTFNNTQDTD 962
                                       557**********99989******322222...........344444559*************99988776 PP

  == domain 6  score: -2.8 bits;  conditional E-value: 3.5
                             DUF11   15 tvtytltvtNtgpas 29  
                                        + ty l ++N g+++
  gi|298676194|ref|YP_003727943.1| 1014 NATYFLELKNLGNTN 1028
                                        789*******99976 PP

  == domain 7  score: -2.8 bits;  conditional E-value: 3.6
                             DUF11   61 v...gsLeagesatlsftvrvtrtaasgaltnv 90  
                                        +   +s+  g+sa  + t+ +++ ++s+ ++n+
  gi|298676194|ref|YP_003727943.1| 1108 SeiiKSVVDGQSAVKNSTIDPSTVKNSL-INNT 1139
                                        1235777888888888888888888876.6665 PP

>> Ail_Lom  Enterobacterial Ail/Lom protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0021       4.7     132     189 ..     601     658 ..     591     666 .. 0.79
   2 !    9.2   0.4   0.00041      0.92     129     192 ..     905     969 ..     881     973 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0021
                           Ail_Lom 132 vrltddkrkkqevltrsddarrsntalaysagvqinptesvvvdlayeasgrgdwrte 189
                                       +++t+  ++k+ +     + r  nt+l  s  v++np e+    l   a  +gd+  +
  gi|298676194|ref|YP_003727943.1| 601 ITITNTGNQKDTYDLTVISPRTNNTSLNNSKPVNLNPGEKTFRKLNVSAPVSGDYNVK 658
                                       56666655555555556789**********************************9865 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00041
                           Ail_Lom 129 gdyvrltddkrkkqev.ltrsddarrsntalaysagvqinptesvvvdlayeasgrgdwrteafi 192
                                          +++t+   +++ + l  +d++  + + la ++  ++np es +vd +++ +   d r ea i
  gi|298676194|ref|YP_003727943.1| 905 SYTIKVTNTGVHTHTYdLKVADNSSNTTANLAINSIPDLNPGESTTVDFTFNNTQDTDRRIEAVI 969
                                       445678887777776437888999999999********************************998 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.3   2.9e+03      27      49 ..     523     545 ..     521     552 .. 0.81
   2 ?    2.0   0.0       0.1   2.3e+02      26      42 ..     836     852 ..     835     861 .. 0.88
   3 ?    5.4   0.0    0.0086        19      28      43 ..     942     957 ..     940     962 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.3
                                       EEE-TT-EEEEEEEEECGGG-EE CS
                          Fn3-like  27 veLapGesktvtftldrkdlsvw 49 
                                       ++L+ G+s tv+  +++++  v+
  gi|298676194|ref|YP_003727943.1| 523 ITLKGGQSDTVEYVVNSSSKGVY 545
                                       67999*******99998776665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.1
                                       EEEE-TT-EEEEEEEEE CS
                          Fn3-like  26 kveLapGesktvtftld 42 
                                       k++L pGes+ +t++++
  gi|298676194|ref|YP_003727943.1| 836 KTTLYPGESTSITVNVS 852
                                       99************986 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0086
                                       EE-TT-EEEEEEEEEC CS
                          Fn3-like  28 eLapGesktvtftldr 43 
                                       +L+pGes+tv ft++ 
  gi|298676194|ref|YP_003727943.1| 942 DLNPGESTTVDFTFNN 957
                                       59***********986 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00017      0.38       4      49 ..    1132    1177 ..    1118    1184 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                    Pentapeptide_4    4 trcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfa 49  
                                        +++  nn++ ++ + ++++l ++++ +++l+n +F++ ++++ +++
  gi|298676194|ref|YP_003727943.1| 1132 KNSLINNTNITDSTVKNSKLVGSTIIDSNLNNIEFRNGHIENNKIY 1177
                                        3333344444444444444444444444444444444444443333 PP

>> BsuPI  Intracellular proteinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.7     0.004       8.9       8      67 ..      83     140 ..      77     160 .. 0.79
   2 ?   -3.0   0.0       3.3   7.4e+03      80      98 ..     191     208 ..     176     209 .. 0.78
   3 ?    7.8   0.8    0.0014       3.2       4      45 ..     479     520 ..     475     527 .. 0.84
   4 ?   -3.2   0.1       3.9   8.6e+03      13      28 ..     596     611 ..     585     615 .. 0.75
   5 ?    2.4   0.0      0.07   1.6e+02      66      99 ..     633     665 ..     629     666 .. 0.89
   6 ?   -3.0   0.3       3.4   7.6e+03       8      27 ..     694     713 ..     690     724 .. 0.69
   7 ?    3.7   0.0     0.028        62      67      98 ..     735     765 ..     732     767 .. 0.88
   8 ?   -2.3   0.2       2.1   4.7e+03       6      33 ..     797     824 ..     795     842 .. 0.79
   9 ?   -2.8   0.1         3   6.7e+03       7      29 ..     897     919 ..     894     930 .. 0.73
  10 ?   -0.3   0.0      0.48   1.1e+03      68      92 ..     943     966 ..     936     974 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.004
                                       EE-SS-EEEEEEEEE-SSS-EEEEESSS--EEEEEE-TT--EEEETTTT-------EEEE CS
                             BsuPI   8 easgeavelaltvtNesdeavtlqFssgqkydlvvkdeegeevwrysegrmFtqalsset 67 
                                       ++ +++v+++l v+N +d  ++  F++ q y       ++++ +++   + F+   +++ 
  gi|298676194|ref|YP_003727943.1|  83 STDSKNVDIKLNVKNYTDYVIEYPFETHQMYTNTS--GKNNVTYQFNGSKYFANKETQVV 140
                                       455668***********************997655..78888888888888887666555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.3
                                       E.S---SEEEEEEEEE--E CS
                             BsuPI  80 wdedlepGeYtleaelvae 98 
                                       + ++l +GeY++ ++l++e
  gi|298676194|ref|YP_003727943.1| 191 F-GNLDAGEYSVLIILRNE 208
                                       4.78999*****9999865 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0014
                                       EEEEEE-SS-EEEEEEEEE-SSS-EEEEESSS--EEEEEE-T CS
                             BsuPI   4 aleaeasgeavelaltvtNesdeavtlqFssgqkydlvvkde 45 
                                       + +++a++ +   ++tvtN+++++ t++ ss+   d+ + ++
  gi|298676194|ref|YP_003727943.1| 479 TTKTTATNTNATYTFTVTNTGNQEHTFNISSTNPSDIGILKN 520
                                       56778888899********************99999888544 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 3.9
                                       -EEEEEEEEE-SSS-E CS
                             BsuPI  13 avelaltvtNesdeav 28 
                                       +   ++t+tN+++++ 
  gi|298676194|ref|YP_003727943.1| 596 NATYNITITNTGNQKD 611
                                       5667899999998765 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.07
                                       EEE-TT-EEEEEEEE.S---SEEEEEEEEE--EE CS
                             BsuPI  66 etlepgesatyeetwdedlepGeYtleaelvaee 99 
                                       ++l+pge++  + ++ + + +G+Y+++++ v+++
  gi|298676194|ref|YP_003727943.1| 633 VNLNPGEKTFRKLNV-SAPVSGDYNVKVVGVSQN 665
                                       5799****9999999.8**********9988876 PP

  == domain 6  score: -3.0 bits;  conditional E-value: 3.4
                                       EE-SS-EEEEEEEEE-SSS- CS
                             BsuPI   8 easgeavelaltvtNesdea 27 
                                       ++ g++v+ ++ v+N+++ +
  gi|298676194|ref|YP_003727943.1| 694 ANPGNTVNYTVNVKNTGNVE 713
                                       55667888888888887644 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.028
                                       EE-TT-EEEEEEEE.S---SEEEEEEEEE--E CS
                             BsuPI  67 tlepgesatyeetwdedlepGeYtleaelvae 98 
                                       +++pg++ +++  + +++ +G+Y+++++ +++
  gi|298676194|ref|YP_003727943.1| 735 NVKPGKTESFDVAI-SNPDSGNYNANITAISK 765
                                       679***********.8*********9987765 PP

  == domain 8  score: -2.3 bits;  conditional E-value: 2.1
                                       EEEE-SS-EEEEEEEEE-SSS-EEEEES CS
                             BsuPI   6 eaeasgeavelaltvtNesdeavtlqFs 33 
                                       e+++++e+v   l ++N+++ + t + s
  gi|298676194|ref|YP_003727943.1| 797 EVTENNENVTYILNIKNTGNIKDTYEIS 824
                                       5778899999999999999877776655 PP

  == domain 9  score: -2.8 bits;  conditional E-value: 3
                                       EEE-SS-EEEEEEEEE-SSS-EE CS
                             BsuPI   7 aeasgeavelaltvtNesdeavt 29 
                                       +++  +a + +++vtN++ ++ t
  gi|298676194|ref|YP_003727943.1| 897 TTKGHNASSYTIKVTNTGVHTHT 919
                                       55566677788889998877665 PP

  == domain 10  score: -0.3 bits;  conditional E-value: 0.48
                                       E-TT-EEEEEEEE.S---SEEEEEE CS
                             BsuPI  68 lepgesatyeetwdedlepGeYtle 92 
                                       l+pges+t++ t+ ++ +  + ++e
  gi|298676194|ref|YP_003727943.1| 943 LNPGESTTVDFTF-NNTQDTDRRIE 966
                                       6777777777777.44444444444 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 ?   -0.6   0.1      0.71   1.6e+03      29      73 ..     391     435 ..     380     444 .. 0.86
   2 ?    2.6   1.9     0.067   1.5e+02      19      82 ..     483     545 ..     467     559 .. 0.81
   3 ?   10.0   0.8   0.00034      0.76      19      68 ..     591     641 ..     589     648 .. 0.95
   4 ?    6.7   0.5    0.0036         8      18      86 ..     735     805 ..     732     821 .. 0.83
   5 ?   -0.5   0.1      0.63   1.4e+03      28      73 ..     808     850 ..     798     854 .. 0.70
   6 ?    8.3   0.7    0.0012       2.7      27      81 ..     906     962 ..     897     980 .. 0.69
   7 ?   -2.2   0.2       2.3   5.1e+03      23      65 ..    1013    1055 ..    1007    1085 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.71
                                       -EEESS-SS--EEEEEEEE--XXXXXXXXXXXXXXXXXXXXXXXX CS
                               ASH  29 LtveNpseepaevkvskvpaaekgfsveetelevqpgesvtltvt 73 
                                       L+++N + ++ +++++k+  +  +   +e+++ v p+e+  ++++
  gi|298676194|ref|YP_003727943.1| 391 LKIKNIGLKKETINLTKTKVRGVNAEFNESQISVMPDETKIIKLK 435
                                       8999999999999999999999999999999*****999888765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.067
                                       ---EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               ASH  19 vkvGssaerlLtveNpseepaevkvskvpaaekgfsveetelevqpgesvtltvtwtPteegav 82 
                                       ++ +++a+ + tv+N+++++++ ++s ++ ++    ++++++++++g+s t++ + + +++g  
  gi|298676194|ref|YP_003727943.1| 483 TATNTNATYTFTVTNTGNQEHTFNISSTN-PSDIGILKNDSITLKGGQSDTVEYVVNSSSKGVY 545
                                       66788999999*********999999999.7777778999999999999999877776666655 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00034
                                       ---EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXX.XXXXXXXXX CS
                               ASH  19 vkvGssaerlLtveNpseepaevkvskvpaaekgfsveete.levqpgesv 68 
                                       v v+++a+ ++t++N+++++ + +++ +++++++ s+++++ +++ pge++
  gi|298676194|ref|YP_003727943.1| 591 VDVNKNATYNITITNTGNQKDTYDLTVISPRTNNTSLNNSKpVNLNPGEKT 641
                                       89**********************************************985 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0036
                                       ----EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXX.XXXXX CS
                               ASH  18 dvkvGssaerlLtveNpseepaevkvskvpaaekgfsveete.levqpgesvtltvtwtPteega.vrevL 86 
                                       +vk G++++  + ++Np+  + + +++ ++++   +s + +  l+v+ + +++++vt +P +e++  +e +
  gi|298676194|ref|YP_003727943.1| 735 NVKPGKTESFDVAISNPDSGNYNANITAISKSYVDISNSVNLsLNVSDKPDHSVSVTANPISEVTeNNENV 805
                                       7999**************************9999999888878*****************99964333333 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 0.63
                                       E-EEESS-SS--EEEEEEEE--XXXXXXXXXXXXXXXXXXXXXXXX CS
                               ASH  28 lLtveNpseepaevkvskvpaaekgfsveetelevqpgesvtltvt 73 
                                        L ++N+++ +   ++  ++ + +  ++  +++++ pges+++tv+
  gi|298676194|ref|YP_003727943.1| 808 ILNIKNTGNIK---DTYEISSELTDANIVDNKTTLYPGESTSITVN 850
                                       45666666632...3333444667888888899**********997 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.0012
                                       EE-EEESS-SS--EEEEEEEE--XXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXX CS
                               ASH  27 rlLtveNpseepaevkvskvpaaekgfsveete...levqpgesvtltvtwtPteega 81 
                                        +++v+N++ ++++ +++ +   + + + + +     ++ pges+t+++t+++t+ + 
  gi|298676194|ref|YP_003727943.1| 906 YTIKVTNTGVHTHTYDLKVAD-NSSNTTANLAInsiPDLNPGESTTVDFTFNNTQDTD 962
                                       457888888877444443333.4444444443334789****************9864 PP

  == domain 7  score: -2.2 bits;  conditional E-value: 2.3
                                        EEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXXXXXXXX CS
                               ASH   23 ssaerlLtveNpseepaevkvskvpaaekgfsveetelevqpg 65  
                                        ++a+ +L+++N ++++ + +++ v ++ek  + +++++++ + 
  gi|298676194|ref|YP_003727943.1| 1013 KNATYFLELKNLGNTNNSFNLEIVEGKEKYTTFKKKSVDLNAS 1055
                                        4667779999999999999999998888888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1301  (0.072564); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.97u 0.29s 00:00:01.26 Elapsed: 00:00:00.52
# Mc/sec: 9173.63
//
Query:       gi|298676195|ref|YP_003727944.1|  [L=181]
Description: hypothetical protein Metev_2336 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-24   85.7   1.5      3e-24   85.7   1.5    1.9  2  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   1.5   1.7e-28     3e-24       1      79 [.      31     106 ..      31     110 .. 0.86
   2 ?   -0.5   0.0      0.14   2.5e+03      26      42 ..     147     163 ..     128     179 .. 0.61

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 1.7e-28
                           Pilin_N   1 eAVSpViGviLmvaitvIlaAviaafvlglasneekapqasievkidssastgknavslehkgGdsidtkdlkivln 77 
                                       +AVSpViGviLmvaitvIlaAvi+++++gl + +e+apqasi+ + d+++st  + ++leh+gG+s+  +d++  l+
  gi|298676195|ref|YP_003727944.1|  31 DAVSPVIGVILMVAITVILAAVIGSYAFGL-GSPEQAPQASISGSADTENST--QIIKLEHQGGESVLFEDTATKLT 104
                                       69****************************.9**********7777777765..56***********9977665544 PP

                           Pilin_N  78 se 79 
                                        +
  gi|298676195|ref|YP_003727944.1| 105 VN 106
                                       43 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.14
                           Pilin_N  26 fvlglasneekapqasi 42 
                                       +v  l+s+ e++++++i
  gi|298676195|ref|YP_003727944.1| 147 SVSHLNSTGETTTSVKI 163
                                       34444555555565555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1101.90
//
Query:       gi|298676196|ref|YP_003727945.1|  [L=123]
Description: response regulator receiver protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-28   97.7   0.1    4.9e-28   97.5   0.1    1.0  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.5   0.1   2.7e-32   4.9e-28       1     111 [.       6     117 ..       6     118 .. 0.97

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 2.7e-32
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpvi 75 
                                       +liv+Dd+ +r+l++++l+ egy  +++a dg+eal+++k++k+ li+lDi++p+++G +ll+e r+ +  +++p+i
  gi|298676196|ref|YP_003727945.1|   6 ILIVEDDKCNRDLISDILDLEGY-YIDTAIDGEEALRKTKNKKYELIILDIKLPKLNGCDLLSEFRKCPetKNTPII 81 
                                       8**********************.*******************************************998899**** PP

                                       EEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  76 iltahseeedavealkagaddflsKpfdpeeLlkal 111
                                       +ltah+   d+++  ++g d++lsKp+d ++ +k +
  gi|298676196|ref|YP_003727945.1|  82 VLTAHAMRGDKEKFESLGCDEYLSKPIDVTKFTKVV 117
                                       *****************************9999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 741.43
//
Query:       gi|298676197|ref|YP_003727946.1|  [L=211]
Description: hypothetical protein Metev_2338 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.071   12.7   0.1       0.12   11.9   0.1    1.4  1  Ras       Ras family
        0.2   11.6   6.8       0.26   11.2   1.1    2.8  3  Imm6      Immunity protein Imm6


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.4e-05      0.12      78     148 ..     120     201 ..     107     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.4e-05
                                       EEETTBHHHHHTHH..HHHHHHHHHST........TTSEEEEEEE.TTTGGGG-SS-HHHHHHHHHHHTSEEEEEBT CS
                               Ras  78 vyditsresfenvk..kwveeikrvae........envpivLvGn.KvDleekravsteegeelakelglkfletSA 143
                                       ++d  + + f+nv+  +w+ e  + a         ++v+ +L    K+D ++++++++e   ++  ++++k++etSA
  gi|298676197|ref|YP_003727946.1| 120 LFDFMKDSGFKNVNnlRWFPEYDEAALdllnknnkNTVETALSKLwKIDWTKNKKITEEMILKYGINIDTKYIETSA 196
                                       57888888899988677888877766556666665667777765459****************************** PP

                                       TTTCT CS
                               Ras 144 ktnen 148
                                         + +
  gi|298676197|ref|YP_003727946.1| 197 CPAAE 201
                                       87665 PP

>> Imm6  Immunity protein Imm6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.023     2e+02      92     108 ..      50      66 ..      44      75 .. 0.82
   2 ?   -0.0   0.0     0.088   7.9e+02      25      54 ..      99     126 ..      75     136 .. 0.65
   3 ?   11.2   1.1   2.9e-05      0.26      11      69 ..     143     201 ..     141     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.023
                              Imm6  92 kkekekylPetlesidd 108
                                       kke+ +y+P +l+ i +
  gi|298676197|ref|YP_003727946.1|  50 KKEYTYYYPGILDLILN 66 
                                       79***********9865 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.088
                              Imm6  25 evveeaLdvckkwlegenvtadeLydlldn 54 
                                       e + + Ld  k++le  +++ d+L+d++  
  gi|298676197|ref|YP_003727946.1|  99 EYIPKGLDLNKNYLE--QLKEDALFDFMKD 126
                                       555666666666665..4556666666654 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 2.9e-05
                              Imm6  11 ekllslikkkddevevveeaLdvckk..wlegenvtadeLydlldnedeedilefaeqeed 69 
                                       e++l l++k+++  + ve aL++ +k  w++++++t + + ++  n d + i + a+ +++
  gi|298676197|ref|YP_003727946.1| 143 EAALDLLNKNNK--NTVETALSKLWKidWTKNKKITEEMILKYGINIDTKYIETSACPAAE 201
                                       667888888887..9**********777***************999999999887776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1203.36
//
Query:       gi|298676198|ref|YP_003727947.1|  [L=171]
Description: hypothetical protein Metev_2339 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.016   15.3   0.3      0.034   14.2   0.3    1.5  1  RAMP4      Ribosome associated membrane protein RAMP4
      0.018   15.0   1.1      0.025   14.5   0.5    1.6  2  GatB_Yqey  GatB domain


Domain annotation for each model (and alignments):
>> RAMP4  Ribosome associated membrane protein RAMP4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   3.8e-06     0.034       3      43 ..      63     106 ..      62     107 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-06
                             RAMP4   3 kremrrknekfakni.tkrGkvpkslk..kkekkspvgpwlLgl 43 
                                       k +++++n  + +   t+rG+v+   k  k+++k+++g+++L++
  gi|298676198|ref|YP_003727947.1|  63 KERQTVQNGEYVNYMdTNRGHVKVIHKriKEKTKKSIGTIMLAI 106
                                       7899999****************99999**************86 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.58   5.2e+03     107     126 ..      10      29 ..       7      31 .. 0.77
   2 ?   14.5   0.5   2.8e-06     0.025      34     105 ..      90     157 ..      52     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.58
                                       HHHHHHTTXXTTSTHHHHHH CS
                         GatB_Yqey 107 kavedyksgkekalkflvGq 126
                                       k v d  ++  k + f+ Gq
  gi|298676198|ref|YP_003727947.1|  10 KNVTDATRKLSKEFTFFTGQ 29 
                                       66778888888889999998 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.8e-06
                                       XTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXHHHHHHHCTXXXXXXSSXHHHHHHHHHHTX CS
                         GatB_Yqey  34 eieelkltpeqlaellkliaegkIskkiakevleelleegkspeeiieekgLkqisdeeeleklveeviaen 105
                                        i+e   t++++  ++  i+ g Is+k  +e+++ ++++     ++ ee      +deee+e++v +v++++
  gi|298676198|ref|YP_003727947.1|  90 RIKE--KTKKSIGTIMLAIKMGLISEKDMEEIVANIMDNFDYYYQMTEEAI--FYTDEEEIENFVLNVLKNE 157
                                       4444..577899999999********************9999999999984..57899***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1015  (0.0566122); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1011.27
//
Query:       gi|298676199|ref|YP_003727948.1|  [L=117]
Description: hypothetical protein Metev_2340 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00075   18.6   0.9    0.00086   18.4   0.9    1.1  1  SNF2_assoc  Bacterial SNF2 helicase associated
  ------ inclusion threshold ------
       0.02   14.7   0.7      0.024   14.5   0.7    1.1  1  GatB_Yqey   GatB domain
      0.057   14.0   0.3       0.11   13.2   0.1    1.6  2  FRP         Photoprotection regulator fluorescence recovery p


Domain annotation for each model (and alignments):
>> SNF2_assoc  Bacterial SNF2 helicase associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.9   1.4e-07   0.00086     252     306 ..      44      99 ..      23     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-07
                        SNF2_assoc 252 sieeegnlLelsfdidgideeElaeilka.yrekkkYyrLkdGsfldLeeeelkel 306
                                       +++++ + L l ++++ i+ee+l++i++  +re   Yy+L  +++ +L+e+e+++l
  gi|298676199|ref|YP_003727948.1|  44 KTKKSIGTLALVIKMGLINEEDLKDIISDtLREFDYYYKLTENAVFKLDEDEVEAL 99 
                                       567778999******************864899999***************99987 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.7   4.1e-06     0.024      38     111 ..      42     113 ..       4     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-06
                                       SSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXHHHHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHH CS
                         GatB_Yqey  38 lkltpeqlaellkliaegkIskkiakevleelleegkspeeiieekgLkqisdeeeleklveeviaenpkaved 111
                                       ++ t++++  l   i+ g I+++  k+++   l e     ++ e    +++ de+e+e+lv  +i+ n+++++ 
  gi|298676199|ref|YP_003727948.1|  42 NSKTKKSIGTLALVIKMGLINEEDLKDIISDTLREFDYYYKLTENA-VFKL-DEDEVEALVMSIISGNEEKIDS 113
                                       3567889999999********************8877777776655.5666.568*************999875 PP

>> FRP  Photoprotection regulator fluorescence recovery protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.8e-05      0.11      50      93 ..      32      75 ..       5      79 .. 0.81
   2 ?   -2.2   0.0       1.1   6.4e+03      15      28 ..      90     103 ..      82     114 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                               FRP 50 akRydidgkydfreskllfvlarlvkeklleleeLeGLeaekla 93
                                       + ++i+ + +++++k + +la ++k +l+++e+L+ + +++l+
  gi|298676199|ref|YP_003727948.1| 32 GHIWTIEKRINSKTKKSIGTLALVIKMGLINEEDLKDIISDTLR 75
                                      4457899*****************************99888876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                               FRP  15 kayereiealiaev 28 
                                       k  e e+eal+ ++
  gi|298676199|ref|YP_003727948.1|  90 KLDEDEVEALVMSI 103
                                       44556677776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 723.28
//
Query:       gi|298676200|ref|YP_003727949.1|  [L=68]
Description: hypothetical protein Metev_2341 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 446.43
//
Query:       gi|298676201|ref|YP_003727950.1|  [L=94]
Description: hypothetical protein Metev_2343 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 589.24
//
Query:       gi|298676202|ref|YP_003727951.1|  [L=361]
Description: hypothetical protein Metev_2344 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-13   49.5  51.1    8.1e-06   26.0  19.6    3.1  2  EamA          EamA-like transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8  23.5   5.4e-10   9.7e-06       2     135 ..      18     177 ..      17     179 .. 0.73
   2 !   26.0  19.6   4.5e-10   8.1e-06       2     137 .]     195     338 ..     194     338 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 5.4e-10
                              EamA   2 lgillallaalfwaiyfvlskil.....lrkv..................spltltfvrfliagilllii..allke 53 
                                       +g+++al+ a+fw+++++   i+     +                        +++++  l+a + l+i+  +ll+ 
  gi|298676202|ref|YP_003727951.1|  18 SGYMWALICAVFWGLWYIPGEIIwninpF--NemlsevshmmsssgsmvvVAAEVSALNALFAVLSLIIWngCLLRL 92 
                                       79******************998554442..0334444544444432221111333355555555555556644444 PP

                              EamA  54 gkl....aklslkd..wllllllgllgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllg 124
                                       + l    +++   +   ++ll  ++lg+ +a +  f+a+  +++++a+++++l Pv+  + ++l++gek+t +  +g
  gi|298676202|ref|YP_003727951.1|  93 NELgrtiKNF---NlcSKWLLAGSVLGGPVAIFGSFMAMAFIGSAFAAVASLLYPVVGSVAAFLWYGEKITRRASIG 166
                                       4445333333...3556999********************************************************* PP

                              EamA 125 ivlillGvlli 135
                                       i++i++G + i
  gi|298676202|ref|YP_003727951.1| 167 IFIIIVGSISI 177
                                       *******9876 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 4.5e-10
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagill.liiallkegkl........aklslkdwlllll 69 
                                       lg+l  l aa  w++ + ++ i+l++ ++ t ++ rf++  ++  lii++++++          a++ + ++  l++
  gi|298676202|ref|YP_003727951.1| 195 LGYLGGLMAASGWGLEGAIAGIGLEFSESDTGLTARFIFELLFWwLIIIPIFAIAGfpmyeyatAVFQPVPLMVLAF 271
                                       79999**********************99999999999777777655555555555556888889999999999999 PP

                              EamA  70 lgllgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllill 137
                                       +g l++ ++++ +++++  +++++   + +l  ++++il  l+ g +++++ ++g +l+++G++++++
  gi|298676202|ref|YP_003727951.1| 272 TG-LASGFCYVTWYKSFPLIGVGRGQGVANLYGLISIILLLLFVGSTPGWTVFIGGLLCVAGAVVMFT 338
                                       99.5777777******************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2132.35
//
Query:       gi|298676203|ref|YP_003727952.1|  [L=59]
Description: hypothetical protein Metev_2345 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 390.76
//
Query:       gi|298676204|ref|YP_003727953.1|  [L=49]
Description: hypothetical protein Metev_2346 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.084   12.6   2.4        0.1   12.4   2.4    1.0  1  Rer1      Rer1 family


Domain annotation for each model (and alignments):
>> Rer1  Rer1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.4   5.6e-06       0.1     121     152 ..      13      44 ..       9      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.6e-06
                              Rer1 121 ltffevfdvpVfwpiLlvyfivlfvltmrrqi 152
                                       + f+++f + ++ p Ll +f+v+ +  mr+++
  gi|298676204|ref|YP_003727953.1|  13 TLFISIFLIAIYAPSLLGFFVVMSIYIMRHRF 44 
                                       56899***********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.29u 0.24s 00:00:00.53 Elapsed: 00:00:00.38
# Mc/sec: 382.17
//
Query:       gi|298676205|ref|YP_003727954.1|  [L=168]
Description: integrase catalytic subunit [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-21   76.7   0.1      2e-21   76.3   0.1    1.2  1  DDE_3     DDE superfamily endonuclease
    9.7e-05   22.1   0.1    0.00012   21.8   0.1    1.3  1  DDE_1     DDE superfamily endonuclease
    0.00031   20.9   0.0    0.00046   20.4   0.0    1.2  1  rve       Integrase core domain


Domain annotation for each model (and alignments):
>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.1   3.4e-25     2e-21       5     144 ..       1     133 [.       1     135 [. 0.87

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 3.4e-25
                             DDE_3   5 iDEsgfqlgtvrrrawakkGkrerleeygrrgrvnligaldekgglafvtfeetlnaedfaeflerlletalqakki 81 
                                       +DEs  q++++ +r w+       +++++   + n++++++ +g   ++ f+++ +++d+ efle++ +      +i
  gi|298676205|ref|YP_003727954.1|   1 MDESSPQTRANTQRLWSFDKPV--IYKNTDYIKANAFAFYSING-NNLIEFKDSSKSDDVCEFLEEISRINHGR-PI 73 
                                       6****************97555..66666667888999999988.4567789999*****************98.** PP

                             DDE_3  82 vlilDnasiHkseslrelveeeadrlellylPpySPelNpiEivwsklkrellkrrsfkslde 144
                                       vli+Dna+ H++ + + ++++   ++ l++lPpySP+lNp+E +w+++kre+   r+++s++ 
  gi|298676205|ref|YP_003727954.1|  74 VLIMDNARAHHALKTTMKAKQ--LGIILVFLPPYSPDLNPVEFIWKSIKREISV-RFVQSKQH 133
                                       **********98666666555..*****************************99.88888765 PP

>> DDE_1  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   1.9e-08   0.00012      72     163 ..      68     155 ..      24     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.9e-08
                             DDE_1  72 aekrkilLlldssrshetvel.leselqniklvflPassasllqPldqgvvselKarYrrqllqalleeqnrlskeq 147
                                       + +r i+L++d++r+h++++  ++ ++  i lvflP+ s + l P++  +++ +K++    ++q  ++ ++ ++   
  gi|298676205|ref|YP_003727954.1|  68 NHGRPIVLIMDNARAHHALKTtMKAKQLGIILVFLPPYSPD-LNPVEF-IWKSIKREISVRFVQSKQHMRSIIKT-- 140
                                       57899************888879999999*******88876.689985.9*********9999999998888887.. PP

                             DDE_1 148 kkltlldalkfikkAw 163
                                         + + + l f +kAw
  gi|298676205|ref|YP_003727954.1| 141 VFMKIGNSLSF-AKAW 155
                                       44444555444.3344 PP

>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   7.7e-08   0.00046      44     118 ..      50     122 ..      43     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 7.7e-08
                               rve  44 demdastvlalleravarfggvepervlsDngseytskafrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                       d++++++v+++le+  +  +g+ p ++++Dn+++  + +++  +++lgi + f +p++p+ n  vE +++ +k+e
  gi|298676205|ref|YP_003727954.1|  50 DSSKSDDVCEFLEEISRINHGR-PIVLIMDNARAHHALKTTMKAKQLGIILVFLPPYSPDLNP-VEFIWKSIKRE 122
                                       455899*******999999999.**********99999**********************997.67777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1071.21
//
Query:       gi|298676206|ref|YP_003727955.1|  [L=170]
Description: ISA1083-3 transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-11   42.9   0.1    1.1e-10   42.0   0.1    1.5  1  HTH_32         Homeodomain-like domain
    3.8e-08   32.9   0.2    1.2e-07   31.3   0.0    1.9  2  HTH_23         Homeodomain-like domain
    1.7e-07   30.7   0.3    1.4e-06   27.8   0.1    2.4  2  HTH_33         Winged helix-turn helix
    7.7e-07   29.1   0.0    1.7e-06   28.0   0.0    1.6  1  HTH_28         Helix-turn-helix domain
    7.4e-06   25.9   0.0    1.6e-05   24.9   0.0    1.4  1  HTH_29         Winged helix-turn helix
     0.0021   17.9   0.3      0.006   16.4   0.1    1.8  2  DUF559         Protein of unknown function (DUF559)
     0.0025   17.8   0.4     0.0043   17.1   0.2    1.5  1  HTH_Tnp_IS630  Transposase
  ------ inclusion threshold ------
       0.03   15.1   0.3      0.057   14.2   0.2    1.5  1  Tau95          RNA polymerase III transcription factor (TF)II
       0.15   12.7   0.0       0.23   12.0   0.0    1.4  1  LZ_Tnp_IS481   leucine-zipper of insertion element IS481
       0.42   10.7   4.4       0.43   10.7   0.3    2.7  3  U3_assoc_6     U3 small nucleolar RNA-associated protein 6


Domain annotation for each model (and alignments):
>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.1   5.9e-14   1.1e-10       1      72 [.      61     132 ..      61     133 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 5.9e-14
                            HTH_32   1 TvsrwlkRyneeGlegLkdrprrgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyri 72 
                                       T + w  R+n++G+e+L +  ++gr +kl++++ ++++++l+e++ W++ ++++ + +++gv++S  +++ i
  gi|298676206|ref|YP_003727955.1|  61 TGYYWQDRWNKGGYEALVPMVSKGREHKLTQQQFDELKDILKERSLWTTNEVRQLVIQKYGVEYSLKQIRII 132
                                       889*****************9********************8889*********999999********9966 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   6.9e-11   1.2e-07       9      49 ..      31      77 ..      24      78 .. 0.79
   2 ?   -1.5   0.0       1.4   2.5e+03       5      23 ..     111     129 ..     107     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 6.9e-11
                            HTH_23  9 rilllla..e....GlsvreIAreLgvsrrTvyrwlkryreeGlegl 49
                                      r+l+ l   +    G+sv+e+A++ g++++T y w  r++++G e+l
  gi|298676206|ref|YP_003727955.1| 31 RMLRRLYfcKfrylGDSVSEAADKVGITKMTGYYWQDRWNKGGYEAL 77
                                      44444444423355*****************************9998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                            HTH_23   5 reRlrillllaeGlsvreI 23 
                                       + R+++++ + + +s ++I
  gi|298676206|ref|YP_003727955.1| 111 EVRQLVIQKYGVEYSLKQI 129
                                       6789999988777777776 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.43   7.7e+02       6      21 ..      16      31 ..      14      35 .. 0.85
   2 !   27.8   0.1   7.8e-10   1.4e-06       2      41 ..     104     143 ..     103     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.43
                            HTH_33  6 tlarlaqlieerfgvs 21
                                      tl++l +li+++++ +
  gi|298676206|ref|YP_003727955.1| 16 TLDQLNTLIKTETNAR 31
                                      9999******998865 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 7.8e-10
                            HTH_33   2 fgrWtlarlaqlieerfgvsysvsgvyrlLkrlGfsyqkP 41 
                                         +Wt+ +++ql+ +++gv+ys ++++ ++   G+   kP
  gi|298676206|ref|YP_003727955.1| 104 RSLWTTNEVRQLVIQKYGVEYSLKQIRIIMIQFGMKHSKP 143
                                       579************************9999999988887 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   9.5e-10   1.7e-06      12      49 ..      45      84 ..      34      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 9.5e-10
                            HTH_28 12 GhsvreaArelgisrrtvyrWikryeegGiagLvp..rrr 49
                                      G+sv+eaA ++gi+  t y W  r+++gG ++Lvp   ++
  gi|298676206|ref|YP_003727955.1| 45 GDSVSEAADKVGITKMTGYYWQDRWNKGGYEALVPmvSKG 84
                                      78********************************964444 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   8.7e-09   1.6e-05      11      61 ..      45      93 ..      43      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 8.7e-09
                            HTH_29 11 GvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprnrlseeq 61
                                      G s vs++A  +g+++ t y w++r+++gG +al +  ++gr  ++l+++q
  gi|298676206|ref|YP_003727955.1| 45 GDS-VSEAADKVGITKMTGYYWQDRWNKGGYEALVPMVSKGRE-HKLTQQQ 93
                                      666.********************************8888987.4799887 PP

>> DUF559  Protein of unknown function (DUF559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.2   2.2e+03      75      94 ..      30      49 ..      10      57 .. 0.64
   2 !   16.4   0.1   3.4e-06     0.006      20      75 ..      96     151 ..      81     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                                      HHHHHHTT-EEEEEEHHHHH CS
                            DUF559 75 telLeslGftvlRfkndevl 94
                                      +++L +l f  +R+  d v 
  gi|298676206|ref|YP_003727955.1| 30 ARMLRRLYFCKFRYLGDSVS 49
                                      34455555555555555555 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.4e-06
                                       HHHHHHGGGTTTT--EEEEEEETTEEEEEEETTTTEEEEEE-----------HHHH CS
                            DUF559  20 kLWqllrnrrlsglkfrRqkpigsYivDfvclkaklivelDGaqhdeeeeyDaeRt 75 
                                       +L   l++r l      Rq +i++Y v++  ++ ++i+   G +h++  +yD ++ 
  gi|298676206|ref|YP_003727955.1|  96 ELKDILKERSLWTTNEVRQLVIQKYGVEYSLKQIRIIMIQFGMKHSKPYTYDYRKP 151
                                       57778999999999999***********************************8875 PP

>> HTH_Tnp_IS630  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   2.4e-06    0.0043      13      97 ..      40     132 ..      29     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.4e-06
                     HTH_Tnp_IS630  13 dyiesGggitkaskvfkvgratvyrWlkreela......atkvetrkrkidrkelke..dvkknpdallkerakkfg 81 
                                       ++   G+++ +a    ++++ t y W +r + +      ++  + r++k+ +++++e  d+ k+      + ++++ 
  gi|298676206|ref|YP_003727955.1|  40 KFRYLGDSVSEAADKVGITKMTGYYWQDRWNKGgyealvPMVSKGREHKLTQQQFDElkDILKERSLWTTNEVRQLV 116
                                       556679*********************997766111111556799*****999887444999999999999****** PP

                     HTH_Tnp_IS630  82 vtpasllyalkklkit 97 
                                       ++   + y lk+++i 
  gi|298676206|ref|YP_003727955.1| 117 IQKYGVEYSLKQIRII 132
                                       ************9985 PP

>> Tau95  RNA polymerase III transcription factor (TF)IIIC subunit HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   3.2e-05     0.057      55     100 ..      81     128 ..      46     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.2e-05
                                       ----...HHHHHHHHHHHHHHHH-SEEEHHHHHTTS-GGGT..TTHHH CS
                             Tau95  55 vkelkekkelqkaveelkklfeerPiwtrraLknklekker..kklkl 100
                                       v++  e+k  q++++elk++++er +wt++++++ + +k    ++lk+
  gi|298676206|ref|YP_003727955.1|  81 VSKGREHKLTQQQFDELKDILKERSLWTTNEVRQLVIQKYGveYSLKQ 128
                                       4555667999*********************99988866655655554 PP

>> LZ_Tnp_IS481  leucine-zipper of insertion element IS481
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.23      27      65 ..      47      85 ..      29     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                      LZ_Tnp_IS481 27 tvaqvarelGvslrtaykwlarfraeGldGlldrssrPr 65
                                      +v ++a ++G+++ t+y w +r+   G + l+   s+ r
  gi|298676206|ref|YP_003727955.1| 47 SVSEAADKVGITKMTGYYWQDRWNKGGYEALVPMVSKGR 85
                                      57899************************9998887665 PP

>> U3_assoc_6  U3 small nucleolar RNA-associated protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.33     6e+02      40      69 ..      14      43 ..       1      59 [. 0.68
   2 ?   10.7   0.3   0.00024      0.43       6      38 ..      95     128 ..      91     136 .. 0.86
   3 ?   -1.0   0.0       1.1   1.9e+03      22      37 ..     154     169 ..     150     170 .] 0.81

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.33
                        U3_assoc_6 40 gkkkedflkYieyElnLeklrkkRrkrlkl 69
                                      + ++++  + i+ E+n   lr+ +  + ++
  gi|298676206|ref|YP_003727955.1| 14 HVTLDQLNTLIKTETNARMLRRLYFCKFRY 43
                                      455666777899999999999988877776 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00024
                        U3_assoc_6   6 peled.leekglFtkeEikeIvkkrrkfEyklqr 38 
                                       +el+d l+e+ l t +E++++v +    Ey+l++
  gi|298676206|ref|YP_003727955.1|  95 DELKDiLKERSLWTTNEVRQLVIQKYGVEYSLKQ 128
                                       566664799**********************985 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.1
                        U3_assoc_6  22 ikeIvkkrrkfEyklq 37 
                                         eI+kk r + y+l+
  gi|298676206|ref|YP_003727955.1| 154 ADEILKKPRRHTYSLK 169
                                       5789999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.38s 00:00:00.86 Elapsed: 00:00:00.88
# Mc/sec: 583.42
//
Query:       gi|298676207|ref|YP_003727956.1|  [L=410]
Description: putative PAS/PAC sensor protein [Methanohalobium evestigatum Z-7303]
Scores for complete 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-40  138.5   1.6    2.9e-40  137.8   1.6    1.4  1  MetOD1         Metanogen output domain 1
    3.9e-23   81.7   1.4    4.2e-11   43.0   0.1    2.8  3  PAS_9          PAS domain
    9.5e-17   60.6   0.2    9.4e-09   35.1   0.0    2.5  2  PAS_8          PAS domain
    5.9e-16   58.7   0.0    1.7e-07   31.5   0.0    2.2  2  PAS_4          PAS fold
    3.9e-13   49.4   0.1    1.2e-05   25.3   0.0    2.7  2  PAS            PAS fold
    4.8e-07   30.0   0.0     0.0082   16.4   0.0    2.5  2  PAS_3          PAS fold
     0.0034   17.3   0.1      0.011   15.6   0.1    2.0  2  DUF3877        Domain of unknown function, E. rectale Gene de
  ------ inclusion threshold ------
       0.21   12.4   1.3       0.73   10.6   1.3    1.9  1  ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrola


Domain annotation for each model (and alignments):
>> MetOD1  Metanogen output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.8   1.6   1.3e-43   2.9e-40       1     153 [.     257     409 ..     257     410 .] 0.95

  Alignments for each domain:
  == domain 1  score: 137.8 bits;  conditional E-value: 1.3e-43
                            MetOD1   1 elkkkkvkaelrsfllsaiPtlaskippeekkilikqfadrveknlkpkfkeelkeaekeeedaekvlkayiewlnq 77 
                                       e ++++ ++++rs+l+ ++Ptl+++ p+e++ +++kq+ d++ek + +    ++ ++e ++ ++++v+ + +e++nq
  gi|298676207|ref|YP_003727956.1| 257 EHDQLEKQNQIRSILTGILPTLLKESPKEKRRVILKQMLDMIEKCMFHGECLNMTQFEYNNINTSNVGYMSCEVINQ 333
                                       678999**************************************77666555999********************** PP

                            MetOD1  78 lfanfgiktekkedeknvlleftnCpWge.earknPifCllcraivsrsftwtglkgsveqkktlgngdekCvFeik 153
                                       l+++f ++t  ++++ ++++++t CpWg  +a++nPi+C+l+ +i+ r+++ ++ + +v+++kt+gngde+C+F i+
  gi|298676207|ref|YP_003727956.1| 334 LGGDFSVDTS-NQNDVQFAIKGTGCPWGIeQAKMNPILCNLTNGIIARTVSNVYKNPNVKTMKTMGNGDECCYFLIH 409
                                       **********.58888999********988********************************************998 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   1.5e-12   3.4e-09       4     104 .]      26     123 ..      23     123 .. 0.93
   2 !   43.0   0.1   1.9e-14   4.2e-11       2     103 ..     143     245 ..     142     245 .. 0.82
   3 ?   -2.7   0.0       3.3   7.4e+03      42      60 ..     283     309 ..     256     331 .. 0.61

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.5e-12
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwvl 79 
                                        ++ +  g+ l++N++a++ lGy ++e+l    + +   +pe +e+++++++q+++ k+ ++e v+i+k+ge+++v+
  gi|298676207|ref|YP_003727956.1|  26 AFVHDLAGNFLDINNTAIQRLGYPKDELLSMGPHSID--APEYAEKVNNIIKQISEeKQLTFESVHITKSGERIPVE 100
                                       556558899*********************9999999..************************************** PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDite 104
                                       ++   ++ +++  ++  +i rDite
  gi|298676207|ref|YP_003727956.1| 101 ISSNIIQYKEQPAIL--SIARDITE 123
                                       ******999988888..*******8 PP

  == domain 2  score: 43.0 bits;  conditional E-value: 1.9e-14
                             PAS_9   2 dgili....dnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirknge 74 
                                       d+i+i     +  g+i++aN++a+++ Gys +e+l+ +itdl  t + a+e+  ++ +  + +   +e+ + +kng+
  gi|298676207|ref|YP_003727956.1| 143 DAIFIlegeGDGTGNIVDANQKAADIHGYSLDEILNMHITDLG-TQSVADEFPLRLKRVFEGEWIKDELNHLDKNGN 218
                                       56666343323445*****************************.55555555555555555578************* PP

                             PAS_9  75 tfwvlltaspvkdddgelvgiivilrDit 103
                                        +w +++a  v  d+ ++++  +i rDit
  gi|298676207|ref|YP_003727956.1| 219 VIWMEVNAGQVELDGHKYIF--AIERDIT 245
                                       ************99999999..******9 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.3
                             PAS_9  42 tdpeanerlraaleqgrk........k 60 
                                       ++++++  l+++l++++k        +
  gi|298676207|ref|YP_003727956.1| 283 PKEKRRVILKQMLDMIEKcmfhgeclN 309
                                       445555556666666665555544442 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   2.3e-08   5.3e-05       4      42 ..      16      55 ..      13      74 .. 0.86
   2 !   35.1   0.0   4.2e-12   9.4e-09       2      52 ..     133     188 ..     132     206 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.3e-08
                             PAS_8  4 ralfesspdgiavvd.lgdrivdvNqaalellGys.adlkg 42
                                        lf++++d+ +v d +g+ ++d+N++a++ lGy+ ++l+ 
  gi|298676207|ref|YP_003727956.1| 16 FYLFNNMNDAAFVHDlAGN-FLDINNTAIQRLGYPkDELLS 55
                                      679**********9*7777.***************777765 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 4.2e-12
                             PAS_8   2 rlralfesspdgiavvd.lgd...rivdvNqaalellGys.adlkgellgqllpvl 52 
                                       r+r lfe ++d+i+++  +gd   +ivd+Nq+a+++ Gys ++++ + + +l++++
  gi|298676207|ref|YP_003727956.1| 133 RYRLLFEKADDAIFILEgEGDgtgNIVDANQKAADIHGYSlDEILNMHITDLGTQS 188
                                       9**************9874445788***************9999987775544444 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   5.9e-09   1.3e-05       1     110 []      19     126 ..      19     126 .. 0.88
   2 !   31.5   0.0   7.6e-11   1.7e-07       1     108 [.     138     247 ..     138     249 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 5.9e-09
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pg 76 
                                       +++++da +v d  g++l++N++a + +g+p +ell + ++++  +e a+ + +++++  e+ + ++f+ ++ + +g
  gi|298676207|ref|YP_003727956.1|  19 FNNMNDAAFVHDLAGNFLDINNTAIQRLGYPKDELLSMGPHSIDAPEYAEKVNNIIKQISEE-KQLTFESVHITkSG 94 
                                       7899*******************9999**************988888999999999998887.566666666667** PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       e+ ++e++ + +     e  ++l i+rDiTer+r
  gi|298676207|ref|YP_003727956.1|  95 ERIPVEISSNIIQY--KEQPAILSIARDITERKR 126
                                       *********88844..4567************97 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 7.6e-11
                             PAS_4   1 ldslpdalavl....dpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleell 73 
                                       +++  da+++l    d  g++++aN+ aa++ g++ +e+l+++  +l ++++a+++   l+rv ege  i+++  +l
  gi|298676207|ref|YP_003727956.1| 138 FEKADDAIFILegegDGTGNIVDANQKAADIHGYSLDEILNMHITDLGTQSVADEFPLRLKRVFEGE-WIKDELNHL 213
                                       6788999****9999***************************************************7.555555555 PP

                             PAS_4  74 l.pgeerhyelrllPlrdesGevigvlvisrDiTer 108
                                       + +g   ++e+++  + + +G    +++i rDiT r
  gi|298676207|ref|YP_003727956.1| 214 DkNGNVIWMEVNAGQV-ELDGH-KYIFAIERDITWR 247
                                       56***********999.68999.9999999999966 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   8.6e-08   0.00019       6     113 .]      18     121 ..      13     121 .. 0.90
   2 !   25.3   0.0   5.3e-09   1.2e-05       2     113 .]     133     244 ..     132     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 8.6e-08
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECT CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklr 82 
                                       +++++ d+ fv D  g++l +N +a + lG++ +e+l+     +i  ++ ae +  + +++++ ++ + + + +++ 
  gi|298676207|ref|YP_003727956.1|  18 LFNNMNDAAFVHDLAGNFLDINNTAIQRLGYPKDELLSMGPH-SIDAPEYAEKVNNIIKQISEEKQLTFESVHITK- 92 
                                       689*********************************998777.999998899999999999999999999999999. PP

                                       TSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  83 dgrpihlevraspvrdaggeilgflgvlrdi 113
                                        g+ i++e+  + +  +++    +l ++rdi
  gi|298676207|ref|YP_003727956.1|  93 SGERIPVEISSNIIQYKEQP--AILSIARDI 121
                                       **********9999999887..888888887 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 5.3e-09
                                       HHHHHHHHSSSEEEEE....ETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECC CS
                               PAS   2 dlraileslpdpifvv....DedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesra 74 
                                       ++r ++e ++d+if++    D  g+i+ +N++a+++ G+s +e+l+ ++ dl        +a+++   l+ ++ +++
  gi|298676207|ref|YP_003727956.1| 133 RYRLLFEKADDAIFILegegDGTGNIVDANQKAADIHGYSLDEILNMHITDLGTQS----VADEFP--LRLKRVFEG 203
                                       899*************55555999****************************9876....777775..555678888 PP

                                       CCEEEEC....TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  75 geisfkl....rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       ++i+ +l    ++g +i++ev+a  v   g++  +++ + rdi
  gi|298676207|ref|YP_003727956.1| 204 EWIKDELnhldKNGNVIWMEVNAGQVELDGHK--YIFAIERDI 244
                                       888888888999***********999888876..777776665 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.7e-06    0.0082       3      79 ..      37     110 ..      35     118 .. 0.88
   2 !   11.1   0.0   0.00016      0.37       2      72 ..     159     226 ..     158     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.7e-06
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirden 79 
                                        ++++  + lGy ++ell+      ++  pe  e+v++ ++++ ++++ +++e   ++k+Ge + ve + ++i++++
  gi|298676207|ref|YP_003727956.1|  37 DINNTAIQRLGYPKDELLSM--GPHSIDAPEYAEKVNNIIKQISEEKQ-LTFESVHITKSGERIPVEISSNIIQYKE 110
                                       6778888899**********..9*******************998888.8999999*****************5544 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00016
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveara 72 
                                       + ++++  +i Gys +e+l+   ++ dl      +++   l++++ +ge ++ e   + k+G ++w+e  a
  gi|298676207|ref|YP_003727956.1| 159 VDANQKAADIHGYSLDEILNM--HITDLGTQSVADEFPLRLKRVF-EGEWIKDELNHLDKNGNVIWMEVNA 226
                                       7899*****************..8888888888888888888888.56658****************9876 PP

>> DUF3877  Domain of unknown function, E. rectale Gene description (DUF3877)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   4.8e-06     0.011      27     152 ..      45     172 ..      14     182 .. 0.73
   2 ?   -2.3   0.0       1.5   3.4e+03      66     103 ..     338     376 ..     319     387 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.8e-06
                           DUF3877  27 rlyyPlssLn....hlleaeedaeelkealeefaeeakeklGevevtekkdrfcveipeegaeyvheeikeneFlke 99 
                                       rl yP + L     h ++a e ae++++ +++++ee++ ++ +v++t++++r+ vei+ +  +y ++  ++   +++
  gi|298676207|ref|YP_003727956.1|  45 RLGYPKDELLsmgpHSIDAPEYAEKVNNIIKQISEEKQLTFESVHITKSGERIPVEISSNIIQYKEQ--PAILSIAR 119
                                       677887777611124456666899***********************************99999433..22233333 PP

                           DUF3877 100 liellkkhectledilelFkkyskkvvvekieedefdyliyFedeeedeyyYc 152
                                        i+  k+ e + ++ + lF+k ++ + + + e d  + ++  ++++ d + Y 
  gi|298676207|ref|YP_003727956.1| 120 DITERKRAELNEKRYRLLFEKADDAIFILEGEGDGTGNIVDANQKAADIHGYS 172
                                       34444444555555666777777777777777777666666666666666665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
                           DUF3877  66 vevt.ekkdrfcveipeegaeyvheeikeneFlkeliel 103
                                        +v  ++++ +++ i  +g+ +  e++k n+ l +l + 
  gi|298676207|ref|YP_003727956.1| 338 FSVDtSNQNDVQFAIKGTGCPWGIEQAKMNPILCNLTNG 376
                                       454315667799999999999999999999999888765 PP

>> ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.3   0.00033      0.73      26     143 ..     288     406 ..     268     408 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00033
                     ATC_hydrolase  26 keiirkal...erlg....kergkklaekakakkdkadvekflalyseifek.enalkfevleedkdeleidvtrCp 94 
                                       + i++++l   e++     + +++++  +++    +++  ++++   e+ ++ ++++ +++  +++ ++ i+ t Cp
  gi|298676207|ref|YP_003727956.1| 288 RVILKQMLdmiEKCMfhgeCLNMTQFEYNNI----NTSNVGYMS--CEVINQlGGDFSVDTSNQNDVQFAIKGTGCP 358
                                       4444443322222222002333333333333....333334444..3555557999********************* PP

                     ATC_hydrolase  95 yceawkkeGlpelgkllCeiDkavaeginpk....vklertktlaeGgdcCdf 143
                                       +          +  ++lC++ + ++    ++     + +  kt++ G++cC f
  gi|298676207|ref|YP_003727956.1| 359 WGIEQA-----KMNPILCNLTNGIIARTVSNvyknPNVKTMKTMGNGDECCYF 406
                                       *64333.....344777766555555544443444456779**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2366.42
//
Query:       gi|298676208|ref|YP_003727957.1|  [L=78]
Description: hypothetical protein Metev_2350 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 525.47
//
Query:       gi|298676209|ref|YP_003727958.1|  [L=1962]
Description: periplasmic copper-binding protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.3e-48  158.3 187.2    0.00053   20.2   2.5   25.7 26  Glug         The GLUG motif
    1.5e-31  109.6  94.6      2e-24   86.2  34.8    6.2  6  NosD         Periplasmic copper-binding protein (NosD)
  ------ inclusion threshold ------
      0.014   15.4   2.6       0.04   13.9   2.6    1.8  1  Trypan_PARP  Procyclic acidic repetitive protein (PARP)


Domain annotation for each model (and alignments):
>> Glug  The GLUG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2      0.22   1.3e+03      18      28 .]     103     114 ..     101     114 .. 0.89
   2 ?    0.7   2.7      0.15     9e+02      13      28 .]     148     167 ..     145     176 .. 0.75
   3 ?   -3.0   0.5       2.2   1.3e+04      17      25 ..     336     344 ..     332     346 .. 0.78
   4 ?    2.3   0.5     0.045   2.7e+02       7      28 .]     544     565 ..     543     565 .. 0.90
   5 !    9.0   2.1   0.00032       1.9       2      28 .]     567     592 ..     566     592 .. 0.90
   6 !    9.6   0.7   0.00022       1.3       5      28 .]     597     619 ..     593     619 .. 0.87
   7 !    9.9   1.0   0.00018       1.1       7      27 ..     626     644 ..     626     645 .. 0.93
   8 ?    3.8   0.1     0.016        94       7      22 ..     785     799 ..     785     799 .. 0.91
   9 ?   -2.9   0.2         2   1.2e+04      14      28 .]     968     983 ..     963     983 .. 0.79
  10 !   14.9   2.6   4.4e-06     0.026       2      28 .]     988    1012 ..     987    1012 .. 0.91
  11 !   13.8   3.8   9.6e-06     0.057       1      28 []    1014    1040 ..    1014    1040 .. 0.94
  12 !   20.2   2.5   8.9e-08   0.00053       1      28 []    1043    1068 ..    1043    1068 .. 0.93
  13 !    7.4   0.7    0.0011       6.5       4      22 ..    1073    1090 ..    1070    1090 .. 0.85
  14 !   18.1   0.8   4.1e-07    0.0025       1      28 []    1273    1299 ..    1273    1299 .. 0.93
  15 !   19.3   1.6   1.7e-07     0.001       4      28 .]    1303    1326 ..    1300    1326 .. 0.91
  16 !    5.1   3.8    0.0057        34       4      28 .]    1330    1359 ..    1327    1359 .. 0.85
  17 !   14.8   2.1   4.7e-06     0.028       2      28 .]    1361    1386 ..    1360    1386 .. 0.92
  18 !   10.5   0.1   0.00011      0.69       4      28 .]    1396    1418 ..    1393    1418 .. 0.89
  19 !   17.7   0.3   5.8e-07    0.0035       1      28 []    1421    1450 ..    1421    1450 .. 0.94
  20 !   20.0   0.4     1e-07   0.00062       1      28 []    1451    1477 ..    1451    1477 .. 0.94
  21 !   13.4   0.0   1.3e-05      0.08       3      27 ..    1480    1503 ..    1478    1504 .. 0.87
  22 !   16.8   1.6   1.1e-06    0.0065       5      28 .]    1523    1545 ..    1520    1545 .. 0.92
  23 !   16.4   0.2   1.4e-06    0.0085       3      27 ..    1550    1575 ..    1548    1576 .. 0.93
  24 !   15.9   0.4     2e-06     0.012       1      27 [.    1577    1602 ..    1577    1603 .. 0.95
  25 !    5.9   1.1    0.0032        19       4      28 .]    1607    1630 ..    1604    1630 .. 0.82
  26 !   11.4   0.2   5.8e-05      0.35       2      21 ..    1633    1652 ..    1632    1653 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.22
                              Glug  18 ienctatg.tvt 28 
                                       ++n+ta++ t++
  gi|298676209|ref|YP_003727958.1| 103 VDNSTAENgTII 114
                                       89******9995 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.15
                              Glug  13 ggg...gsienctatg.tvt 28 
                                       +g     s++n++++g ++t
  gi|298676209|ref|YP_003727958.1| 148 TGStisISVDNVNVSGfNIT 167
                                       54456678888888888887 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.2
                              Glug  17 sienctatg 25 
                                        i n+++tg
  gi|298676209|ref|YP_003727958.1| 336 KINNSSVTG 344
                                       6899***98 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.045
                              Glug   7 GLvGgaggggsienctatg.tvt 28 
                                       GL G+++g+ si+n++ ++ ++t
  gi|298676209|ref|YP_003727958.1| 544 GLFGYTDGN-SISNVSLKDvNIT 565
                                       6779****9.*******999987 PP

  == domain 5  score: 9.0 bits;  conditional E-value: 0.00032
                              Glug   2 atavGGLvGgaggggsienctatgtvt 28 
                                        +avG LvG++  +g +  +++tg+vt
  gi|298676209|ref|YP_003727958.1| 567 DSAVGALVGYNN-DGFVYQSYSTGNVT 592
                                       689********6.59**********98 PP

  == domain 6  score: 9.6 bits;  conditional E-value: 0.00022
                              Glug   5 vGGLvGgaggggsienctatgtvt 28 
                                       vGGLvG+    ++++ +++ ++vt
  gi|298676209|ref|YP_003727958.1| 597 VGGLVGYIN-ESNVTKSYSIANVT 619
                                       9*****995.5********99998 PP

  == domain 7  score: 9.9 bits;  conditional E-value: 0.00018
                              Glug   7 GLvGgaggggsienctatgtv 27 
                                       G+vG++   g+i+n+++ gtv
  gi|298676209|ref|YP_003727958.1| 626 GFVGYSS--GNISNSYSIGTV 644
                                       9*****8..5**********9 PP

  == domain 8  score: 3.8 bits;  conditional E-value: 0.016
                              Glug   7 GLvGgaggggsienct 22 
                                       GL+G+++  g+++n++
  gi|298676209|ref|YP_003727958.1| 785 GLIGYNDE-GTVDNSY 799
                                       9*****97.8****96 PP

  == domain 9  score: -2.9 bits;  conditional E-value: 2
                              Glug  14 gggsienctatg.tvt 28 
                                       g++ ++n+  ++ +vt
  gi|298676209|ref|YP_003727958.1| 968 GNSKVSNVGLENiNVT 983
                                       3489999999998887 PP

  == domain 10  score: 14.9 bits;  conditional E-value: 4.4e-06
                              Glug    2 atavGGLvGgaggggsienctatgtvt 28  
                                        + +vGGLvG+++  g++  +++tg+vt
  gi|298676209|ref|YP_003727958.1|  988 YAYVGGLVGHSY--GTVNQSYSTGNVT 1012
                                        569********7..6***********8 PP

  == domain 11  score: 13.8 bits;  conditional E-value: 9.6e-06
                              Glug    1 gatavGGLvGgaggggsienctatgtvt 28  
                                        ++++vGGLvG ++g g++  +++t +vt
  gi|298676209|ref|YP_003727958.1| 1014 SGYSVGGLVGWNDG-GTVNQSYSTSNVT 1040
                                        589**********8.8*********998 PP

  == domain 12  score: 20.2 bits;  conditional E-value: 8.9e-08
                              Glug    1 gatavGGLvGgaggggsienctatgtvt 28  
                                        g+++vGGLvG ++  gsi+ +++tg+vt
  gi|298676209|ref|YP_003727958.1| 1043 GSSSVGGLVGWNY--GSIDQSYSTGNVT 1068
                                        6899********7..6***********8 PP

  == domain 13  score: 7.4 bits;  conditional E-value: 0.0011
                              Glug    4 avGGLvGgaggggsienct 22  
                                        +vGGLvG +   gs +n++
  gi|298676209|ref|YP_003727958.1| 1073 YVGGLVGLNNS-GSTDNSY 1090
                                        8********65.8999986 PP

  == domain 14  score: 18.1 bits;  conditional E-value: 4.1e-07
                              Glug    1 gatavGGLvGgaggggsienctatgtvt 28  
                                        ga  vGGLvG +++ g++ ++++tg+v+
  gi|298676209|ref|YP_003727958.1| 1273 GAKLVGGLVGWNDQ-GTVNHSYSTGDVN 1299
                                        5778*********9.8**********97 PP

  == domain 15  score: 19.3 bits;  conditional E-value: 1.7e-07
                              Glug    4 avGGLvGgaggggsienctatgtvt 28  
                                         vGGLvG++++ g++ ++++tg+v+
  gi|298676209|ref|YP_003727958.1| 1303 DVGGLVGYNYQ-GTVNHSYSTGDVN 1326
                                        69********9.8**********97 PP

  == domain 16  score: 5.1 bits;  conditional E-value: 0.0057
                              Glug    4 avGGLvGgaggg.......gsienctatgtvt 28  
                                        +vGGLvG    +       g++  +++tg+v+
  gi|298676209|ref|YP_003727958.1| 1330 NVGGLVGEY--NvgtvdhvGTVYQSYSTGNVS 1359
                                        8******66..4558**************995 PP

  == domain 17  score: 14.8 bits;  conditional E-value: 4.7e-06
                              Glug    2 atavGGLvGgaggggsienctatgtvt 28  
                                        +  vGGL+G++ g ++i  ++a+gtvt
  gi|298676209|ref|YP_003727958.1| 1361 SEDVGGLAGINKG-ATILQSSASGTVT 1386
                                        677********98.9***********8 PP

  == domain 18  score: 10.5 bits;  conditional E-value: 0.00011
                              Glug    4 avGGLvGgaggggsienctatgtvt 28  
                                        + GGL+G +   g+ie ++atg+v+
  gi|298676209|ref|YP_003727958.1| 1396 NFGGLIGFNI--GHIELSNATGDVN 1418
                                        67*******8..5**********97 PP

  == domain 19  score: 17.7 bits;  conditional E-value: 5.8e-07
                              Glug    1 gatavGGLvGgaggg..gsienctatgtvt 28  
                                        gat+vGGLvG++++    +++ ++atg+++
  gi|298676209|ref|YP_003727958.1| 1421 GATYVGGLVGYNLASepKTVSESYATGDIS 1450
                                        79***********87**9*********995 PP

  == domain 20  score: 20.0 bits;  conditional E-value: 1e-07
                              Glug    1 gatavGGLvGgaggggsienctatgtvt 28  
                                        g+ +vGGLvG+++++  +++++atg+v+
  gi|298676209|ref|YP_003727958.1| 1451 GYEYVGGLVGQNEND-FVTDSYATGDVS 1477
                                        689***********8.**********95 PP

  == domain 21  score: 13.4 bits;  conditional E-value: 1.3e-05
                              Glug    3 tavGGLvGgaggggsienctatgtv 27  
                                         ++GGLvG++   g+i+n++a g+v
  gi|298676209|ref|YP_003727958.1| 1480 RNLGGLVGRNKR-GTIDNSSAMGKV 1503
                                        689*******88.8******97776 PP

  == domain 22  score: 16.8 bits;  conditional E-value: 1.1e-06
                              Glug    5 vGGLvGgaggggsienctatgtvt 28  
                                         GGLvG ++g g+++ ++atg++t
  gi|298676209|ref|YP_003727958.1| 1523 FGGLVGFNLG-GTVKTSNATGDIT 1545
                                        6********8.8***********8 PP

  == domain 23  score: 16.4 bits;  conditional E-value: 1.4e-06
                              Glug    3 tavGGLvGgaggg.gsienctatgtv 27  
                                        ++vGGL+G++  g ++++ ++atg+v
  gi|298676209|ref|YP_003727958.1| 1550 NNVGGLIGYNSKGlTTVKQSYATGSV 1575
                                        79*********88***********98 PP

  == domain 24  score: 15.9 bits;  conditional E-value: 2e-06
                              Glug    1 gatavGGLvGgaggggsienctatgtv 27  
                                        g+ +vGGL+G ++++  ++n +a g+v
  gi|298676209|ref|YP_003727958.1| 1577 GNENVGGLIGWNEYD-LVTNTYALGDV 1602
                                        799**********97.********998 PP

  == domain 25  score: 5.9 bits;  conditional E-value: 0.0032
                              Glug    4 avGGLvGgaggggsienctatgtvt 28  
                                        +vGGLvG +   g++  +++tg vt
  gi|298676209|ref|YP_003727958.1| 1607 NVGGLVGLNSP-GTVNLSYSTGEVT 1630
                                        8******9975.7888888888886 PP

  == domain 26  score: 11.4 bits;  conditional E-value: 5.8e-05
                              Glug    2 atavGGLvGgaggggsienc 21  
                                        ++ +GGL+G++++++++e++
  gi|298676209|ref|YP_003727958.1| 1633 GSTIGGLIGTNENDATVEDA 1652
                                        6789**************97 PP

>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.1  14.3         3   1.8e+04      38     133 ..      52     155 ..      23     161 .. 0.69
   2 !   39.4  51.7   6.3e-14   3.8e-10      23     173 ..     155     309 ..     142     316 .. 0.91
   3 !   86.2  34.8   3.4e-28     2e-24     119     238 ..     310     444 ..     306     447 .. 0.92
   4 ?  -14.3  18.3         3   1.8e+04      46     154 ..     525     644 ..     454     699 .. 0.53
   5 ?   -7.7   6.0         3   1.8e+04      99     102 ..    1094    1097 ..    1002    1146 .. 0.48
   6 ?   -3.1   0.8      0.63   3.8e+03      26      78 ..    1633    1685 ..    1619    1710 .. 0.55

  Alignments for each domain:
  == domain 1  score: -6.1 bits;  conditional E-value: 3
                              NosD  38 rdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnn.tlenNtisnnen..yGills 111
                                       ++++ll n+s+n i g   e +++G+++ n++s+ + +     n++ ia+++  +n t en ti+  ++  +  +l+
  gi|298676209|ref|YP_003727958.1|  52 KQQVLLINNSDNVIAG-LWEGNNSGVYYYNNSSTSWVNESG-VNNKTIAIQRAVDNsTAENGTIIVGDGlyN-GSLK 125
                                       4455788888888888.5888899****9999966665555.555689999999888***999999888643.3333 PP

                              NosD 112 dssn..ntisnNti......snnnkGifle 133
                                         +   +++++N+       +n+++ i+++
  gi|298676209|ref|YP_003727958.1| 126 IDNPnvTELTYNNSkpvidgLNTGSTISIS 155
                                       333312445555555665555555555555 PP

  == domain 2  score: 39.4 bits;  conditional E-value: 6.3e-14
                              NosD  23 nsegseisnneisnsrdgi.lldnssnntitgntienlryGihlensesntiedntlssne.....sGialmsssnn 93 
                                       ++++  +s+ +i+ns++++  ++n++ +++t+n i+++++G+ l++s++++++dn + +n+     ++i+l+ss+++
  gi|298676209|ref|YP_003727958.1| 155 SVDNVNVSGFNITNSSNTLvNVSNANYINLTNNNITDNSKGVILQKSNNSNVKDNYFINNGgdgfdYAICLESSNKT 231
                                       458888999999999999978899999999******************************99888889*******99 PP

                              NosD  94 tlenNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFi 170
                                        ++ N++++n +  i   +s++n++ nNt++nn + i+ +ns+sn it+N+i++n + Gi ll +s++n++++N  i
  gi|298676209|ref|YP_003727958.1| 232 NVSSNIFKENYI-CICSFNSNYNNLVNNTFLNNLATIYNRNSESNNITNNYIANN-SLGIGLLGTSSKNNVTGNKII 306
                                       **********99.******************************************.********************7 PP

                              NosD 171 nns 173
                                       n +
  gi|298676209|ref|YP_003727958.1| 307 NTT 309
                                       754 PP

  == domain 3  score: 86.2 bits;  conditional E-value: 3.4e-28
                              NosD 119 snNtisnnnkGiflens.ssntitgNriesnqkiGilllssseg......ntiynNyFinnsenvkydgsn.nneWn 187
                                        ++t+  ++ Gi ++++ ++n++ gN+i+++  +Gi  l+++++      n+iynNy+ nn++n++ ++s  +n+Wn
  gi|298676209|ref|YP_003727958.1| 310 YDDTVDTSGVGILISGNsENNKVNGNKINNSSVTGIS-LDQNSNgnapsnNLIYNNYL-NNTNNAYVNDSCtGNNWN 384
                                       567888999*****98769******************.887766688888********.********99989***** PP

                              NosD 188 ttktsgtniiggpylgGNyWsdydg.......eDadgDGigDtpYeindgv..iDylplv 238
                                        +k+sgtni+ggpylgGNyW++ +g        D++gDGi+D++Y+in++   +D+lpl 
  gi|298676209|ref|YP_003727958.1| 385 ISKKSGTNIMGGPYLGGNYWANRSGdgfsqtnIDENGDGICDSSYTINSNTdsVDNLPLN 444
                                       ************************************************777779****96 PP

  == domain 4  score: -14.3 bits;  conditional E-value: 3
                              NosD  46 ssnntitgntienl...ryGihlenses.....ntiedntlssne.sGialmsssnntlenNtisnnen....yGil 109
                                        ++ +i++ +i+ l   + G++  ++++     + ++d  +++++  G ++ ++++ ++ ++ +++n +     G l
  gi|298676209|ref|YP_003727958.1| 525 GNGYNISNLVINRLgenNVGLF-GYTDGnsisnVSLKDVNITGDSaVGALVGYNNDGFVYQSYSTGNVTgsekVGGL 600
                                       2333333333333342233333.333332344444444444444457777777777766655444444334336777 PP

                              NosD 110 lsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGil 154
                                       + +++++++++     n +G++ ++     +++ +i+++ +iG +
  gi|298676209|ref|YP_003727958.1| 601 VGYINESNVTKSYSIANVTGFSETS-GFVGYSSGNISNSYSIGTV 644
                                       7777777777766655555544333.3344444444444444444 PP

  == domain 5  score: -7.7 bits;  conditional E-value: 3
                              NosD   99 tisn 102 
                                        + s+
  gi|298676209|ref|YP_003727958.1| 1094 ETSG 1097
                                        1111 PP

  == domain 6  score: -3.1 bits;  conditional E-value: 0.63
                              NosD   26 gseisnneisnsrdgilldnssnntitgntienlryGihlenses..ntiedntl 78  
                                        gs+i +   +n++d+   d+ ++ + tg t +++  G  l++se+  n + dn +
  gi|298676209|ref|YP_003727958.1| 1633 GSTIGGLIGTNENDATVEDAYWDTDTTGQTSSDG--GTALTTSEMvgNAAMDNMA 1685
                                        5555555555555555555555555555555554..4444444444455555555 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.6   6.7e-06      0.04      78     116 ..    1907    1945 ..    1899    1957 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.7e-06
                       Trypan_PARP   78 epetepeeepepepepepepepepepepepepepgaatl 116 
                                        e et  ee++epepe ep+p++e +   e e  pg ++l
  gi|298676209|ref|YP_003727958.1| 1907 EIETVEEEKTEPEPETEPKPDTEQNESEESESTPGFSSL 1945
                                        345555556666666666666666655666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1962 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 1.03u 0.31s 00:00:01.34 Elapsed: 00:00:00.50
# Mc/sec: 11893.99
//
Query:       gi|298676210|ref|YP_003727959.1|  [L=128]
Description: hypothetical protein Metev_2353 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.4   9.0       0.15   12.1   9.0    1.2  1  DUF5094   Domain of unknown function (DUF5094)


Domain annotation for each model (and alignments):
>> DUF5094  Domain of unknown function (DUF5094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   9.0   8.4e-06      0.15      19      96 ..      22     101 ..       2     118 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.4e-06
                           DUF5094  19 kknklssknlkeke.nvkvkeaeekkeekvtstkenkenekqdkdsllkeikdienelieaykeeNeyLrsl.knev 93 
                                       +k++ +   ++  + ++  +++e++++ k+++ ++n++n++ d ++++ +i++i  + +  +++e  +L++  k+++
  gi|298676210|ref|YP_003727959.1|  22 SKKPNPVVVTETLNlYFYGSKKEDENNYKSADDNNNNANNQTDDNKMILDINSIMYQWVYDLRAERDTLKEQlKEKD 98 
                                       333333333333335555555555555555555666666666666*************************8534444 PP

                           DUF5094  94 llt 96 
                                       +l 
  gi|298676210|ref|YP_003727959.1|  99 SLD 101
                                       444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1821  (0.101567); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.35s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 712.48
//
Query:       gi|298676211|ref|YP_003727960.1|  [L=120]
Description: hypothetical protein Metev_2354 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.41
# Mc/sec: 882.72
//
Query:       gi|298676212|ref|YP_003727961.1|  [L=192]
Description: hypothetical protein Metev_2355 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score 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   13.0   0.0       0.21   12.2   0.0    1.5  1  ThiS      ThiS family
       0.15   13.0   0.4       0.42   11.6   0.4    1.9  1  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.4e-05      0.21      40      66 ..     109     136 ..      71     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                                       TTTTEEEEETTEEEGC.CTTTSB--TTC CS
                              ThiS  40 lerrvavavNgeivpr.lwldtelkdgD 66 
                                        ++   v +Nge +++ l++dt lk+gD
  gi|298676212|ref|YP_003727961.1| 109 TKEETTVKINGEKINYyLGEDTNLKKGD 136
                                       568889*********************9 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   4.7e-05      0.42      32      78 ..      73     119 ..      40     122 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.7e-05
                           Pilin_N  32 sneekapqasievkidssastgkna..vslehkgGdsidt..kdlkivlns 78 
                                         +ekapq si  + d+ ++    +  ++l+h+ G+si+   +++++ +n+
  gi|298676212|ref|YP_003727961.1|  73 VSTEKAPQLSIGASFDTIKG----NkvIKLKHQWGESITFtkEETTVKING 119
                                       34566777777555555554....235***********9855666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1245.37
//
Query:       gi|298676213|ref|YP_003727962.1|  [L=82]
Description: hypothetical protein Metev_2356 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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: 0.30u 0.22s 00:00:00.52 Elapsed: 00:00:00.37
# Mc/sec: 655.83
//
Query:       gi|298676214|ref|YP_003727963.1|  [L=90]
Description: plasmid stabilization system [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-06   27.9   0.5    4.1e-06   27.3   0.5    1.3  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
    0.00015   21.8   0.0    0.00018   21.6   0.0    1.1  1  Gp49             Phage derived protein Gp49-like (DUF891)
    0.00017   21.5   0.5    0.00026   20.9   0.5    1.3  1  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a
     0.0034   17.2   0.4     0.0041   16.9   0.4    1.0  1  DUF4364          Domain of unknown function (DUF4364)


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.5   9.1e-10   4.1e-06       1      90 []       5      85 ..       5      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 9.1e-10
                                      EEEEHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEECTSTC.....CTTEEEEEECTEEEEEEEETS CS
                        ParE_toxin  1 vrltprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrprrelg.....lkglrririgdyriiYridde 74
                                      v +t +A+k lkk+ + i      a+ ++  +    ++l  np    +    +        +++ r+g yr+i +i+++
  gi|298676214|ref|YP_003727963.1|  5 VTYTTKARKNLKKLPEEI------ARNIIYSI----DELRHNPYYSVK----KisgtgKHSIYSHRVGQYRVILTIENN 69
                                      679***********8877......65555555....666666655544....222355889****************** PP

                                      TTEEEEEEEEEHHHHC CS
                        ParE_toxin 75 elvvvilrvlhrsedy 90
                                      e v+ +l ++ r+ +y
  gi|298676214|ref|YP_003727963.1| 70 EMVIMVLELGDRKHIY 85
                                      **********999765 PP

>> Gp49  Phage derived protein Gp49-like (DUF891)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   3.9e-08   0.00018       2      67 ..      14      75 ..      13      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.9e-08
                              Gp49  2 eldalpkkarakilaaldlleeggpdlgkplvkkledglwElrpksaggiiRvlyafdpgrkvilL 67
                                       l++lp+++ ++i++ +d l+++     k++ +++++ ++  r+    g++Rv+ +   ++ vi++
  gi|298676214|ref|YP_003727963.1| 14 NLKKLPEEIARNIIYSIDELRHNPYYSVKKISGTGKHSIYSHRV----GQYRVILTIENNEMVIMV 75
                                      699*****************999888******************....9*********99988775 PP

>> ParE-like_toxin  ParE-like toxin of type II bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.5   5.9e-08   0.00026       2      85 ..       6      87 ..       5      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.9e-08
                   ParE-like_toxin  2 lqtrrfkkalkklkeklkadldkavkeiiedPelGeeKkGDLsgvfvykfklnkqltllaYeldekkrvlvlllvGthe 80
                                      + t++++k lkkl e+ ++++   ++e+ ++P+   +K        +y  ++   ++++  +++++++v+++l +G ++
  gi|298676214|ref|YP_003727963.1|  6 TYTTKARKNLKKLPEEIARNIIYSIDELRHNPYYSVKKISGTGKHSIYSHRV--GQYRVILTIENNEMVIMVLELGDRK 82
                                      67899******************************99976666555555554..57888889***************** PP

                   ParE-like_toxin 81 NfYre 85
                                        Yr+
  gi|298676214|ref|YP_003727963.1| 83 HIYRK 87
                                      ***96 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.4   9.2e-07    0.0041      61     132 ..       6      78 ..       2      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.2e-07
                           DUF4364  61 kiTekGketlelfenripksirekideylkenkeelkkesev.kadyykkengeytVklkikekdstllelkl 132
                                       + T k +++l+ + ++i+ +i   ide  ++  +++kk s + k  +y ++ g+y+V l+i ++++ ++ l+l
  gi|298676214|ref|YP_003727963.1|   6 TYTTKARKNLKKLPEEIARNIIYSIDELRHNPYYSVKKISGTgKHSIYSHRVGQYRVILTIENNEMVIMVLEL 78 
                                       6799************************999998888876553899***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 602.90
//
Query:       gi|298676215|ref|YP_003727964.1|  [L=76]
Description: hypothetical protein Metev_2358 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00061   19.7   0.0    0.00073   19.5   0.0    1.1  1  Gag_p24   gag gene protein p24 (core nucleocapsid protein)


Domain annotation for each model (and alignments):
>> Gag_p24  gag gene protein p24 (core nucleocapsid protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   4.1e-08   0.00073     115     154 ..       7      47 ..       3      56 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.1e-08
                                       HHHH--S.-CCC----TT--HHHHHHHHHHHH..HH----HH CS
                           Gag_p24 115 prsgsktesladirQGpkEpyqdfvaRlekal..rkeladek 154
                                       +++ +k   l+++rQ pkEpy++ ++Rl   +  ++el+de+
  gi|298676215|ref|YP_003727964.1|   7 VNPQTKE-MLNELRQYPKEPYNSVIERLARMAidDNELSDEA 47 
                                       5555555.9*******************87543345666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.30u 0.21s 00:00:00.51 Elapsed: 00:00:00.36
# Mc/sec: 638.48
//
Query:       gi|298676216|ref|YP_003727965.1|  [L=73]
Description: hypothetical protein Metev_2359 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 475.61
//
Query:       gi|298676217|ref|YP_003727966.1|  [L=203]
Description: zinc finger C2H2-type domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for 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-08   32.3  34.4     0.0031   18.2   1.6    5.9  6  zf-C2H2_4       C2H2-type zinc finger
    3.9e-07   30.2  19.8       0.08   13.3   0.1    4.0  3  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
    8.3e-07   29.1  12.4    0.00033   20.9   2.5    4.6  3  zf-C2H2_jaz     Zinc-finger double-stranded RNA-binding
    0.00054   19.9  13.0      0.015   15.3   1.7    3.2  3  DZR             Double zinc ribbon
     0.0014   19.0  38.9      0.016   15.6   3.3    5.7  6  zf-C2H2         Zinc finger, C2H2 type
     0.0061   16.4   4.8      0.084   12.8   0.4    4.4  4  zf-C2HC_2       zinc-finger of a C2HC-type
      0.008   16.5  27.1        0.1   12.9   6.0    3.6  3  zf-C2H2_2       C2H2 type zinc-finger (2 copies)
  ------ inclusion threshold ------
      0.013   15.9  18.9       0.22   12.0   1.8    4.1  3  zf-met          Zinc-finger of C2H2 type
      0.018   14.9  12.9      0.098   12.6   0.4    3.3  3  PyrI_C          Aspartate carbamoyltransferase regulatory cha
      0.019   14.1   0.3        1.8    7.6   0.0    2.0  2  NAD_binding_4   Male sterility protein
      0.029   13.8   1.8        3.8    6.8   0.1    2.3  2  HSP33           Hsp33 protein
       0.03   14.4   0.4        4.8    7.3   0.0    2.9  3  NinD            Family of unknown function
      0.056   13.4  14.1        1.4    8.9   0.9    3.8  4  zinc-ribbons_6  zinc-ribbons
      0.085   12.7   0.4       0.12   12.2   0.4    1.2  1  DUF4370         Domain of unknown function (DUF4370)
      0.096   12.8  13.4        1.5    9.0   0.1    4.3  5  zf-CHCC         Zinc-finger domain
        0.1   12.8   7.3        6.6    7.0   0.0    4.1  4  zf-RING_7       C4-type zinc ribbon domain
       0.12   12.0  11.7        3.4    7.3   0.2    3.7  3  Sgf11           Sgf11 (transcriptional regulation protein)
        0.4   10.5   3.7       0.88    9.4   0.2    2.2  2  T6PP_N          Trehalose-6-phosphate phosphatase N-terminal 
       0.58    8.6  17.9        2.5    6.5   2.6    3.2  3  DUF629          Protein of unknown function (DUF629)
          1    9.7  14.4        4.7    7.6   2.4    3.5  3  GFA             Glutathione-dependent formaldehyde-activating
        1.3    9.1  13.6       0.85    9.7   0.4    3.7  3  CpXC            CpXC protein
        1.7    8.7  11.7        5.1    7.1   0.3    3.4  2  zf-TFIIIC       Putative zinc-finger of transcription factor 
        3.1    8.1  10.0         27    5.1   1.9    3.1  2  BolA            BolA-like protein
        3.2    8.0  29.9       0.26   11.5   1.5    3.8  4  zf-AN1          AN1-like Zinc finger
        9.4    6.5  24.4        1.5    9.0   0.4    4.8  5  HNH             HNH endonuclease


Domain annotation for each model (and alignments):
>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.6       7.9   5.6e+03       3       8 ..       4       9 ..       3      10 .. 0.82
   2 ?    1.2   0.2       1.2   8.9e+02       3       9 ..      17      24 ..      16      33 .. 0.73
   3 !   17.3   0.4   8.2e-06    0.0059       1      24 []      77     100 ..      77     100 .. 0.96
   4 !   18.2   1.6   4.4e-06    0.0031       1      24 []     104     127 ..     104     127 .. 0.96
   5 ?    2.2   0.3      0.61   4.4e+02       9      24 .]     137     151 ..     136     151 .. 0.85
   6 !   15.1   1.8   4.4e-05     0.032       1      24 []     155     178 ..     155     178 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 7.9
                         zf-C2H2_4 3 CpiCgk 8
                                     C+ Cgk
  gi|298676217|ref|YP_003727966.1| 4 CKNCGK 9
                                     9***97 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.2
                         zf-C2H2_4  3 CpiC.gks 9 
                                      C +C ++s
  gi|298676217|ref|YP_003727966.1| 17 CQQCgTRS 24
                                      ****5555 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 8.2e-06
                         zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlkthH 24 
                                       ++C iC+  F  k++L +H+++ H
  gi|298676217|ref|YP_003727966.1|  77 HICGICSSEFDGKNKLINHMEKKH 100
                                       68********************99 PP

  == domain 4  score: 18.2 bits;  conditional E-value: 4.4e-06
                         zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlkthH 24 
                                       f+C++C++ F s +aL++H + +H
  gi|298676217|ref|YP_003727966.1| 104 FTCEYCSRKFISEHALNQHKNDVH 127
                                       89*****************99988 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.61
                         zf-C2H2_4   9 sFsskkaLlrHlkthH 24 
                                       +F sk++ l H+++ H
  gi|298676217|ref|YP_003727966.1| 137 TFDSKNK-LIHMEKKH 151
                                       6888888.89**9999 PP

  == domain 6  score: 15.1 bits;  conditional E-value: 4.4e-05
                         zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlkthH 24 
                                       f+C++C++ F s + L++H + +H
  gi|298676217|ref|YP_003727966.1| 155 FTCEYCSRKFISEHVLNQHKNDVH 178
                                       89*****************99988 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   0.00011      0.08      28      54 .]      73     101 ..      68     101 .. 0.82
   2 !   12.3   5.1   0.00022      0.16       2      32 ..     103     134 ..     102     152 .. 0.90
   3 !   12.1   2.4   0.00025      0.18       2      30 ..     154     183 ..     153     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                           zf-Di19  28 eskevvCPvCaekvt..kdlvaHltleha 54 
                                       ++++++C +C+++ +  + l++H++ +h+
  gi|298676217|ref|YP_003727966.1|  73 KKHNHICGICSSEFDgkNKLINHMEKKHG 101
                                       6789*******88653269******9996 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00022
                           zf-Di19   2 sftCPyCgke.ltvkeLveHvedeHrveskev 32 
                                       +ftC yC+++ +++++L +H +d H+ ++++ 
  gi|298676217|ref|YP_003727966.1| 103 EFTCEYCSRKfISEHALNQHKNDVHHTSKESL 134
                                       7*******9659**************999876 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00025
                           zf-Di19   2 sftCPyCgke.ltvkeLveHvedeHrvesk 30 
                                       +ftC yC+++ ++++ L +H +d H+  ++
  gi|298676217|ref|YP_003727966.1| 154 EFTCEYCSRKfISEHVLNQHKNDVHHAFKE 183
                                       7*******9659***********9987555 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.4     0.016        11       2      21 ..      77      96 ..      76     100 .. 0.90
   2 !   20.9   2.5   4.6e-07   0.00033       2      22 ..     104     124 ..     103     124 .. 0.95
   3 !   20.5   2.4   5.8e-07   0.00042       2      22 ..     155     175 ..     154     175 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.016
                                      CBBTTTTBBBSSHHHHHCCT CS
                       zf-C2H2_jaz  2 fYCvlCdKyFksenaldnHl 21
                                      + C +C+  F   n l nH+
  gi|298676217|ref|YP_003727966.1| 77 HICGICSSEFDGKNKLINHM 96
                                      78*****************8 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 4.6e-07
                                       CBBTTTTBBBSSHHHHHCCTT CS
                       zf-C2H2_jaz   2 fYCvlCdKyFksenaldnHlk 22 
                                       f C++C++ F+se+al +H++
  gi|298676217|ref|YP_003727966.1| 104 FTCEYCSRKFISEHALNQHKN 124
                                       99*****************87 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 5.8e-07
                                       CBBTTTTBBBSSHHHHHCCTT CS
                       zf-C2H2_jaz   2 fYCvlCdKyFksenaldnHlk 22 
                                       f C++C++ F+se++l +H++
  gi|298676217|ref|YP_003727966.1| 155 FTCEYCSRKFISEHVLNQHKN 175
                                       99*****************87 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.7   2.1e-05     0.015       1      21 [.       4      23 ..       4      42 .. 0.88
   2 !    9.3   0.5    0.0016       1.2       7      42 ..      71     117 ..      67     121 .. 0.87
   3 ?    4.2   1.6     0.061        44      14      41 ..     105     167 ..     103     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                               DZR  1 CpqCgeelppdarfCseCgtk 21
                                      C++Cg++ p++  fC++Cgt+
  gi|298676217|ref|YP_003727966.1|  4 CKNCGKK-PNHFGFCQQCGTR 23
                                      9****99.9**********98 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0016
                               DZR   7 elppdarfCseCgtklkavaa...........edrCpsCgekvdpea 42 
                                       +++++++ C+ C ++ +  ++           e +C  C++k  +e+
  gi|298676217|ref|YP_003727966.1|  71 KNKKHNHICGICSSEFDGKNKlinhmekkhglEFTCEYCSRKFISEH 117
                                       68999**********9877779999999************9977766 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.061
                               DZR  14 fCseCgtklkavaa...................................edrCpsCgekvdpe 41 
                                       +C++C  k  ++ a                                   e +C  C++k  +e
  gi|298676217|ref|YP_003727966.1| 105 TCEYCSRKFISEHAlnqhkndvhhtskeslistfdsknklihmekkhslEFTCEYCSRKFISE 167
                                       689999887766667888888888888888888888888888888988888999999886655 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.9       0.5   3.6e+02       2       8 ..       3       9 ..       2      10 .. 0.87
   2 ?    0.3   0.2       1.6   1.1e+03       3       9 ..      17      24 ..      16      30 .. 0.74
   3 !   10.8   0.6   0.00075      0.54       1      23 []      77     100 ..      77     100 .. 0.95
   4 !   15.6   3.3   2.3e-05     0.016       1      23 []     104     127 ..     104     128 .. 0.94
   5 ?   -1.6   0.1       6.8   4.9e+03      15      23 .]     142     151 ..     137     151 .. 0.69
   6 !   12.5   3.5   0.00023      0.16       1      23 []     155     178 ..     155     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.5
                                     EETTTTE CS
                           zf-C2H2 2 kCpdCgk 8
                                     +C+ Cgk
  gi|298676217|ref|YP_003727966.1| 3 VCKNCGK 9
                                     7*****9 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.6
                                      ETTTT.EE CS
                           zf-C2H2  3 CpdCg.ks 9 
                                      C  Cg +s
  gi|298676217|ref|YP_003727966.1| 17 CQQCGtRS 24
                                      99999555 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00075
                                       EEETTTTEEESSHHHHHHHHHC.C CS
                           zf-C2H2   1 ykCpdCgksFkrksnLkrHirt.H 23 
                                       + C++C+  F  k  L +H+ + H
  gi|298676217|ref|YP_003727966.1|  77 HICGICSSEFDGKNKLINHMEKkH 100
                                       67******************9999 PP

  == domain 4  score: 15.6 bits;  conditional E-value: 2.3e-05
                                       EEETTTTEEESSHHHHHHHHHC.C CS
                           zf-C2H2   1 ykCpdCgksFkrksnLkrHirt.H 23 
                                       ++C++C+++F + + L++H +  H
  gi|298676217|ref|YP_003727966.1| 104 FTCEYCSRKFISEHALNQHKNDvH 127
                                       89*****************98776 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 6.8
                                       HHHHHHHC.C CS
                           zf-C2H2  15 nLkrHirt.H 23 
                                       n   H+ + H
  gi|298676217|ref|YP_003727966.1| 142 NKLIHMEKkH 151
                                       5567998888 PP

  == domain 6  score: 12.5 bits;  conditional E-value: 0.00023
                                       EEETTTTEEESSHHHHHHHHHC.C CS
                           zf-C2H2   1 ykCpdCgksFkrksnLkrHirt.H 23 
                                       ++C++C+++F + + L++H +  H
  gi|298676217|ref|YP_003727966.1| 155 FTCEYCSRKFISEHVLNQHKNDvH 178
                                       89*****************98776 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.4      0.33   2.4e+02       5      11 ..       4      10 ..       1      10 [. 0.82
   2 ?   -0.2   0.2       1.4   9.9e+02       4      20 ..      78      95 ..      77      99 .. 0.72
   3 !   12.8   0.4   0.00012     0.084       4      21 ..     105     123 ..     103     124 .. 0.81
   4 !   12.5   0.4   0.00015      0.11       4      20 ..     156     173 ..     154     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.33
                         zf-C2HC_2  5 CpkCgRs 11
                                      C++Cg +
  gi|298676217|ref|YP_003727966.1|  4 CKNCGKK 10
                                      *****76 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.4
                         zf-C2HC_2  4 pCpkCgRsF.npdrlekH 20
                                       C +C+  F +   l +H
  gi|298676217|ref|YP_003727966.1| 78 ICGICSSEFdGKNKLINH 95
                                      588898777777788888 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00012
                         zf-C2HC_2   4 pCpkCgRsF.npdrlekHe 21 
                                        C++C+R+F  + +l  H+
  gi|298676217|ref|YP_003727966.1| 105 TCEYCSRKFiSEHALNQHK 123
                                       7********7777777775 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00015
                         zf-C2HC_2   4 pCpkCgRsF.npdrlekH 20 
                                        C++C+R+F  +  l  H
  gi|298676217|ref|YP_003727966.1| 156 TCEYCSRKFiSEHVLNQH 173
                                       7********666666666 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   3.5    0.0007       0.5      51      74 ..      77     100 ..       3     104 .. 0.79
   2 !   12.9   6.0   0.00014       0.1      37      77 ..      90     130 ..      90     136 .. 0.93
   3 !    7.6  15.7    0.0065       4.6       2      77 ..     106     181 ..     105     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0007
                         zf-C2H2_2  51 leClyCekefkslealreHmkkkg 74 
                                       ++C +C++ef+ +++l +Hm+kk+
  gi|298676217|ref|YP_003727966.1|  77 HICGICSSEFDGKNKLINHMEKKH 100
                                       556666666666666666665543 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00014
                         zf-C2H2_2  37 eglleylrekieekleClyCekefkslealreHmkkkgHck 77 
                                       ++l++++++k   +++C yC+++f s +al++H ++ +H+ 
  gi|298676217|ref|YP_003727966.1|  90 NKLINHMEKKHGLEFTCEYCSRKFISEHALNQHKNDVHHTS 130
                                       589**********************************9986 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0065
                         zf-C2H2_2   2 ClfcekkskeveellehmskkhgffipereylvdleglleylrekieekleClyCekefkslealreHmkkkgHck 77 
                                       C +c++k+ + ++l +h ++ h+   ++  +  d+++ l ++++k + +++C yC+++f s + l++H ++ +H  
  gi|298676217|ref|YP_003727966.1| 106 CEYCSRKFISEHALNQHKNDVHHTSKESLISTFDSKNKLIHMEKKHSLEFTCEYCSRKFISEHVLNQHKNDVHHAF 181
                                       999*999999999999999999887775544446666666777777888*******************99999975 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.6      0.35   2.5e+02       2      21 ..      78      97 ..      77     100 .. 0.85
   2 ?   12.0   1.8   0.00031      0.22       1      21 [.     104     124 ..     104     124 .. 0.94
   3 ?   11.4   1.9   0.00047      0.33       1      21 [.     155     175 ..     155     175 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.35
                            zf-met  2 yCelCnvtfnsesqlksHlq 21
                                       C +C   f +++ l++H+ 
  gi|298676217|ref|YP_003727966.1| 78 ICGICSSEFDGKNKLINHME 97
                                      5****999999999999986 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00031
                            zf-met   1 fyCelCnvtfnsesqlksHlq 21 
                                       f+Ce C ++f se +l++H +
  gi|298676217|ref|YP_003727966.1| 104 FTCEYCSRKFISEHALNQHKN 124
                                       89*****************75 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00047
                            zf-met   1 fyCelCnvtfnsesqlksHlq 21 
                                       f+Ce C ++f se +l++H +
  gi|298676217|ref|YP_003727966.1| 155 FTCEYCSRKFISEHVLNQHKN 175
                                       89*****************75 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2       4.8   3.5e+03      36      42 ..       4      10 ..       2      13 .. 0.77
   2 ?    9.0   2.0    0.0018       1.3      26      44 ..      96     114 ..      75     117 .. 0.79
   3 ?   12.6   0.4   0.00014     0.098      24      47 ..     145     168 ..     129     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.8
                                      ETTT--E CS
                            PyrI_C 36 CkYCeke 42
                                      Ck C+k+
  gi|298676217|ref|YP_003727966.1|  4 CKNCGKK 10
                                      9999987 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0018
                                       EEETTTTEEEETTT--EEE CS
                            PyrI_C  26 vedkekvklkCkYCekeis 44 
                                       +e+k+ +++ C+YC +++ 
  gi|298676217|ref|YP_003727966.1|  96 MEKKHGLEFTCEYCSRKFI 114
                                       488999********99985 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00014
                                       EEEEETTTTEEEETTT--EEEHHH CS
                            PyrI_C  24 FkvedkekvklkCkYCekeiseee 47 
                                        ++e+k+ +++ C+YC +++  e+
  gi|298676217|ref|YP_003727966.1| 145 IHMEKKHSLEFTCEYCSRKFISEH 168
                                       35588************9987665 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.014        10     156     191 ..      60     123 ..       4     128 .. 0.75
   2 ?    7.6   0.0    0.0025       1.8     147     208 ..     130     188 ..     124     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.014
                                       ................................HHH--EEEETTTCCCHHHHHHHHHHHHHHHHH CS
                     NAD_binding_4 156 e............................keekldederaklkglpntYeqsKalaEklvrear 191
                                                                    k++  + +e++++ +++ +Y   K+++E+ +++++
  gi|298676217|ref|YP_003727966.1|  60 VgkrkkttsggknkkhnhicgicssefdgKNKLINHMEKKHGLEFTCEYCSRKFISEHALNQHK 123
                                       0444444455566777778888888888899999***************************998 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0025
                                       --SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                     NAD_binding_4 147 veekvyeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                        +e ++++ ++++kl  +e++++ +++ +Y   K+++E+++++++  +++    ++ s it+
  gi|298676217|ref|YP_003727966.1| 130 SKESLISTFDSKNKLIHMEKKHSLEFTCEYCSRKFISEHVLNQHK--NDVH-HAFKESLITS 188
                                       4566666667899999***************************99..4554.5566666665 PP

>> HSP33  Hsp33 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0087       6.2     243     264 ..      93     113 ..      88     115 .. 0.80
   2 ?    6.8   0.1    0.0053       3.8     238     264 ..     138     164 ..     127     167 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0087
                                       HHHHHHCCTEEEEE-TTT--EE CS
                             HSP33 243 leeileedgkievtCefCgkkY 264
                                       ++++ e+++++e tCe+C++k+
  gi|298676217|ref|YP_003727966.1|  93 INHM-EKKHGLEFTCEYCSRKF 113
                                       4566.66999*********986 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0053
                                       T-CHH.HHHHHHCCTEEEEE-TTT--EE CS
                             HSP33 238 lgkee.leeileedgkievtCefCgkkY 264
                                       ++ +  l ++ e+++++e tCe+C++k+
  gi|298676217|ref|YP_003727966.1| 138 FDSKNkLIHM-EKKHSLEFTCEYCSRKF 164
                                       5444424455.669***********986 PP

>> NinD  Family of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.6         5   3.6e+03       1      13 [.       1      13 [.       1      25 [. 0.64
   2 ?    7.3   0.0    0.0067       4.8      27      53 ..     106     132 ..     102     136 .. 0.91
   3 ?    3.9   0.0     0.081        58      27      51 ..     157     181 ..     149     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5
                              NinD  1 mkrcyrcGesked 13
                                      m  c  cG+  + 
  gi|298676217|ref|YP_003727966.1|  1 MSVCKNCGKKPNH 13
                                      5667777765444 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0067
                              NinD  27 clrcersPvGvlPlPeekedvwrdsde 53 
                                       c  c r  +    l ++k+dv + s e
  gi|298676217|ref|YP_003727966.1| 106 CEYCSRKFISEHALNQHKNDVHHTSKE 132
                                       7789********************988 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.081
                              NinD  27 clrcersPvGvlPlPeekedvwrds 51 
                                       c  c r  +    l ++k+dv +  
  gi|298676217|ref|YP_003727966.1| 157 CEYCSRKFISEHVLNQHKNDVHHAF 181
                                       78899****************9965 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.9     0.002       1.4      18      38 ..       3      23 ..       1      29 [. 0.85
   2 ?    0.6   0.1      0.79   5.7e+02      14      27 ..      74      87 ..      62      92 .. 0.65
   3 ?    6.2   1.3     0.014       9.9       3      30 ..      79     117 ..      77     132 .. 0.72
   4 ?    5.0   0.2     0.033        23      10      30 ..     147     168 ..     140     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                                      E-TTT--EEEEEEE-SSS-S- CS
                    zinc-ribbons_6 18 hCeaCqedlkkealCpeCeqe 38
                                       C++C ++ +   +C++C+ +
  gi|298676217|ref|YP_003727966.1|  3 VCKNCGKKPNHFGFCQQCGTR 23
                                      599999999999999999875 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.79
                                      SSEEE-TTT--EEE CS
                    zinc-ribbons_6 14 geqyhCeaCqedlk 27
                                      +++  C  C+++++
  gi|298676217|ref|YP_003727966.1| 74 KHNHICGICSSEFD 87
                                      34556777766665 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.014
                                       -SSS-S--E.E-S..........SEEE-TTT--EEEEEE CS
                    zinc-ribbons_6   3 CpeCqqele.krg..........eqyhCeaCqedlkkea 30 
                                       C  C +e + k++           +++Ce C++++  e 
  gi|298676217|ref|YP_003727966.1|  79 CGICSSEFDgKNKlinhmekkhgLEFTCEYCSRKFISEH 117
                                       6666666664333666666666699*******9987665 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.033
                                       -E.E-SSEEE-TTT--EEEEEE CS
                    zinc-ribbons_6  10 le.krgeqyhCeaCqedlkkea 30 
                                       +e k++ +++Ce C++++  e 
  gi|298676217|ref|YP_003727966.1| 147 MEkKHSLEFTCEYCSRKFISEH 168
                                       554566899******9987665 PP

>> DUF4370  Domain of unknown function (DUF4370)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   0.00017      0.12      15     102 ..     109     195 ..      96     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                           DUF4370  15 aaassrlsaaaaasaalekhlssrslfavlsasskavlsdlrsp..lalslGsvrsfsedvshlPeikdsevkkafk 89 
                                       + ++    +a++++++  +h+s+ sl++ + +++k + ++ ++   ++++  s+++ se v    + + ++v++afk
  gi|298676217|ref|YP_003727966.1| 109 CSRKFISEHALNQHKNDVHHTSKESLISTFDSKNKLIHMEKKHSleFTCEYCSRKFISEHV---LNQHKNDVHHAFK 182
                                       566666777888888999999******9988888887777776522677778888888755...567889******* PP

                           DUF4370  90 dllaaswdelPda 102
                                       + l +s + l + 
  gi|298676217|ref|YP_003727966.1| 183 ESLITSKESLISN 195
                                       *999998888665 PP

>> zf-CHCC  Zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2       4.7   3.4e+03      29      35 ..       3       9 ..       2      10 .. 0.81
   2 ?   -1.4   0.1       3.6   2.6e+03      30      36 ..      17      23 ..      12      23 .. 0.84
   3 ?    2.2   0.0      0.26   1.9e+02      24      37 .]      73      86 ..      71      86 .. 0.87
   4 ?    8.6   0.2    0.0026       1.9      29      37 .]     105     113 ..      96     113 .. 0.86
   5 ?    9.0   0.1     0.002       1.5      28      37 .]     155     164 ..     145     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.7
                                      EETTTTE CS
                           zf-CHCC 29 dCgYCgl 35
                                      +C+ Cg+
  gi|298676217|ref|YP_003727966.1|  3 VCKNCGK 9 
                                      6999*97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.6
                                      ETTTTEE CS
                           zf-CHCC 30 CgYCglr 36
                                      C+ Cg+r
  gi|298676217|ref|YP_003727966.1| 17 CQQCGTR 23
                                      999**98 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.26
                                      TTSEEEETTTTEEE CS
                           zf-CHCC 24 kkgpvdCgYCglrF 37
                                      kk+ + Cg C+  F
  gi|298676217|ref|YP_003727966.1| 73 KKHNHICGICSSEF 86
                                      8899******9887 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0026
                                       EETTTTEEE CS
                           zf-CHCC  29 dCgYCglrF 37 
                                       +C YC+++F
  gi|298676217|ref|YP_003727966.1| 105 TCEYCSRKF 113
                                       8******99 PP

  == domain 5  score: 9.0 bits;  conditional E-value: 0.002
                                       EEETTTTEEE CS
                           zf-CHCC  28 vdCgYCglrF 37 
                                        +C YC+++F
  gi|298676217|ref|YP_003727966.1| 155 FTCEYCSRKF 164
                                       58******99 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       2.2   1.6e+03      26      30 ..       4       8 ..       1       9 [. 0.82
   2 ?    0.3   0.5       1.2   8.3e+02      25      30 ..      16      21 ..      12      22 .. 0.91
   3 ?    7.0   0.0    0.0091       6.6      21      31 ..     101     111 ..      90     111 .. 0.74
   4 ?    6.2   0.0     0.016        12      24      31 ..     155     162 ..     140     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.2
                                      -TTT- CS
                         zf-RING_7 26 CpeCG 30
                                      C +CG
  gi|298676217|ref|YP_003727966.1|  4 CKNCG 8 
                                      99**9 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.2
                                      E-TTT- CS
                         zf-RING_7 25 tCpeCG 30
                                      +C +CG
  gi|298676217|ref|YP_003727966.1| 16 FCQQCG 21
                                      7****9 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0091
                                       TB-EE-TTT-- CS
                         zf-RING_7  21 devvtCpeCGR 31 
                                       +  +tC++C+R
  gi|298676217|ref|YP_003727966.1| 101 GLEFTCEYCSR 111
                                       5569*****99 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.016
                                       EE-TTT-- CS
                         zf-RING_7  24 vtCpeCGR 31 
                                       +tC++C+R
  gi|298676217|ref|YP_003727966.1| 155 FTCEYCSR 162
                                       8*****99 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.9     0.099        71       6      16 ..       3      13 ..       1      21 [. 0.78
   2 ?    6.6   0.2    0.0079       5.7       5      13 ..     104     112 ..     102     113 .. 0.90
   3 ?    7.3   0.2    0.0048       3.4       4      13 ..     154     163 ..     151     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.099
                                      E-TTTSSEEEG CS
                             Sgf11  6 tCpnCgRqiaa 16
                                      +C+nCg++ ++
  gi|298676217|ref|YP_003727966.1|  3 VCKNCGKKPNH 13
                                      7*****98555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0079
                                       EE-TTTSSE CS
                             Sgf11   5 vtCpnCgRq 13 
                                       +tC++C+R+
  gi|298676217|ref|YP_003727966.1| 104 FTCEYCSRK 112
                                       9*******6 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0048
                                       EEE-TTTSSE CS
                             Sgf11   4 yvtCpnCgRq 13 
                                        +tC++C+R+
  gi|298676217|ref|YP_003727966.1| 154 EFTCEYCSRK 163
                                       79*******6 PP

>> T6PP_N  Trehalose-6-phosphate phosphatase N-terminal helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.5      0.24   1.7e+02      23      62 ..     113     152 ..     108     159 .. 0.76
   2 ?    9.4   0.2    0.0012      0.88      15      53 ..     161     200 ..     153     203 .] 0.80

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.24
                            T6PP_N  23 vLkgieirehfvesLknakesLeadcetgtevlelrttee 62 
                                        +++ ++++h +++ + +kesL    +++++ ++++++++
  gi|298676217|ref|YP_003727966.1| 113 FISEHALNQHKNDVHHTSKESLISTFDSKNKLIHMEKKHS 152
                                       5677888899999999999999977778888888888743 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0012
                            T6PP_N  15 vRrqIvervLkgie..irehfvesLknakesLeadcetgte 53 
                                        R+ I e+vL++ +  ++++f esL  +kesL  ++ ++++
  gi|298676217|ref|YP_003727966.1| 161 SRKFISEHVLNQHKndVHHAFKESLITSKESLI-SNIDENQ 200
                                       6999******985433****************9.5554444 PP

>> DUF629  Protein of unknown function (DUF629)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.2    0.0042         3      57      86 ..      77     106 ..      69     111 .. 0.87
   2 ?    4.1   3.3     0.019        14      57      97 ..     104     139 ..     102     152 .. 0.71
   3 ?    6.5   2.6    0.0035       2.5      57      98 ..     155     198 ..     141     202 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0042
                            DUF629  57 WvCrtCsekfsdaeeckqHlvqeHvaklkp 86 
                                        +C +Cs +f   ++  +H++++H  ++  
  gi|298676217|ref|YP_003727966.1|  77 HICGICSSEFDGKNKLINHMEKKHGLEFTC 106
                                       57**********************988865 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.019
                            DUF629  57 WvCrtCsekfsdaeeckqHlvqeHvaklkpklqkvlpqevd 97 
                                       ++C  Cs+kf++     +H +++H +++++ ++++l  + d
  gi|298676217|ref|YP_003727966.1| 104 FTCEYCSRKFIS-----EHALNQHKNDVHHTSKESLISTFD 139
                                       58*********9.....555666666666656655555555 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0035
                            DUF629  57 WvCrtCsekfsdaeeckqHlvqeHvak..lkpklqkvlpqevdk 98 
                                       ++C  Cs+kf++ +  +qH  + H a       ++++l  ++d+
  gi|298676217|ref|YP_003727966.1| 155 FTCEYCSRKFISEHVLNQHKNDVHHAFkeSLITSKESLISNIDE 198
                                       68**********87777777777765211333445555666655 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.4    0.0066       4.7      45      67 ..       9      32 ..       1      38 [. 0.71
   2 ?    5.4   0.1     0.032        23      38      59 ..      64      86 ..      41     101 .. 0.71
   3 ?    3.5   1.2      0.12        88       5      63 ..     106     168 ..     102     184 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0066
                               GFA 45 nkvtr.sfCpeCgsplyseesaap 67
                                      +k ++  fC++Cg++ y+ ++++ 
  gi|298676217|ref|YP_003727966.1|  9 KKPNHfGFCQQCGTRSYVVSDEKY 32
                                      4444559*********98766554 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.032
                               GFA 38 kkt.adsgnkvtrsfCpeCgspl 59
                                      kkt +  +nk+++++C  C s++
  gi|298676217|ref|YP_003727966.1| 64 KKTtSGGKNKKHNHICGICSSEF 86
                                      4442556677777******9986 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.12
                               GFA   5 CsdCrkasgsaftanavvkaealellegelkeykkt...adsgnkvtr.sfCpeCgsplysee 63 
                                       C+ C +   s +++n   ++ + +  e+ +++++++    + ++k++    C+ C  +++se 
  gi|298676217|ref|YP_003727966.1| 106 CEYCSRKFISEHALNQHKNDVHHTSKESLISTFDSKnklIHMEKKHSLeFTCEYCSRKFISEH 168
                                       999999999999999877766666555588888877555445555554367999999888764 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   2.5       2.6   1.9e+03      40      49 ..      17      26 ..       2      42 .. 0.74
   2 ?    9.7   0.4    0.0012      0.85      24      68 ..      90     139 ..      71     152 .. 0.76
   3 ?    6.6   0.2     0.011       7.6      35      58 ..     152     175 ..     141     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.6
                              CpXC 40 CpkCgatakl 49
                                      C++Cg++ ++
  gi|298676217|ref|YP_003727966.1| 17 CQQCGTRSYV 26
                                      7777776655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                              CpXC  24 pelkeklldgslfeatCpkCgatakleapll.....yhdpekellillvp 68 
                                       ++l + + ++  +e+tC++C +++  e+ l      +h  +ke li  + 
  gi|298676217|ref|YP_003727966.1|  90 NKLINHMEKKHGLEFTCEYCSRKFISEHALNqhkndVHHTSKESLISTFD 139
                                       56666666777789***************996666666666666665555 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.011
                              CpXC  35 lfeatCpkCgatakleapllyhdp 58 
                                        +e+tC++C +++  e+ l  h+ 
  gi|298676217|ref|YP_003727966.1| 152 SLEFTCEYCSRKFISEHVLNQHKN 175
                                       579***********9998886664 PP

>> zf-TFIIIC  Putative zinc-finger of transcription factor IIIC complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   6.1      0.16   1.2e+02      53      82 ..     103     133 ..       3     147 .. 0.85
   2 ?    7.1   0.3    0.0071       5.1      53      77 ..     154     178 ..     135     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.16
                         zf-TFIIIC  53 skvCilcstevldeelveaqelik.eeseks 82 
                                       + +C  cs+++++e+ +++++ +  ++s++s
  gi|298676217|ref|YP_003727966.1| 103 EFTCEYCSRKFISEHALNQHKNDVhHTSKES 133
                                       448***********99998884441333333 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0071
                         zf-TFIIIC  53 skvCilcstevldeelveaqelike 77 
                                       + +C  cs+++++e+++++++ + +
  gi|298676217|ref|YP_003727966.1| 154 EFTCEYCSRKFISEHVLNQHKNDVH 178
                                       448**********999988874442 PP

>> BolA  BolA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.9     0.037        27      12      49 ..      51      95 ..      44     136 .. 0.69
   2 ?    3.6   2.1      0.11        79      15      59 ..     139     184 ..     126     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.037
                              BolA 12 vedeShkhagha......eaggetHFk.vvivseaFegkslvarh 49
                                      +++ S   ++ +      ++++++H + + i+s++F+gk+++  h
  gi|298676217|ref|YP_003727966.1| 51 IVNSSVPSEVGKrkkttsGGKNKKHNHiCGICSSEFDGKNKLINH 95
                                      555555544444444544223444443167888888888887666 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.11
                              BolA  15 eShkhaghaeaggetHFkvvivseaFegkslvarhRl.vyalLkee 59 
                                       +S+++  h e++    F+++ +s +F  +  +++h+  v+++ ke 
  gi|298676217|ref|YP_003727966.1| 139 DSKNKLIHMEKKHSLEFTCEYCSRKFISEHVLNQHKNdVHHAFKES 184
                                       5666667767788889*******************95477777776 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   5.2      0.41   2.9e+02       1      21 [.       4      22 ..       4      23 .. 0.87
   2 ?   -2.4   0.4         8   5.7e+03      15      21 ..      78      84 ..      72      86 .. 0.55
   3 ?   11.5   1.5   0.00036      0.26       8      30 ..      98     120 ..      94     123 .. 0.85
   4 ?   11.1   1.9   0.00049      0.35       8      30 ..     149     171 ..     146     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.41
                            zf-AN1  1 CsfksCkkkdflpfkCryCgk 21
                                      C+  +C+kk +  + C++Cg 
  gi|298676217|ref|YP_003727966.1|  4 CK--NCGKKPNHFGFCQQCGT 22
                                      55..8*****999******96 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8
                            zf-AN1 15 kCryCgk 21
                                       C  C+ 
  gi|298676217|ref|YP_003727966.1| 78 ICGICSS 84
                                      4556655 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00036
                            zf-AN1   8 kkdflpfkCryCgkvFClkHrlp 30 
                                       kk  l f+C+yC+++F ++H l 
  gi|298676217|ref|YP_003727966.1|  98 KKHGLEFTCEYCSRKFISEHALN 120
                                       566788**********9999875 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00049
                            zf-AN1   8 kkdflpfkCryCgkvFClkHrlp 30 
                                       kk +l f+C+yC+++F ++H l 
  gi|298676217|ref|YP_003727966.1| 149 KKHSLEFTCEYCSRKFISEHVLN 171
                                       566778**********9999775 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2      0.96   6.9e+02       1       7 [.       4      10 ..       1      14 [. 0.64
   2 ?   -2.3   0.6       7.5   5.4e+03       1       5 [.      17      21 ..      17      25 .. 0.81
   3 ?    4.1   0.3     0.076        54       1      23 [.      79     100 ..      79     103 .. 0.85
   4 ?    9.0   0.4    0.0021       1.5       1      22 [.     106     132 ..     106     144 .. 0.85
   5 ?    8.9   0.8    0.0024       1.7       1      33 [.     157     196 ..     157     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.96
                               HNH  1 CeyCgrk 7 
                                      C +Cg+k
  gi|298676217|ref|YP_003727966.1|  4 CKNCGKK 10
                                      5555554 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.5
                               HNH  1 CeyCg 5 
                                      C+ Cg
  gi|298676217|ref|YP_003727966.1| 17 CQQCG 21
                                      89998 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.076
                               HNH   1 CeyCgrkfhksealevdHiipis 23 
                                       C +C ++f+++  + ++H++ ++
  gi|298676217|ref|YP_003727966.1|  79 CGICSSEFDGK-NKLINHMEKKH 100
                                       9*********9.88888887665 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0021
                               HNH   1 CeyCgrkfhks.....ealevdHiipi 22 
                                       CeyC rkf  +       + v+H    
  gi|298676217|ref|YP_003727966.1| 106 CEYCSRKFISEhalnqHKNDVHHTSKE 132
                                       ********9999999889999998665 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0024
                               HNH   1 CeyCgrkfhks.....ealevdHiipisq..ggaddieNl 33 
                                       CeyC rkf  +       + v+H    s   +++  i+N+
  gi|298676217|ref|YP_003727966.1| 157 CEYCSRKFISEhvlnqHKNDVHHAFKESLitSKESLISNI 196
                                       ********99899999999999987777555666667775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1360  (0.0758548); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1124.70
//
Query:       gi|298676218|ref|YP_003727967.1|  [L=197]
Description: transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-32  111.3   0.1      4e-32  111.0   0.1    1.1  1  DDE_3     DDE superfamily endonuclease
  ------ inclusion threshold ------
      0.057   12.9   0.2       0.11   12.0   0.1    1.5  2  AviRa     RRNA methyltransferase AviRa
        0.1   12.2   0.0       0.17   11.5   0.0    1.5  1  SMC_ScpB  Segregation and condensation complex subunit ScpB


Domain annotation for each model (and alignments):
>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.0   0.1   6.7e-36     4e-32       2     142 ..      18     164 ..      17     167 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 6.7e-36
                             DDE_3   2 vvfiDEsgfqlgt.vrrrawakkGkrer.leeygrrgrvnligaldekgglafvtfeetlnaedfaeflerlletal 76 
                                       vv++DEs+ ql + +r +  a  Gk e+ ++ey+r+ ++n+++a ++ +g+++v+++++ +++d+++f+e+++ ++ 
  gi|298676218|ref|YP_003727967.1|  18 VVCMDESPKQLISeTRNKIQASAGKPEKyDYEYRRKCSCNIFMACEPLTGERIVQITKRKTKKDWVQFIEKIATKYN 94 
                                       9************9************999************************************************ PP

                             DDE_3  77 qakkivlilDnasiHkseslrelveee.....adrlellylPpySPelNpiEivwsklkrellkrrsfksl 142
                                       +ak+i li+Dn ++H+  s++e+++ e     +dr+el+++P++ ++lN+ Ei  ++l++++l+ r++ ++
  gi|298676218|ref|YP_003727967.1|  95 SAKRITLIMDNYNTHTPGSFYEAFHPEkakqlLDRFELVFTPKHGSWLNMAEIELNVLNKQCLN-RRIGDI 164
                                       ****************************************************************.887765 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.67     4e+03     224     224 ..      87      87 ..      64     119 .. 0.53
   2 ?   12.0   0.1   1.8e-05      0.11      89     141 ..     139     191 ..     121     197 .] 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.67
                             AviRa 224 r 224
                                       +
  gi|298676218|ref|YP_003727967.1|  87 E 87 
                                       1 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.8e-05
                             AviRa  89 eevlelakkNLsLLtkeglakreeelrelaeeyekeshaealesaerleella 141
                                        + l++a+  L++L k+ l++r+ +++ + ++ e+  h+e  ++ae + +ll+
  gi|298676218|ref|YP_003727967.1| 139 GSWLNMAEIELNVLNKQCLNRRIGDIQVSLTKSEHGNHIEMRNTAESIGNLLH 191
                                       67899************************************999999999884 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.9e-05      0.17       7      46 ..      58      98 ..      52     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.9e-05
                          SMC_ScpB  7 LfvageplsleeLakilels.keeveealeeLkeeyeeedr 46
                                      +f+a epl+ e++ +i++ + k++  + +e+++++y++++r
  gi|298676218|ref|YP_003727967.1| 58 IFMACEPLTGERIVQITKRKtKKDWVQFIEKIATKYNSAKR 98
                                      899**************86679**************77666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1178.17
//
Query:       gi|298676219|ref|YP_003727968.1|  [L=152]
Description: transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-10   41.8   0.0    4.3e-10   40.1   0.0    1.8  2  HTH_32    Homeodomain-like domain
    6.4e-10   38.9   0.0      1e-09   38.3   0.0    1.3  1  HTH_29    Winged helix-turn helix
    4.7e-05   23.0   0.1    0.00016   21.3   0.0    1.9  2  HTH_23    Homeodomain-like domain
  ------ inclusion threshold ------
       0.03   14.2   0.3      0.051   13.4   0.3    1.4  1  Clathrin  Region in Clathrin and VPS
       0.17   11.7   1.4        3.4    7.5   0.1    2.0  2  ATG27     Autophagy-related protein 27


Domain annotation for each model (and alignments):
>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.68   2.4e+03      28      41 ..      11      24 ..       5      40 .. 0.72
   2 !   40.1   0.0   1.2e-13   4.3e-10       2      73 .]      69     148 ..      68     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.68
                            HTH_32 28 klsdevrariiall 41
                                      +l++e+r+++  ++
  gi|298676219|ref|YP_003727968.1| 11 TLTKEERKELESIV 24
                                      47788888887776 PP

  == domain 2  score: 40.1 bits;  conditional E-value: 1.2e-13
                            HTH_32   2 vsrwlkRyneeGle.gLkdrprrg.rprklsdevrariiallreep.....rWsprqlaarlaere.gvkvShstvy 70 
                                       + r+ kR+ e+Gl+ +L  ++  +   +k++ + +a+iial +++p     + s+r+la++++e e  +++S++++ 
  gi|298676219|ref|YP_003727968.1|  69 IDRVKKRFVEDGLDmALNGKEYERtYEKKIDGDMEAHIIALSCSDPsqghsQCSLRLLADKVVELEyIDSISYESIK 145
                                       67999*************88554223358***************999**99***********88885777******* PP

                            HTH_32  71 riL 73 
                                       r+L
  gi|298676219|ref|YP_003727968.1| 146 RVL 148
                                       *98 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   2.8e-13     1e-09       1      63 []      36     104 ..      36     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 2.8e-13
                            HTH_29   1 RaqallllaeGvs.....tvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprn.rlseeqea 63 
                                       +a++ll+++eG++     t   +  +l++ +r+++r++krf+e+Gl+ +l++++  r ++ ++++++ea
  gi|298676219|ref|YP_003727968.1|  36 NALILLNCDEGEYqkqkhTNEVVSSVLNIGMRKIDRVKKRFVEDGLDMALNGKEYERTYEkKIDGDMEA 104
                                       589************************************************87755555559****997 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   4.6e-08   0.00016       6      48 ..      35      83 ..      31      85 .. 0.89
   2 ?   -2.2   0.1       1.1     4e+03      29      40 ..     139     150 ..     138     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.6e-08
                            HTH_23  6 eRlrillllae......GlsvreIAreLgvsrrTvyrwlkryreeGleg 48
                                      + ++ill ++e      +++ + ++  L++  r ++r++kr++e+Gl+ 
  gi|298676219|ref|YP_003727968.1| 35 QNALILLNCDEgeyqkqKHTNEVVSSVLNIGMRKIDRVKKRFVEDGLDM 83
                                      67899999997777788*****************************986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                            HTH_23  29 vsrrTvyrwlkr 40 
                                       +s+  + r+lk+
  gi|298676219|ref|YP_003727968.1| 139 ISYESIKRVLKK 150
                                       788999999886 PP

>> Clathrin  Region in Clathrin and VPS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   1.4e-05     0.051      30      60 ..      20      50 ..      11      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                                      HCCHHHCHTS--HHHHHHHHHHHHHTT-HHH CS
                          Clathrin 30 Lekvlkedskenpalqtallelyakyddpqe 60
                                      Le+++++++++++++q+al+ l+++++++q+
  gi|298676219|ref|YP_003727968.1| 20 LESIVSKGKHKSQKYQNALILLNCDEGEYQK 50
                                      9*************************99987 PP

>> ATG27  Autophagy-related protein 27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.3     0.001       3.7     114     169 ..      12      65 ..       5      68 .. 0.74
   2 ?    7.5   0.1   0.00094       3.4      90     146 ..      52     112 ..      46     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.001
                             ATG27 114 lkesdekeglrlelkggkygkkkqkaiieflCdekslkfksydeeeeeekdvlrle 169
                                       l+++++ke  ++  kg++ ++k q+a i + Cde + + +++++e    + vl++ 
  gi|298676219|ref|YP_003727968.1|  12 LTKEERKELESIVSKGKHKSQKYQNALILLNCDEGEYQKQKHTNEV--VSSVLNIG 65 
                                       444456677788889999999***********99888888877743..45556665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00094
                             ATG27  90 kdekdeitqvipiggksldpkvtrlkesdekeglrlelkggky........gkkkqkaiieflCd 146
                                       k+ ++ +++v++ig +++d   +r+     ++gl + l+g++y         + +   ii + C 
  gi|298676219|ref|YP_003727968.1|  52 KHTNEVVSSVLNIGMRKIDRVKKRF----VEDGLDMALNGKEYertyekkiDGDMEAHIIALSCS 112
                                       3345559999999888888888888....889**********99999988877888889999994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1049  (0.0585086); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 1190.40
//
Query:       gi|298676220|ref|YP_003727969.1|  [L=941]
Description: fibronectin type III domain-containing protein [Methanohalobium evestigatum Z-7303]
Scores for complete 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-05   23.5   1.6    5.2e-05   23.5   1.6    3.3  3  fn3              Fibronectin type III domain
  ------ inclusion threshold ------
        2.2    8.9   7.2        1.2    9.8   0.2    4.1  4  YtkA             YtkA-like


Domain annotation for each model (and alignments):
>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.89     8e+03      12      44 ..      55      87 ..      49     119 .. 0.61
   2 !   23.5   1.6   5.8e-09   5.2e-05       1      85 []     154     236 ..     154     236 .. 0.93
   3 ?   -3.4   0.1       1.5   1.3e+04      32      57 ..     646     675 ..     641     678 .. 0.50

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.89
                                      SSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTS CS
                               fn3 12 tstsltvsWeppkdgggpitgYeveyrekgsee 44
                                      ++ ++ ++ +p  d + ++++ +v+ +++++ +
  gi|298676220|ref|YP_003727969.1| 55 NNETAEINITPLADNSVDLSSISVTSQNTSNDG 87
                                      556666777777767777777777766654444 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 5.8e-09
                                       TCECEEEEEEESSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEEEEE CS
                               fn3   1 saPsnlsvsevtstsltvsWeppkdgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVqavn 77 
                                       ++P+++++s+ +   ++++W+  +dgg+ +  Y+v  +e+++++  +e+t +++t + t +gL++g+ Y  +V av 
  gi|298676220|ref|YP_003727969.1| 154 PQPTGITASP-SQGDINLNWNGVSDGGSGLKEYNVYRAETETGS-YTEITDSSDT-QETDSGLTEGKYYYYKVSAVD 227
                                       6899******.888*********************999999998.9999999999.9999***************** PP

                                       TSE.EEEEE CS
                               fn3  78 ggg.egpes 85 
                                        +g egp s
  gi|298676220|ref|YP_003727969.1| 228 YAGnEGPNS 236
                                       999888766 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.5
                                       EEEEEEEETTSTS......TEEEEEECSTSSE CS
                               fn3  32 gYeveyrekgsee......ewneftvprttts 57 
                                       +  v++r +++++      ++ +f v++t++s
  gi|298676220|ref|YP_003727969.1| 646 N--VTVRAQDNTDskneniKEWSFEVDSTEPS 675
                                       3..44444444432255555555666666655 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00013       1.2      33      85 ..     482     531 ..     447     532 .. 0.70
   2 ?   -2.0   0.0      0.64   5.8e+03      66      80 ..     610     625 ..     547     629 .. 0.66
   3 ?   -0.1   0.3      0.17   1.5e+03      19      42 ..     658     683 ..     642     713 .. 0.67
   4 ?   -3.4   0.0       1.8   1.6e+04      19      52 ..     753     787 ..     741     791 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00013
                              YtkA  33 kpVedadvkvefwmpameGmeemttkvelke.sedGvYeaevnfsmeGtWqvql 85 
                                        + +d +v++++ + a   m+  + + ++++ s + vY a++  s +G+++v+l
  gi|298676220|ref|YP_003727969.1| 482 GETNDINVTITGAENA--EMD--NNNFSTEDsSAPYVYTATYESSTDGDYTVTL 531
                                       4445556666666664..344..6777777788*******************98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.64
                              YtkA  66 dGvYeae.vnfsmeGt 80 
                                       +  Y +  +nf+++Gt
  gi|298676220|ref|YP_003727969.1| 610 NKTYAGDhINFTESGT 625
                                       4467777778888876 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.17
                              YtkA  19 agen..tivvtvtqggkpVedadvkv 42 
                                       ++en  +++++v+ ++  Ve a+++ 
  gi|298676220|ref|YP_003727969.1| 658 KNENikEWSFEVDSTEPSVEHATIES 683
                                       33443368888888888888888764 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 1.8
                              YtkA  19 agenti.vvt..vtqggkpVe.dadvkvefwmpameGm 52 
                                        ++ +i +++   ++ g+ +e +++v+++ ++     m
  gi|298676220|ref|YP_003727969.1| 753 SNDYEIvEFNgiSDEAGNNIElNENVEINTFRRG---M 787
                                       3333431444557788888884556888888773...3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (941 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.50
# Mc/sec: 5708.74
//
Query:       gi|298676221|ref|YP_003727970.1|  [L=369]
Description: Gram-positive anchor protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00058   19.7   0.1     0.0012   18.7   0.1    1.5  1  Gram_pos_anchor  LPXTG cell wall anchor motif
     0.0018   18.4   1.3        1.6    8.9   0.2    2.8  2  MG4              Macroglobulin domain MG4
     0.0064   16.7   1.7      0.013   15.8   0.2    2.3  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
      0.022   14.8   0.1      0.022   14.8   0.1    3.1  4  Big_1            Bacterial Ig-like domain (group 1)
      0.023   15.0   0.6      0.088   13.2   0.0    2.2  2  Pollen_Ole_e_I   Pollen proteins Ole e I like
      0.026   15.1   2.2       0.12   12.9   0.7    2.5  2  SEP              SEP domain
       0.21   12.3   3.4       0.65   10.7   0.1    2.9  3  TTR-52           Transthyretin-like family
        0.7   10.4   3.6          2    8.9   1.9    2.5  2  Glyco_hydro_108  Glycosyl hydrolase 108
        1.2    9.3   4.4        3.2    7.9   3.2    2.3  2  Cupredoxin_1     Cupredoxin-like domain
        7.8    7.5   5.9        6.4    7.8   0.1    3.1  2  Pilin_N          Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   6.7e-07    0.0012      13      38 ..     340     366 ..     340     369 .] 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.7e-07
                                       XX.XXXXXXXXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor  13 Ge.ngnifltaaGllallggllLlvkr 38 
                                       Ge +g++++ta Glla+ +++++l+++
  gi|298676221|ref|YP_003727970.1| 340 GEsQGMPGFTAIGLLAAGASAAFLKRK 366
                                       6449*********99999999997766 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0027       4.9      25      79 ..      41      99 ..      37     118 .. 0.84
   2 !    8.9   0.2    0.0009       1.6      42      89 ..     143     190 ..     126     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0027
                               MG4 25 pdgspaknvpVkiealk.....seteekeslttdedGtakfsintpedaksltitvktkd 79
                                       dg+ ++++ Vkie+ +     ++++   s++td++G  k+  n  +d+k+l++ v  kd
  gi|298676221|ref|YP_003727970.1| 41 DDGNGVNGIKVKIET-DdgtklTNDKTYVSTKTDSEGYYKLKPNGLQDGKTLSLYVDGKD 99
                                      68999**********.4455677788888899**********999999999999887665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0009
                               MG4  42 seteekeslttdedGtakfsintpedaksltitvktkdpslpeenqat 89 
                                       s++e k+ + + ++G a+++i   +++ +++i+ + +d++ +e+++ +
  gi|298676221|ref|YP_003727970.1| 143 SDQETKQIKAELKNGKANTNIKQINKGDEVSIELESEDKDQKEQQSIK 190
                                       4455566666889***************************99888754 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   7.1e-06     0.013       2      43 ..      35      81 ..      35     117 .. 0.79
   2 ?   -2.2   0.1         3   5.4e+03      16      36 ..     202     221 ..     195     222 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.1e-06
                   CarboxypepD_reg  2 isGrVtdasgapiagatVtvtnadtg......tvastttdadGafrlr 43
                                      ++G+++d +g+++ g +V ++++d++      t  st+td++G+++l+
  gi|298676221|ref|YP_003727970.1| 35 VHGYIKD-DGNGVNGIKVKIETDDGTkltndkTYVSTKTDSEGYYKLK 81
                                      6889998.899**********76654555555789**********996 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3
                   CarboxypepD_reg  16 gatVtvtnadtgtvastttda 36 
                                        +++++t+  ++t+ +t+td+
  gi|298676221|ref|YP_003727970.1| 202 DVNIEITD-HGETKPETVTDS 221
                                       57777773.455666777775 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.2e-05     0.022      17      50 ..      42      80 ..      35      90 .. 0.85
   2 ?   -3.1   0.0       4.5   8.1e+03      45      55 ..     156     166 ..     150     170 .. 0.74
   3 ?   -1.2   0.1       1.2   2.1e+03      24      44 ..     201     221 ..     196     222 .. 0.75
   4 ?   -2.1   0.1       2.2     4e+03      21      43 ..     245     268 ..     241     269 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                             Big_1 17 ngnpvagatVtfsvsggals.....assgtTdanGkatv 50
                                      +gn v+g++V++++++g+ +       s++Td++G +  
  gi|298676221|ref|YP_003727970.1| 42 DGNGVNGIKVKIETDDGTKLtndktYVSTKTDSEGYYKL 80
                                      8***************66666999999********9875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.5
                             Big_1  45 nGkatvtltst 55 
                                       nGka ++++  
  gi|298676221|ref|YP_003727970.1| 156 NGKANTNIKQI 166
                                       88888888765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.2
                             Big_1  24 atVtfsvsg.galsassgtTda 44 
                                       + V++++++ g +  ++++Td+
  gi|298676221|ref|YP_003727970.1| 201 QDVNIEITDhGET-KPETVTDS 221
                                       6789999996666.66777775 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2.2
                             Big_1  21 vagatVtfsvsggals.assgtTd 43 
                                       +  a++tf+v+++ +  ++ g Td
  gi|298676221|ref|YP_003727970.1| 245 IDSASITFEVDKDWVKeNNAGPTD 268
                                       567889999998544446666666 PP

>> Pollen_Ole_e_I  Pollen proteins Ole e I like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.9e-05     0.088      24      62 ..      46      83 ..      39      93 .. 0.79
   2 ?   -1.7   0.1       2.1   3.8e+03      25      55 ..     168     198 ..     153     222 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.9e-05
                    Pollen_Ole_e_I 24 lkgakvkveCknkkkeeeevklsasaktdknGyFkvelp 62
                                      ++g+kvk+e ++ +k +++ k+++s+ktd++Gy+k++ +
  gi|298676221|ref|YP_003727970.1| 46 VNGIKVKIETDDGTKLTND-KTYVSTKTDSEGYYKLKPN 83
                                      6899******995455444.789************9855 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                    Pollen_Ole_e_I  25 kgakvkveCknkkkeeeevklsasaktdknG 55 
                                       kg +v++e ++++k+++e ++++s + ++nG
  gi|298676221|ref|YP_003727970.1| 168 KGDEVSIELESEDKDQKEQQSIKSISFKSNG 198
                                       5666777766655666666666666666666 PP

>> SEP  SEP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.7   6.9e-05      0.12      19      75 ..     143     198 ..     140     199 .. 0.87
   2 ?    0.5   0.0      0.53   9.5e+02      45      65 ..     279     299 ..     246     306 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.9e-05
                               SEP  19 ddpenaeflesikkGevPeelekvekgeevevnledrrneeykppkkpkfkaFsGsG 75 
                                       +d+e++++ +++k+G++  ++++++kg+ev+++le  ++++ k++++ k  +F+ +G
  gi|298676221|ref|YP_003727970.1| 143 SDQETKQIKAELKNGKANTNIKQINKGDEVSIELE-SEDKDQKEQQSIKSISFKSNG 198
                                       68999*****************************9.667777777666788898877 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.53
                               SEP  45 geevevnledrrneeykppkk 65 
                                        +evev++ d+++ +y  + k
  gi|298676221|ref|YP_003727970.1| 279 WDEVEVSMFDETEDKYIYKAK 299
                                       47899******9999987654 PP

>> TTR-52  Transthyretin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00036      0.65       8      45 ..      43      82 ..      37      99 .. 0.83
   2 ?    0.9   0.1      0.41   7.4e+02      11      38 ..     200     227 ..     196     252 .. 0.77
   3 ?   -1.9   0.0       3.2   5.8e+03       9      35 ..     277     300 ..     275     324 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                                      T-GGSS-EEEEEEHHHH..TS--EEEEEE--TTSEEEEEE CS
                            TTR-52  8 gkpaknvkVkLwekdtl..dpddlldetkTdedGnFelsg 45
                                      g+ ++++kVk+  +d +  ++d+++ +tkTd++G+++l+ 
  gi|298676221|ref|YP_003727970.1| 43 GNGVNGIKVKIETDDGTklTNDKTYVSTKTDSEGYYKLKP 82
                                      566788999998876556799****************984 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.41
                                       GSS-EEEEEEHHHHTS--EEEEEE--TT CS
                            TTR-52  11 aknvkVkLwekdtldpddlldetkTded 38 
                                       a++v+++++++  ++p+++ d+  +d +
  gi|298676221|ref|YP_003727970.1| 200 AQDVNIEITDHGETKPETVTDSGDSDTE 227
                                       7889999999877788888888888764 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.2
                                       -GGSS-EEEEEEHHHHTS--EEEEEE- CS
                            TTR-52   9 kpaknvkVkLwekdtldpddlldetkT 35 
                                       +   +v+V+++++    +d+ + ++kT
  gi|298676221|ref|YP_003727970.1| 277 DDWDEVEVSMFDET---EDKYIYKAKT 300
                                       56678899999973...5666666666 PP

>> Glyco_hydro_108  Glycosyl hydrolase 108
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.9    0.0011         2       5      40 ..     114     149 ..     112     242 .. 0.83
   2 ?   -0.3   0.0      0.83   1.5e+03      18      45 ..     263     285 ..     258     300 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                                       CHCCH-EEE-TCGGCG-EECTEEHHHCCCTT-BS.. CS
                   Glyco_hydro_108   5 lahEGgyvndpkDkGGeTnkGItkktlralrkekai 40 
                                       ++hEG y  d +D  G +  GI++    + ++e+++
  gi|298676221|ref|YP_003727970.1| 114 VNHEGNYLSDSSDDDGGSSGGISAPGTGKSDQETKQ 149
                                       68*****99999999999****99877666544432 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.83
                                       GCG-EECTEEHHHCCCTT-BS....-CC CS
                   Glyco_hydro_108  18 kGGeTnkGItkktlralrkekaidadvk 45 
                                       + G+T  G+ + + +++++ +     v 
  gi|298676221|ref|YP_003727970.1| 263 NAGPTDVGVKRFHGDDWDEVE-----VS 285
                                       569999999999999995544.....33 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.5   4.4e+03      34      42 ..      46      54 ..       9      81 .. 0.51
   2 ?    7.9   3.2    0.0018       3.2      15      65 ..     142     193 ..     135     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.5
                      Cupredoxin_1 34 Pskievkag 42
                                       + i+vk +
  gi|298676221|ref|YP_003727970.1| 46 VNGIKVKIE 54
                                      444444433 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0018
                      Cupredoxin_1  15 aaaaaektveitvkdggfePskievkagekvklkiknkdktp.eefesedlg 65 
                                       ++++++k+++ ++k+g+ + +  ++++g +v+++++ +dk   e+ ++++++
  gi|298676221|ref|YP_003727970.1| 142 KSDQETKQIKAELKNGKANTNIKQINKGDEVSIELESEDKDQkEQQSIKSIS 193
                                       45788999*******************************9974444444444 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0036       6.4      15      79 ..       7      73 ..       5      75 .. 0.71
   2 ?    0.2   1.5      0.84   1.5e+03      57      57 ..     192     192 ..     135     257 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0036
                           Pilin_N 15 itvIlaAviaafvlgl.asneekapqasievkidssastgkna..vslehkgGdsidtkdlkivlnse 79
                                      +t+++  ++ ++++g  + +++ +p   ++  i+++++   n   v++e ++G  ++++++ + ++ +
  gi|298676221|ref|YP_003727970.1|  7 LTILITIFLFVSMVGAaSADTNPTPPHLVHGYIKDDGNG-VNGikVKIETDDGTKLTNDKTYVSTKTD 73
                                      677777778888888855555566666665555555554.44469**************999988765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.84
                           Pilin_N  57 v 57 
                                       +
  gi|298676221|ref|YP_003727970.1| 192 I 192
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1253  (0.0698868); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2205.79
//
Query:       gi|298676222|ref|YP_003727971.1|  [L=43]
Description: hypothetical protein Metev_2365 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 309.07
//
Query:       gi|298676223|ref|YP_003727972.1|  [L=2559]
Description: hypothetical protein Metev_2366 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0023   18.2   1.2     0.0023   18.2   1.2   11.5 12  DUF4625   Domain of unknown function (DUF4625)
     0.0033   18.1  18.8     0.0046   17.7   9.0   18.0 19  Big_7     Bacterial Ig domain
     0.0049   16.3   1.0     0.0049   16.3   1.0    2.0  2  DUF1616   Protein of unknown function (DUF1616)
  ------ inclusion threshold ------
        3.3    7.7   8.2        6.7    6.7   0.0    5.3  4  Y_Y_Y     Y_Y_Y domain
        4.9    6.5   7.4        4.7    6.6   0.1    3.9  3  DUF5462   Family of unknown function (DUF5462)
        5.3    6.8   8.9        4.5    7.1   0.0    5.2  6  Big_3_4   Domain of unknown function


Domain annotation for each model (and alignments):
>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.18   5.3e+02      88     130 ..     193     239 ..     151     242 .. 0.75
   2 !   18.2   1.2   7.6e-07    0.0023      10      82 ..     242     310 ..     226     335 .. 0.79
   3 !   11.9   1.2   6.8e-05       0.2      10      64 ..     347     400 ..     330     440 .. 0.79
   4 ?   -2.1   0.1       1.4   4.1e+03      10      61 ..     562     605 ..     555     644 .. 0.61
   5 ?   -1.4   0.1      0.84   2.5e+03      35      62 ..     820     849 ..     803     879 .. 0.79
   6 ?   -1.5   0.0      0.92   2.8e+03      38      84 ..    1301    1351 ..    1273    1365 .. 0.63
   7 ?    1.2   0.0      0.13   3.9e+02      38      85 ..    1403    1448 ..    1374    1467 .. 0.70
   8 ?    2.1   0.7     0.069   2.1e+02       6      55 ..    1627    1678 ..    1609    1709 .. 0.69
   9 ?   -1.6   0.0      0.99     3e+03      11      47 ..    1796    1832 ..    1788    1879 .. 0.67
  10 ?    2.7   1.0     0.046   1.4e+02      87     125 ..    1941    1979 ..    1828    1985 .. 0.80
  11 ?    1.3   0.6      0.13   3.9e+02      10      87 ..    1985    2058 ..    1979    2090 .. 0.61
  12 ?    2.8   0.5     0.045   1.3e+02      56      95 ..    2152    2207 ..    2078    2215 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.18
                           DUF4625  88 skkeyelheeieiPad....aeaGdYhlvirvtDasGneteesreik 130
                                        +k  + + +i+iP++     e G   +++  +D++G    +  +++
  gi|298676223|ref|YP_003727972.1| 193 VAKGGSTKLSITIPESetenLESGTHTITVETLDNDGEGDTTTSQVE 239
                                       4455677899999976555599*************998877776665 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 7.6e-07
                           DUF4625  10 edtekPvidllevsaepeeeevlkiGetlhfeaklsdnealasykvdihnnfDhhshsseakegekewsfeks 82 
                                        d+e P i+ ++++ + + ++v+++G+t+++ a++sd  a++s++ d  ++fD  + + + +    + ++  +
  gi|298676223|ref|YP_003727972.1| 242 VDQEPPDISNVTIDDDDDGNDVVATGDTVTLSADVSDASAISSVTFDA-SDFDAGTVQLSGS---GNGTYTTD 310
                                       499********************************************9.99*9988777653...34444444 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 6.8e-05
                           DUF4625  10 edtekPvidllevsaepeeeevlkiGetlhfeaklsdnealasykvdihnnfDhh 64 
                                        d++kP i+ ++++ e + +  ++  +++++ a++sd + ++s++ d  n f   
  gi|298676223|ref|YP_003727972.1| 347 VDNTKPDISNVNITDETDGNGNVTANDSVNITANVSDANGIKSVTADA-NSFGLS 400
                                       69******************************************9997.666544 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 1.4
                           DUF4625  10 edtekPvidllevsaepeeeevlkiGetlhfeaklsdnealasykvdihnnf 61 
                                       +d  +Pvi++++        ++   G++++++++ s++  ++++++   +n 
  gi|298676223|ref|YP_003727972.1| 562 TDGANPVISDFT--------ATNPSGQSINIKFNSSEELSIKNVSITGPENV 605
                                       577888888883........33456777777777777777777777655555 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 0.84
                           DUF4625  35 Get.lhfeaklsdnealasykvdihnnf.D 62 
                                       G++  ++ ++l+d +++ +++v+++++  D
  gi|298676223|ref|YP_003727972.1| 820 GDEsGTVTINLNDTVNVDNITVSLQSDGiD 849
                                       4444788999************99776544 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 0.92
                           DUF4625   38 lhfeaklsdnealasykvdihnnfDhhshsseakeg......ekewsfeksyd 84  
                                         ++ ++++  e+la + +d+  + D+  ++ + ++       + ++ +  +y+
  gi|298676223|ref|YP_003727972.1| 1301 QNVSIEINSSEKLATIGIDL--DIDELGDKLTLDKSnftksgDGPYIYTATYE 1351
                                        45667777778888877776..4444444444443333445566777766664 PP

  == domain 7  score: 1.2 bits;  conditional E-value: 0.13
                           DUF4625   38 lhfeaklsdnealasykvdih.nnfDhhshsseakegekewsfeksydl 85  
                                         +++++++  e+l+ ++v ++ + fD+++ s ++   + ++ + ++y++
  gi|298676223|ref|YP_003727972.1| 1403 REINVTINTSEELSTINVGLDgKTFDENDFSLDS---NAPYIYTHTYSA 1448
                                        457888999999******9973457888888776...689999999854 PP

  == domain 8  score: 2.1 bits;  conditional E-value: 0.069
                           DUF4625    6 ddeeedtekPvidllevsaepeeeevl.kiGet.lhfeaklsdnealasykv 55  
                                        d++  d++kP+++++ +++e ++ +++ + ++t l+  ++++dn++    ++
  gi|298676223|ref|YP_003727972.1| 1627 DEKMDDSTKPTVEITGLTQETTDLSSVnYADSTtLTGTVEITDNDEDTTGSI 1678
                                        3444688999999998888755544440444444677777888876555444 PP

  == domain 9  score: -1.6 bits;  conditional E-value: 0.99
                           DUF4625   11 dtekPvidllevsaepeeeevlkiGetlhfeaklsdn 47  
                                        d+ kP i+ ++++++p + + +   +t++++++ s n
  gi|298676223|ref|YP_003727972.1| 1796 DNLKPGISSASITNAPINVSDVGDTQTVTLNFNESMN 1832
                                        6678888888777766665555444445555444444 PP

  == domain 10  score: 2.7 bits;  conditional E-value: 0.046
                           DUF4625   87 gskkeyelheeieiPadaeaGdYhlvirvtDasGnetee 125 
                                        gs+k  e++e+    + a +Gd +++++++D +Gn+  +
  gi|298676223|ref|YP_003727972.1| 1941 GSNKIDEANESSWDSTKASDGDIDFTLTAEDDAGNTGTV 1979
                                        4445555566655667899****************8765 PP

  == domain 11  score: 1.3 bits;  conditional E-value: 0.13
                           DUF4625   10 edtekPvidllevsaepeeeevlkiGetlhfeaklsdnealasykv..dihnnfDhhshsseakeg..ekewsfe 80  
                                         d+++Pvi+ ++v+ +          e+ ++ ++++  e+la + +  di+++ D+ + + ++     + ++ + 
  gi|298676223|ref|YP_003727972.1| 1985 VDNTEPVINEFKVTDPDV--------ENQNISIEVNSSEQLATIGIdlDIDEEGDEAALDLNNFTKsgDGPYIYT 2051
                                        578888888884444211........2235556666666666665511566666666655543222447777777 PP

                           DUF4625   81 ksydlsg 87  
                                         +y+ s+
  gi|298676223|ref|YP_003727972.1| 2052 ATYEGSK 2058
                                        7775444 PP

  == domain 12  score: 2.8 bits;  conditional E-value: 0.045
                           DUF4625   56 dihnnfDhhshsseakeg................ekewsfeksydlsgskkeyelh 95  
                                        +++  fD  +h+ + ++g                +kewsfe + +++  kk+y ++
  gi|298676223|ref|YP_003727972.1| 2152 EVEFTFDPAAHDVTLNDGevivnvsatdtksntqTKEWSFEVDTKAPDLKKTYPIN 2207
                                        45556788888888888888888888888888889999999999999999887665 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   3.8     0.012        35      12      70 .]     150     222 ..     142     222 .. 0.71
   2 !    6.5   0.4    0.0047        14       4      43 ..     202     248 ..     200     258 .. 0.82
   3 !   16.4  10.3   3.9e-06     0.012      11      70 .]     261     326 ..     251     326 .. 0.80
   4 !   17.7   9.0   1.5e-06    0.0046       3      70 .]     357     433 ..     356     433 .. 0.83
   5 ?   -5.1   3.6         6   1.8e+04      16      42 ..     515     541 ..     500     562 .. 0.51
   6 !   16.5   2.1   3.6e-06     0.011      13      67 ..     575     636 ..     572     638 .. 0.87
   7 ?   -2.7   0.2       3.5   1.1e+04      12      31 ..     772     792 ..     767     798 .. 0.73
   8 ?   -5.0   5.8         6   1.8e+04      20      42 ..     825     847 ..     813     945 .. 0.73
   9 ?   -0.9   1.9      0.97   2.9e+03      22      68 ..    1100    1152 ..    1082    1155 .. 0.76
  10 ?   -2.7   0.2       3.5   1.1e+04      44      67 ..    1233    1255 ..    1203    1263 .. 0.59
  11 ?    0.7   0.4       0.3   8.9e+02      43      69 ..    1330    1361 ..    1290    1371 .. 0.66
  12 !    9.6   1.8    0.0005       1.5      13      69 ..    1396    1457 ..    1382    1458 .. 0.80
  13 ?   -2.7   0.8       3.6   1.1e+04      23      65 ..    1537    1578 ..    1526    1580 .. 0.75
  14 ?  -13.9  20.0         6   1.8e+04      17      60 ..    1717    1766 ..    1635    1776 .. 0.75
  15 ?   -5.6   5.7         6   1.8e+04       7      60 ..    1810    1868 ..    1804    1879 .. 0.53
  16 ?   -1.8   1.0       1.9   5.7e+03      44      60 ..    1955    1971 ..    1899    1985 .. 0.48
  17 ?    0.2   4.5      0.44   1.3e+03      15      69 ..    2003    2065 ..    1954    2066 .. 0.78
  18 ?   -0.3   0.2      0.64   1.9e+03      16      42 ..    2168    2181 ..    2153    2217 .. 0.62
  19 ?   -0.6   0.4      0.81   2.4e+03      13      32 ..    2271    2293 ..    2261    2335 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.012
                                       --EB.TSEEEEEEEEE-SS-E...EEEEEEETTEE........EEEE-SSSEEEEEE-.....-...SEEEEEEE CS
                             Big_7  12 atvs.ggtvtisasAsddggv...skVefyvdgtl.g......lgtdtsapysltwtt.....taltagthtltV 70 
                                       +++s g++ t++++ ++ gg+    + ++++d ++ +      +++   +   l++t+     ++l++gtht+tV
  gi|298676223|ref|YP_003727972.1| 150 EKISaGDSATVQVDIENTGGIqykYNTVLSLDSSSiKskttesVAKG--GSTKLSITIpesetENLESGTHTITV 222
                                       5789999**************77667788999888444443334444..4444444445576455*********9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0047
                                       EEEE--TT--EB.TSEEEEEEEEE-S.....S-EEEEEEEETTEE.. CS
                             Big_7   4 titsPangatvs.ggtvtisasAsdd.....ggvskVefyvdgtl.g 43 
                                       +it P++ ++   +gt ti++++ d+     ++ s+Ve+ vd ++  
  gi|298676223|ref|YP_003727972.1| 202 SITIPESETENLeSGTHTITVETLDNdgegdTTTSQVEVIVDQEPpD 248
                                       89999999988889*********999877777779999999987644 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 3.9e-06
                                       T--EB.TSEEEEEEEEE-SS-EEEEEEEETTEE.....EEEE-SSSEEEEEE--....SEEEEEEE CS
                             Big_7  11 gatvs.ggtvtisasAsddggvskVefyvdgtl.g...lgtdtsapysltwttta.ltagthtltV 70 
                                       +++v  g+tvt+sa++sd++++s+V+f + +   g   l+ + +++y++ ++  +  t+g++++tV
  gi|298676223|ref|YP_003727972.1| 261 NDVVAtGDTVTLSADVSDASAISSVTFDASDFDaGtvqLSGSGNGTYTTDIDVGSsPTEGNQSVTV 326
                                       44677899*******************76644333333999999*********8878999999998 PP

  == domain 4  score: 17.7 bits;  conditional E-value: 1.5e-06
                                       EEEEE--TT-.-EB.TSEEEEEEEEE-SS-EEEEEEEET.....TEE...EEEE-SSSEEEEEE--.....SEEEEE CS
                             Big_7   3 vtitsPanga.tvs.ggtvtisasAsddggvskVefyvd.....gtlg..lgtdtsapysltwttta..ltagthtl 68 
                                       v+it  ++g+ +v+ +++v+i+a++sd++g+++V+  ++        +  l+++ +++y+ t+t ++  ++ g+++l
  gi|298676223|ref|YP_003727972.1| 357 VNITDETDGNgNVTaNDSVNITANVSDANGIKSVTADANsfglsS--QvsLTNNGDGTYTKTITVNSklAKLGSQSL 431
                                       5666666666688999*******************9999664421..256999999*********88889999**99 PP

                                       EE CS
                             Big_7  69 tV 70 
                                       tV
  gi|298676223|ref|YP_003727972.1| 432 TV 433
                                       98 PP

  == domain 5  score: -5.1 bits;  conditional E-value: 6
                                       TSEEEEEEEEE-SS-EEEEEEEETTEE CS
                             Big_7  16 ggtvtisasAsddggvskVefyvdgtl 42 
                                       g++vt++ s + d++ s+  +  d t 
  gi|298676223|ref|YP_003727972.1| 515 GDQVTVELSSEVDNTASTTNVTYDSTA 541
                                       444555555544444444444444444 PP

  == domain 6  score: 16.5 bits;  conditional E-value: 3.6e-06
                                       -EB.TSEEEEEEEEE-SS-EEEEEE......EETTEE.EEEE-SSSEEEEEE--....SEEEE CS
                             Big_7  13 tvs.ggtvtisasAsddggvskVef......yvdgtlglgtdtsapysltwttta.ltagtht 67 
                                       t + g++++i+ + s   ++++V +      y++    ++t +sapy++t t ++  ++g +t
  gi|298676223|ref|YP_003727972.1| 575 TNPsGQSINIKFNSSEELSIKNVSItgpenvYLNSGF-STTENSAPYEYTATCDTiTSDGDYT 636
                                       556699*****************88555555788888.*****************999**999 PP

  == domain 7  score: -2.7 bits;  conditional E-value: 3.5
                                       --EBTSEEEEEEEEE-S.S-E CS
                             Big_7  12 atvsggtvtisasAsdd.ggv 31 
                                       ++v  +++ti ++ sd+ +g 
  gi|298676223|ref|YP_003727972.1| 772 EVVGVDKTTIDVTFSDSgSGL 792
                                       555567899******996665 PP

  == domain 8  score: -5.0 bits;  conditional E-value: 6
                                       EEEEEEE-SS-EEEEEEEETTEE CS
                             Big_7  20 tisasAsddggvskVefyvdgtl 42 
                                       t++ + +d ++v++++++++   
  gi|298676223|ref|YP_003727972.1| 825 TVTINLNDTVNVDNITVSLQSDG 847
                                       67777777777777777765433 PP

  == domain 9  score: -0.9 bits;  conditional E-value: 0.97
                                        EEEEE-SS-EEEEEEEETTEE........EEEE-SSSEEEEEE--...SEEEEE CS
                             Big_7   22 sasAsddggvskVefyvdgtl.g......lgtdtsapysltwtttaltagthtl 68  
                                        s++  d+g+++k +f++ + +        ++ dts++ ++++  + ++a + t+
  gi|298676223|ref|YP_003727972.1| 1100 SGTGLDNGTIDKNDFSLSTGViSsiepsiTSGDTSGTVTINLENK-VDAENVTV 1152
                                        46667889********99999768999988888888888888775.44444444 PP

  == domain 10  score: -2.7 bits;  conditional E-value: 3.5
                                        EEEE-SSSEEEEEE--...SEEEE CS
                             Big_7   44 lgtdtsapysltwtttaltagtht 67  
                                        ++ dts++ ++++  + ++a t t
  gi|298676223|ref|YP_003727972.1| 1233 INGDTSGTVTINLKNK-VNADTVT 1255
                                        5556666666655554.3333333 PP

  == domain 11  score: 0.7 bits;  conditional E-value: 0.3
                                        ......EEEE-SSSEEEEEE--...SEEEEEE CS
                             Big_7   43 g.....lgtdtsapysltwtttaltagthtlt 69  
                                        +     ++++ ++py +t t +   +g +t t
  gi|298676223|ref|YP_003727972.1| 1330 TldksnFTKSGDGPYIYTATYEGSVDGKYTAT 1361
                                        24444477888899999999988888888876 PP

  == domain 12  score: 9.6 bits;  conditional E-value: 0.0005
                                        -EB.TSEEEEEEEEE-SS-EEEEEEEETTEE.....EEEE-SSSEEEEEE--...SEEEEEE CS
                             Big_7   13 tvs.ggtvtisasAsddggvskVefyvdgtl.g...lgtdtsapysltwtttaltagthtlt 69  
                                        +v+  +  +i+++ + + + s++ + +dg++     ++ d++apy +t t +a+++g +t t
  gi|298676223|ref|YP_003727972.1| 1396 KVNnPTGREINVTINTSEELSTINVGLDGKTfDendFSLDSNAPYIYTHTYSAGSDGDYTAT 1457
                                        5554444456666666677***********987899999*********************87 PP

  == domain 13  score: -2.7 bits;  conditional E-value: 3.6
                                        EEEE-SS-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEE CS
                             Big_7   23 asAsddggvskVefyvdgtlglgtdtsapysltwtttaltagt 65  
                                        a+ s +++v +++++ ++   + ++ +++  +t++ ++ ++g+
  gi|298676223|ref|YP_003727972.1| 1537 AEFSYSTQVLNITLSENNDA-YLKNGNDGLAVTLNNDNISDGS 1578
                                        55666677888888888888.7888888888888888888887 PP

  == domain 14  score: -13.9 bits;  conditional E-value: 6
                                        SEEEEEEEEE-S..S-EEEEEE..EETTEE.....EEEE-SSSEEEEEE--. CS
                             Big_7   17 gtvtisasAsdd..ggvskVef..yvdgtlg....lgtdtsapysltwttta 60  
                                        g+  ++ s +d+  ++vs++++  + d+++g    +gt  s+p+ +t + t+
  gi|298676223|ref|YP_003727972.1| 1717 GN--VTLSSTDNtgDSVSSITWkfSTDTSSGtyseIGTGDSYPWDTTEQVTD 1766
                                        44..444555555599999966214555553577788888888888776665 PP

  == domain 15  score: -5.6 bits;  conditional E-value: 6
                                        E--TT--EB.TSEEEEEEEEE-SS-EE.EEEEEETTEE......EEEE-SSSEEEEEE--. CS
                             Big_7    7 sPangatvs.ggtvtisasAsddggvs.kVefyvdgtl.g....lgtdtsapysltwttta 60  
                                        +P n + v  ++tvt++ + s +++vs +V++   +++      +++d  + ++ t+t+++
  gi|298676223|ref|YP_003727972.1| 1810 APINVSDVGdTQTVTLNFNESMNTSVSpSVQITGTNKTySveesSYSD--SVWEGTVTIDD 1868
                                        688888888677777777777777774244443333332233222222..55666666655 PP

  == domain 16  score: -1.8 bits;  conditional E-value: 1.9
                                        EEEE-SSSEEEEEE--. CS
                             Big_7   44 lgtdtsapysltwttta 60  
                                        +++ +++   +t+t+++
  gi|298676223|ref|YP_003727972.1| 1955 STKASDGDIDFTLTAED 1971
                                        33333333333333322 PP

  == domain 17  score: 0.2 bits;  conditional E-value: 0.44
                                        BTSEEEEEEEEE-SS-EEEEEEEETTEE.........EEEE-SSSEEEEEE--...SEEEEEE CS
                             Big_7   15 sggtvtisasAsddggvskVefyvdgtl.g.......lgtdtsapysltwtttaltagthtlt 69  
                                        ++++++i+++ s + +   +++ +d +  +       ++++ ++py +t t +  ++gt++ t
  gi|298676223|ref|YP_003727972.1| 2003 ENQNISIEVNSSEQLATIGIDLDIDEEGdEaaldlnnFTKSGDGPYIYTATYEGSKDGTYNAT 2065
                                        3456666666666655555555555443335688777888889**********9******976 PP

  == domain 18  score: -0.3 bits;  conditional E-value: 0.64
                                        TSEEEEEEEEE-SS-EEEEEEEETTEE CS
                             Big_7   16 ggtvtisasAsddggvskVefyvdgtl 42  
                                         g v +++sA+d              +
  gi|298676223|ref|YP_003727972.1| 2168 DGEVIVNVSATDT-------------K 2181
                                        5555555555554.............3 PP

  == domain 19  score: -0.6 bits;  conditional E-value: 0.81
                                        -EBTSEEEEEEEEE-S..S-E.E CS
                             Big_7   13 tvsggtvtisasAsdd..ggv.s 32  
                                        t+++g+v +++sA+d   + + +
  gi|298676223|ref|YP_003727972.1| 2271 TFEEGQVVVNVSANDTnsNKMnK 2293
                                        55567777777777764333342 PP

>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.89   2.7e+03     140     177 ..       7      44 ..       5      62 .. 0.75
   2 !   16.3   1.0   1.6e-06    0.0049     181     258 ..     142     223 ..     108     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.89
                           DUF1616 140 alnvlLvvsivlavaalgyavvaPkegekfTelyllge 177
                                       +l+vl+v+s+ + + al    ++++ g +   +++ g+
  gi|298676223|ref|YP_003727972.1|   7 ILSVLMVLSVFITGIALTATTASAAGGPTVDYVEISGN 44 
                                       68999999999999999888887776666555555555 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.6e-06
                           DUF1616 181 elvaenypteltagesqevivgieNhEheevnYtvvvllqev.tdeeevevlerteldrrevtladnet...weqel 253
                                            n p++++ag+s +v+v ieN ++ + +Y++v+ l+ +  +++++e +++   ++ ++t+ + et   ++ ++
  gi|298676223|ref|YP_003727972.1| 142 SILNLNAPEKISAGDSATVQVDIENTGGIQYKYNTVLSLDSSsIKSKTTESVAKGGSTKLSITIPESETenlESGTH 218
                                       5566799*********************************99877778888899999999****9999954445556 PP

                           DUF1616 254 evepe 258
                                       ++++e
  gi|298676223|ref|YP_003727972.1| 219 TITVE 223
                                       66665 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0022       6.7      34      65 ..     211     242 ..     180     243 .. 0.87
   2 ?    1.5   0.1     0.095   2.8e+02      24      50 ..     394     422 ..     385     434 .. 0.72
   3 ?   -3.5   0.2       3.5   1.1e+04      29      43 ..    1343    1360 ..    1332    1367 .. 0.72
   4 ?   -1.9   0.2       1.2   3.5e+03      45      65 ..    2281    2299 ..    2275    2310 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0022
                                       ES--SEEEEEEEEEEETTS-B-SS-EEEEEEE CS
                             Y_Y_Y  34 tnlppGdYtlkVkakdndgqwnyditslsfti 65 
                                        nl++G+ t++V++ dndg+ +  + ++++++
  gi|298676223|ref|YP_003727972.1| 211 ENLESGTHTITVETLDNDGEGDTTTSQVEVIV 242
                                       79******************998888888876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.095
                                       ESSTS...EEEEES--SEEEEEEEEEEET CS
                             Y_Y_Y  24 asdysq..easytnlppGdYtlkVkakdn 50 
                                       a++++   ++s tn+  G+Yt ++ + ++
  gi|298676223|ref|YP_003727972.1| 394 ANSFGLssQVSLTNNGDGTYTKTITVNSK 422
                                       44444466************976666555 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 3.5
                                        ....EEEEES--SEEEEE CS
                             Y_Y_Y   29 q...easytnlppGdYtl 43  
                                        +   +a+y     G+Yt 
  gi|298676223|ref|YP_003727972.1| 1343 PyiyTATYEGSVDGKYTA 1360
                                        255689999999****95 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 1.2
                                        EEEEETTS-B-SS-EEEEEEE CS
                             Y_Y_Y   45 Vkakdndgqwnyditslsfti 65  
                                        V+a d ++++ +  ++++fti
  gi|298676223|ref|YP_003727972.1| 2281 VSANDTNSNKMN--KKWNFTI 2299
                                        444444444433..6777776 PP

>> DUF5462  Family of unknown function (DUF5462)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0016       4.7      62     110 ..     202     250 ..     192     276 .. 0.79
   2 ?    0.9   0.7     0.088   2.6e+02      30      63 ..     366     399 ..     365     447 .. 0.65
   3 ?   -1.5   0.1      0.48   1.4e+03      73     115 ..     908     950 ..     895     954 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0016
                           DUF5462  62 sLvirnAelrkasggevlvtvketlpdgsearvtlkveLvvdgkkvsis 110
                                       s++i + e  + ++g++ +tv+ +  dg+   +t +ve++vd     is
  gi|298676223|ref|YP_003727972.1| 202 SITIPESETENLESGTHTITVETLDNDGEGDTTTSQVEVIVDQEPPDIS 250
                                       6899999999*************9999999999*********9754333 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.088
                           DUF5462  30 NGqvqgnsvvkvtrtlsdpvLfraqekdellksL 63 
                                       NG+v++n+ v++t   sd   +++  +d     L
  gi|298676223|ref|YP_003727972.1| 366 NGNVTANDSVNITANVSDANGIKSVTADANSFGL 399
                                       9************999998777666555544444 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.48
                           DUF5462  73 asggevlvtvketlpdgsearvtlkveLvvdgkkvsisvkqrg 115
                                       + +  +++ v  +   ++ ++vt++++  vd   v++s ++ g
  gi|298676223|ref|YP_003727972.1| 908 NTKTDFSIDVSDINNGENRGNVTINLNNPVDTNTVNVSLQNDG 950
                                       566778889999887789999***************9999887 PP

>> Big_3_4  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2      0.26   7.8e+02      11      39 ..     237     265 ..     233     270 .. 0.91
   2 ?   -4.0   0.0       4.2   1.2e+04      32      49 ..    1450    1468 ..    1440    1469 .. 0.81
   3 ?   -2.0   0.1         1     3e+03      20      48 ..    1856    1888 ..    1840    1903 .. 0.59
   4 ?    7.1   0.0    0.0015       4.5      32      87 ..    1959    2014 ..    1943    2030 .. 0.79
   5 ?   -1.1   0.0       0.5   1.5e+03      32      48 ..    2167    2183 ..    2163    2196 .. 0.85
   6 ?   -3.4   0.0       2.7     8e+03      33      49 ..    2274    2290 ..    2272    2328 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.26
                           Big_3_4  11 gievefdrseGdiWnvpvPldedGeyvve 39 
                                        +ev+ d+   di nv++  d dG+ vv+
  gi|298676223|ref|YP_003727972.1| 237 QVEVIVDQEPPDISNVTIDDDDDGNDVVA 265
                                       57999********************9997 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 4.2
                           Big_3_4   32 edGeyvvel.laedeaGnq 49  
                                         dG+y   l  a+d aGn 
  gi|298676223|ref|YP_003727972.1| 1450 SDGDYTATLnTAKDAAGND 1468
                                        6899999884689999996 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1
                           Big_3_4   20 eGdiWnvpvPldedGeyvvell....aedeaGn 48  
                                           +W+ +v +d d e + + +    aed aGn
  gi|298676223|ref|YP_003727972.1| 1856 SDSVWEGTVTIDDDNEDLTAEInvsgAEDLAGN 1888
                                        345677777777777655432212235666666 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0015
                           Big_3_4   32 edGeyvvellaedeaGnqayiakllyvvdienicvevrpldylsekleteftieav 87  
                                         dG+    l aed+aGn   ++    v ++e +  e ++ d   e+++  ++++  
  gi|298676223|ref|YP_003727972.1| 1959 SDGDIDFTLTAEDDAGNTGTVTGTATVDNTEPVINEFKVTDPDVENQNISIEVNSS 2014
                                        5677777899***************************9999888888888877753 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 0.5
                           Big_3_4   32 edGeyvvellaedeaGn 48  
                                        +dGe +v++ a d   n
  gi|298676223|ref|YP_003727972.1| 2167 NDGEVIVNVSATDTKSN 2183
                                        799*******9998777 PP

  == domain 6  score: -3.4 bits;  conditional E-value: 2.7
                           Big_3_4   33 dGeyvvellaedeaGnq 49  
                                        +G+ vv++ a+d   n+
  gi|298676223|ref|YP_003727972.1| 2274 EGQVVVNVSANDTNSNK 2290
                                        78888888888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.93u 0.27s 00:00:01.20 Elapsed: 00:00:00.54
# Mc/sec: 14179.09
//
Query:       gi|298676224|ref|YP_003727973.1|  [L=633]
Description: chromosome segregation ATPase-like protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-06   26.0  74.7      0.013   14.4  24.1    3.9  4  Spc7             Spc7 kinetochore protein
    1.2e-05   24.2  73.8    8.7e-05   21.4  34.1    2.3  2  AAA_13           AAA domain
    0.00049   20.7 100.6     0.0027   18.2  45.6    4.7  2  AAA_23           AAA domain
  ------ inclusion threshold ------
      0.015   15.6  76.1       0.23   11.8  12.9    4.4  4  OmpH             Outer membrane protein (OmpH-like)
       0.02   15.0   0.9       0.02   15.0   0.9    4.7  4  Spore_III_AB     Stage III sporulation protein AB (spore_III_
       0.28   11.0  51.7       0.19   11.5  15.5    2.4  2  ERM              Ezrin/radixin/moesin family
        0.4   10.8  84.2        1.1    9.3  13.5    4.5  4  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.43   11.0  41.9       0.14   12.7   8.9    4.9  5  T3SSipB          Type III cell invasion protein SipB
        1.6    9.0  65.7        0.5   10.6  14.9    5.0  5  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        1.6    9.1  64.9       0.35   11.3  24.0    3.9  4  Fez1             Fez1
        2.6    7.8  70.5      0.027   14.3  31.3    3.5  2  TACC_C           Transforming acidic coiled-coil-containing p
        2.9    5.9  76.1       0.68    8.0  36.0    2.1  2  HOOK             HOOK protein
        3.8    7.8  50.7      0.049   13.9   4.9    5.1  4  FliJ             Flagellar FliJ protein
        4.1    6.1  68.3       0.16   10.8  11.9    4.2  4  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
        4.3    6.6  84.1       0.69    9.2  23.2    3.9  3  GAS              Growth-arrest specific micro-tubule binding
        4.5    7.6   7.0        1.6    9.0   0.5    3.3  3  MHB              Haemophore, haem-binding
        9.3    6.3  62.3        2.5    8.1  11.3    5.1  5  Laminin_II       Laminin Domain II
        9.7    7.0  10.2        1.2    9.9   1.2    3.2  3  LTXXQ            LTXXQ motif family protein


Domain annotation for each model (and alignments):
>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   8.3    0.0018       1.8     220     283 ..     140     202 ..     118     207 .. 0.78
   2 !   13.3  29.5   2.8e-05     0.028     156     290 ..     147     289 ..     139     307 .. 0.78
   3 !   14.4  24.1   1.4e-05     0.013     137     277 ..     317     456 ..     314     459 .. 0.86
   4 !    5.8  14.2    0.0053       5.3     162     266 ..     419     508 ..     416     523 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0018
                              Spc7 220 kelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltg 283
                                       +++ +l++ql + +++i++ ++q ++le++++++ ++++ + +++++e+++l ee ++le+++ 
  gi|298676224|ref|YP_003727973.1| 140 TNIPDLKNQLSKYDSQIKDNENQLNTLENKLKNETELYK-NLSITRNEIEKLDEEKSKLEKEYT 202
                                       477888899999999999999999999999886666555.778899999999999999888764 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.8e-05
                              Spc7 156 elLekqeeeldellpeleeekaeleeeleklqe...aaeelesid..keeLee...lreelaelkaeieekkkelae 224
                                       ++L+k  +++++  ++l++ +++l++e e  ++    ++e+e++d  k +Le+   +++  +e ++e++e  ++l++
  gi|298676224|ref|YP_003727973.1| 147 NQLSKYDSQIKDNENQLNTLENKLKNETELYKNlsiTRNEIEKLDeeKSKLEKeytAKKIDDETNKEYKEAVNKLNK 223
                                       4555555555555555555555555555555555555566666554455666533366666789999999999**** PP

                              Spc7 225 lqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgwkivsls 290
                                        q+ ++ele+ki+  k++++elee  ++ e+ le+ ++ ++ +v++l++e k++ e+ + +i +++
  gi|298676224|ref|YP_003727973.1| 224 IQQSIKELENKINYNKKRYKELEETKQKYENDLEQVQHNENIDVNTLENEIKNINEKIDSNISKMK 289
                                       *********************************************************999999986 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 1.4e-05
                              Spc7 137 legLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelka 213
                                       +++L e+l+  + g + dk++Le+q++ l+++ ++l+ee ++l+++  + qe  ++ ++ +++e++++ +++ + ++
  gi|298676224|ref|YP_003727973.1| 317 IDSLAESLNCPFCGTNCDKSKLEEQKSHLTSIRDSLKEENKSLKQKSSEKQELIDSYKK-KENEINKINSKIIDTEN 392
                                       77899999999999*************************************98877544.78899999999999999 PP

                              Spc7 214 eieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevka 277
                                        i+e ++++++ q++l +++++  e ++  s+++ee++ +   + ++ +  + +++++k++ ++
  gi|298676224|ref|YP_003727973.1| 393 LISETNEQIKKAQNKLRDIKQQKIEQEDIVSKFKEEVETETADITNRLSKVNAQLESYKNKEDQ 456
                                       9999999999999999999999999999999999999988888877777777777777776655 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.0053
                              Spc7 162 eeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekiee 238
                                       e+ ++++++e+e+e a+++++l k +++ e+ ++ +++++++  e+ + +k++++e+k+++++l++++ +l++ki++
  gi|298676224|ref|YP_003727973.1| 419 EDIVSKFKEEVETETADITNRLSKVNAQLESYKN-KEDQINKSIENNRLNKEKYDELKTKIDDLNDKRSNLQKKINN 494
                                       4444555555555555555555444443333222.344444444444455555555555555555555555555555 PP

                              Spc7 239 lkeqkseleeeiaeaervleeckgwses 266
                                       +++               ++e+ +   +
  gi|298676224|ref|YP_003727973.1| 495 IEQ--------------NVRENFNNHIK 508
                                       444..............43333333333 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5  31.7   0.00068      0.68     285     444 ..     142     300 ..     130     311 .. 0.90
   2 !   21.4  34.1   8.7e-08   8.7e-05     255     450 ..     323     511 ..     311     520 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00068
                            AAA_13 285 qerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvk 361
                                       + +L++ ++k++s+++   ++l+++ ++ + + +  ++ +  ++e+e+l+e+  +l+++ +aK+ +  ++ e++++ 
  gi|298676224|ref|YP_003727973.1| 142 IPDLKNQLSKYDSQIKDNENQLNTLENKLKNETELYKNLSITRNEIEKLDEEKSKLEKEYTAKKIDDETNKEYKEAV 218
                                       7789******************99999988889999999999*********************************** PP

                            AAA_13 362 akiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeae 438
                                       +k+++i+++++e+++ i+ + ++ ++lee k++ +++le+  ++e   +++++++++k+++++i ++  ++k  ++ 
  gi|298676224|ref|YP_003727973.1| 219 NKLNKIQQSIKELENKINYNKKRYKELEETKQKYENDLEQVQHNEN-IDVNTLENEIKNINEKIDSNISKMKTLNTY 294
                                       ****************************************888876.788899999999999998888887777777 PP

                            AAA_13 439 lkklee 444
                                       +  ++e
  gi|298676224|ref|YP_003727973.1| 295 IDGIDE 300
                                       766665 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 8.7e-08
                            AAA_13 255 sdtCpFCgqplpaerkaaLeahFddefeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeae 331
                                       s +CpFCg + +++  ++ ++h ++      ++L++  +++++k+se +e +++  ++++e ++ ++++ + ++ ++
  gi|298676224|ref|YP_003727973.1| 323 SLNCPFCGTNCDKSKLEEQKSHLTS----IRDSLKEENKSLKQKSSEKQELIDSYKKKENEINKINSKIIDTENLIS 395
                                       469********************99....44579999999999999999999999999999999999********** PP

                            AAA_13 332 aleeqLkglqraleaKrkepfksvelesvkaki.esikklvaeineliakhNekvanleeekeeakkklelhlveel 407
                                       +++eq+k++q++l + +    +++e+e++ +k  e+++ + a+i +  +k N++ +++++++ +++k++e  +++  
  gi|298676224|ref|YP_003727973.1| 396 ETNEQIKKAQNKLRDIK---QQKIEQEDIVSKFkEEVETETADITNRLSKVNAQLESYKNKEDQINKSIENNRLN-- 467
                                       *********99998877...567888888888878899***********************************99.. PP

                            AAA_13 408 eseldeykkkykklekaieklekelkeeeaelk.kleeeikeLe 450
                                       ++++de+k+k+++l+++ ++l+k+++++e++++ + ++ ike  
  gi|298676224|ref|YP_003727973.1| 468 KEKYDELKTKIDDLNDKRSNLQKKINNIEQNVReNFNNHIKEVY 511
                                       88999*********************999887515677788765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2  45.6   2.7e-06    0.0027       2     199 ..      10     235 ..       9     282 .. 0.53
   2 ?    0.1  25.9         1     1e+03      88     196 ..     268     412 ..     258     417 .. 0.52

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.7e-06
                            AAA_23   2 LkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese....gkvkay 74 
                                       ++++n++ ++++++  ++gl++I  pN +GKT++l+ + l       + + ++++ + +s+ +++s     +++++y
  gi|298676224|ref|YP_003727973.1|  10 ISLKNVGGLKEKNLTVKSGLNIIEAPNASGKTSLLRGFLLSVLP---NGKANHYSYLLHSKSNFGSVkitdANGQEY 83 
                                       89**********************************99986543...334444444444444433333333344455 PP

                            AAA_23  75 veltfenkdgry..trsiererelskkkgkttkkaklellei....deleqfisellgskkiilnlilflgqerfee 145
                                        +  +++k+  +   ++i +  +++  +  t+ +++ ++l+     ++l++++ e+ ++ +  ++l+ +  q + +e
  gi|298676224|ref|YP_003727973.1|  84 TKEIVKDKNSVSikGDNIVDPEKENLVSRFTIAGNTNKILDAvrtgQNLKDILLEYTNIPDLKNQLSKYDSQIKDNE 160
                                       33333333333344222333333333333333333333333322234444444444444444555555555555444 PP

                            AAA_23 146 felkdkke..........rleelekeleeledekkllekl...........eqekekek......eleeleeeleei 195
                                       ++l++ ++           l   ++e+e+l +ek++lek+           +      +      +l+++++ ++e+
  gi|298676224|ref|YP_003727973.1| 161 NQLNTLENklknetelykNLSITRNEIEKLDEEKSKLEKEytakkiddetnK------EykeavnKLNKIQQSIKEL 231
                                       4443333311122223333333344444444444444444444444442222......0223444666666666666 PP

                            AAA_23 196 lkel 199
                                       ++++
  gi|298676224|ref|YP_003727973.1| 232 ENKI 235
                                       6665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
                            AAA_23  88 rsiererelskkkg.kttkkaklelleideleqfisellgskkiil.nlilflgqer.................... 142
                                        ++e+e++++ +k  ++++k k+ +++id  ++fi+++l++ + +  n i+ l+++                     
  gi|298676224|ref|YP_003727973.1| 268 NTLENEIKNINEKIdSNISKMKTLNTYIDGIDEFINSSLDIADVQGnNSIDSLAESLncpfcgtncdkskleeqksh 344
                                       55666666555544256677789999999999999998887766542555666666578888888666555544444 PP

                            AAA_23 143 .........feefelkdkkerleelekeleeledekkllekl.....eqekekekeleeleeeleeil 196
                                                +e+++lk+k+++ +el+++++++e+e+++++ +     + + e ++++++ +++l +i+
  gi|298676224|ref|YP_003727973.1| 345 ltsirdslkEENKSLKQKSSEKQELIDSYKKKENEINKINSKiidteNLISETNEQIKKAQNKLRDIK 412
                                       44444433222222233333333333333333333333333344443333334446666666665554 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   8.1    0.0061       6.1      12      86 ..     140     200 ..     118     205 .. 0.49
   2 ?   11.2  17.3   0.00036      0.36      17     105 ..     203     288 ..     200     295 .. 0.74
   3 ?   -0.6  19.9       1.6   1.6e+03      29     106 ..     339     416 ..     334     438 .. 0.45
   4 ?   11.8  12.9   0.00023      0.23      26     111 ..     434     516 ..     417     535 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0061
                                       HHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  12 eespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqelqkk 86 
                                       ++ p+ k+  +++++++k+ +++l+++e++l+++ e ++              l   ++e+++ +++++ +l+k+
  gi|298676224|ref|YP_003727973.1| 140 TNIPDLKNQLSKYDSQIKDNENQLNTLENKLKNETELYK-------------NLSITRNEIEK-LDEEKSKLEKE 200
                                       344445555555555555555555555555555555553.............33333333333.33333333322 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00036
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  17 gkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.ekeekeqelqkkeqelqqkqqqkaqelqkkqqellk 92 
                                       +k+++++ +k++k+  ++l++ ++++++l+++++    ++   +e e+  qk e++l+q q +++ +++  ++e+ k
  gi|298676224|ref|YP_003727973.1| 203 AKKIDDETNKEYKEAVNKLNKIQQSIKELENKIN---YNKkRYKELEETKQKYENDLEQVQHNENIDVNTLENEI-K 275
                                       79999****************************8...33211555555566666666665555557788888774.5 PP

                                       HHHHHHHHHHHHH CS
                              OmpH  93 pildkinkaikev 105
                                       +i +ki+  i++ 
  gi|298676224|ref|YP_003727973.1| 276 NINEKIDSNISKM 288
                                       5999999888775 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  29 kklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqka...qelqkkqqellkpildkinkai 102
                                       ++ +  l++ +++l+++ + l++k+++  k+e    ++kke+e+++  + k    ++l ++ +e +k+ ++k++++ 
  gi|298676224|ref|YP_003727973.1| 339 EEQKSHLTSIRDSLKEENKSLKQKSSE--KQELIDSYKKKENEINK-INSKIidtENLISETNEQIKKAQNKLRDIK 412
                                       444555555555555555555543333..22222224444444444.333333433344444444444444433333 PP

                                       HHHH CS
                              OmpH 103 keva 106
                                       ++  
  gi|298676224|ref|YP_003727973.1| 413 QQKI 416
                                       3322 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00023
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  26 kkfkklqaeleakekelqklqeelqkkakkl.ekeekeqelqkkeqelqqkqqqkaqelqkkqqellkpildkinka 101
                                       ++++++  +++a+ +++++++++++k+ +++  ++ek+ el++k ++l++k+++ ++++++ +q ++++     n+ 
  gi|298676224|ref|YP_003727973.1| 434 ADITNRLSKVNAQLESYKNKEDQINKSIENNrLNKEKYDELKTKIDDLNDKRSNLQKKINNIEQNVREN----FNNH 506
                                       223444455555666666677777666666544999999999999999997777777777777665555....5555 PP

                                       HHHHHHHTT- CS
                              OmpH 102 ikevakekgy 111
                                       ikev  e g+
  gi|298676224|ref|YP_003727973.1| 507 IKEVYDELGF 516
                                       5555555554 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.4      0.29   2.9e+02     120     159 ..     143     182 ..     130     184 .. 0.82
   2 ?   15.0   0.9     2e-05      0.02      21      95 ..     212     287 ..     209     318 .. 0.76
   3 ?    4.0   2.3     0.049        49     114     154 ..     330     370 ..     328     373 .. 0.91
   4 ?    0.4   9.5       0.6     6e+02      36     143 ..     393     510 ..     371     515 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.29
                                       -SHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                      Spore_III_AB 120 sdregqlkalelaleeleeeieeareeakkkeklyrtlGv 159
                                        d+++ql+  +  +++ e+++  ++++ k+ + ly+ l++
  gi|298676224|ref|YP_003727973.1| 143 PDLKNQLSKYDSQIKDNENQLNTLENKLKNETELYKNLSI 182
                                       5788888888888888999999999999999999999987 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2e-05
                                       XXXXHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHHHHHCS-TTHHHHHHHHHHHHH.S....TSS-HHHHHHHHH CS
                      Spore_III_AB  21 krlkrrlkeleelkralellegeirygatpLpealeklaeksesplseffeevaerleek....egesfeeaweeav 93 
                                       k++k+ +++l+++++ ++ le++i+y+++  +e le++++k+e++l+++ ++  e+++ +    e ++++e + +++
  gi|298676224|ref|YP_003727973.1| 212 KEYKEAVNKLNKIQQSIKELENKINYNKKRYKE-LEETKQKYENDLEQVQHN--ENIDVNtlenEIKNINEKIDSNI 285
                                       89****************************999.999999***999998332..22222211114444444444444 PP

                                       HH CS
                      Spore_III_AB  94 ek 95 
                                       +k
  gi|298676224|ref|YP_003727973.1| 286 SK 287
                                       44 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.049
                                       HHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXX CS
                      Spore_III_AB 114 geslgysdregqlkalelaleeleeeieeareeakkkekly 154
                                       g +  +s +e+q+++l  ++  l+ee + +++++ +k+ l+
  gi|298676224|ref|YP_003727973.1| 330 GTNCDKSKLEEQKSHLTSIRDSLKEENKSLKQKSSEKQELI 370
                                       66778999****************************99886 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.6
                                       HHHHHHHHHHH-SS-H..........HHHHHHHHHCS-TTHHHHHHHHHHHHH..STSS-HHHHHHHHHHHHGGGS- CS
                      Spore_III_AB  36 alellegeirygatpL..........pealeklaeksesplseffeevaerlee.kegesfeeaweeavekllkkla 101
                                       +++  + +i+ +++ L          +++++k++e++e       +++ +rl++ + + + ++  e++++k++++  
  gi|298676224|ref|YP_003727973.1| 393 LISETNEQIKKAQNKLrdikqqkieqEDIVSKFKEEVE----TETADITNRLSKvNAQLESYKNKEDQINKSIENNR 465
                                       34444444444444442222111111334444444444....4455555555554666677777788888888889* PP

                                       --HHHHHHHHHHHHHHT..--SHHHHHHHHH.HHHHHHHHHHHHH CS
                      Spore_III_AB 102 Lkkedkeilkelgeslg..ysdregqlkale.laleeleeeieea 143
                                       L+ke  + lk+  + l   +s++++ ++++e +++e++++ i+e 
  gi|298676224|ref|YP_003727973.1| 466 LNKEKYDELKTKIDDLNdkRSNLQKKINNIEqNVRENFNNHIKEV 510
                                       ***********9999972255666666666425666777766665 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  15.5   0.00019      0.19      10     131 ..     145     269 ..     142     318 .. 0.68
   2 ?    4.9  28.2      0.02        20       8     179 ..     339     508 ..     333     518 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                               ERM  10 leerLkqlqeeaekaqeaLreseet...aelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerk 83 
                                       l+++L ++ ++++ ++++L+  e++     +L +++ + ++e e+L+++++++e+e ++ k++ e ++e ke+++ k
  gi|298676224|ref|YP_003727973.1| 145 LKNQLSKYDSQIKDNENQLNTLENKlknETELYKNLSITRNEIEKLDEEKSKLEKEYTAKKIDDETNKEYKEAVN-K 220
                                       7889999999999999987766655111568999*************************9999999999998764.5 PP

                               ERM  84 lreaeleaarleeeserkeeeaerLkeeleeareaeeeak.eklleals 131
                                       l++ ++ +++le++ +  ++  ++L+e  ++ ++++e+ + ++  ++ +
  gi|298676224|ref|YP_003727973.1| 221 LNKIQQSIKELENKINYNKKRYKELEETKQKYENDLEQVQhNENIDVNT 269
                                       6666666666666655555555555555555555554444122222222 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.02
                               ERM   8 releerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerkl 84 
                                       +e +  L+++++  ++ ++ L+++  + ++L  + ++ e+e ++ + k  + e+ i++ +e+ +k +++ ++++++ 
  gi|298676224|ref|YP_003727973.1| 339 EEQKSHLTSIRDSLKEENKSLKQKSSEKQELIDSYKKKENEINKINSKIIDTENLISETNEQIKKAQNKLRDIKQQK 415
                                       56677899********************************************************************* PP

                               ERM  85 reaeleaarleeeserkeeeaerLkeeleeareaeeeakekllealstpskses.eenveeseteeeeenseeesae 160
                                        e e  +++++ee+e    e+    ++l ++++++e  k+k  ++ ++ +++   +e+ +e +t+ ++ n++ ++ +
  gi|298676224|ref|YP_003727973.1| 416 IEQEDIVSKFKEEVET---ETADITNRLSKVNAQLESYKNKEDQINKSIENNRLnKEKYDELKTKIDDLNDKRSNLQ 489
                                       *************998...8888999999999999999999888888886553336667777777777777777777 PP

                               ERM 161 letdeveklsleieeeRvt 179
                                        + +++e++++e+ +++++
  gi|298676224|ref|YP_003727973.1| 490 KKINNIEQNVRENFNNHIK 508
                                       7777787877777666655 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 ?   -0.4  34.6         1     1e+03      63     177 ..     158     258 ..     112     308 .. 0.49
   2 ?    5.9  21.9     0.012        12      65     148 ..     333     419 ..     318     430 .. 0.60
   3 ?    0.4  21.2      0.61     6e+02      69     179 ..     386     492 ..     383     493 .. 0.78
   4 ?    9.3  13.5    0.0011       1.1      57     142 ..     425     512 ..     421     524 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1
                           UPF0242  63 ekl.ekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkl 138
                                        +  + ++le+k ++ tel ++l++ ++++e+l ee+ +L++e+ ak+   e  ke ++ ++ kl++i++    + +
  gi|298676224|ref|YP_003727973.1| 158 DNEnQLNTLENKLKNETELYKNLSITRNEIEKLDEEKSKLEKEYTAKKIDDETNKEYKEAVN-KLNKIQQ----SIK 229
                                       11124444455555555555555555555555555555555555554444444333333333.3333222....222 PP

                           UPF0242 139 eleeqLaekqellqeyqetieeqrsvlekrqdqieqLes 177
                                       ele+++++ +++ +e++et          +q++ ++Le 
  gi|298676224|ref|YP_003727973.1| 230 ELENKINYNKKRYKELEET----------KQKYENDLEQ 258
                                       2233333333333333332..........3333333332 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
                           UPF0242  65 lekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkee...nqqLqekleaiaedfeelkl 138
                                        +ksklee+++ lt+ +++lk+++++l++  +e++eL + +++ke+e+++ + +    ++L +++++  +  ++ ++
  gi|298676224|ref|YP_003727973.1| 333 CDKSKLEEQKSHLTSIRDSLKEENKSLKQKSSEKQELIDSYKKKENEINKINSKiidTENLISETNEQIKKAQNKLR 409
                                       47888899999999988888888888888888888888888888888888765411122333333222222222333 PP

                           UPF0242 139 eleeqLaekq 148
                                       ++++q  e++
  gi|298676224|ref|YP_003727973.1| 410 DIKQQKIEQE 419
                                       3333222222 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.61
                           UPF0242  69 kleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLa 145
                                       k+   e++++e++e++k+ +++l++ ++++ e ++ +++ +ee+e    e + +  +l+++ ++ e +k   e+q++
  gi|298676224|ref|YP_003727973.1| 386 KIIDTENLISETNEQIKKAQNKLRDIKQQKIEQEDIVSKFKEEVE---TETADITNRLSKVNAQLESYKN-KEDQIN 458
                                       556678899999999999999999998888887777777777665...5667788888888888888765.588888 PP

                           UPF0242 146 ekqellqeyqetieeqrsvlekrqdqieqLeskV 179
                                       +  e     +e+  e++  ++  +d+ ++L+ k+
  gi|298676224|ref|YP_003727973.1| 459 KSIENNRLNKEKYDELKTKIDDLNDKRSNLQKKI 492
                                       8888888888889999999999999999999887 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0011
                           UPF0242  57 wekalkeklekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae.. 131
                                       ++++++  +e+  + ++ +k+ ++ e++k+ke++++++ e+++  ke++d+ ++++  l+ +  +Lq+k ++i +  
  gi|298676224|ref|YP_003727973.1| 425 FKEEVE--TETADITNRLSKVNAQLESYKNKEDQINKSIENNRLNKEKYDELKTKIDDLNDKRSNLQKKINNIEQnv 499
                                       433333..489999999******************************************************999955 PP

                           UPF0242 132 ..dfeelklelee 142
                                         +f+++ +e+ +
  gi|298676224|ref|YP_003727973.1| 500 reNFNNHIKEVYD 512
                                       5555555555555 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   2.8      0.15   1.5e+02      21      78 ..     143     199 ..     135     212 .. 0.80
   2 ?   12.7   8.9   0.00014      0.14      22     113 ..     175     262 ..     173     290 .. 0.81
   3 ?    5.1   2.8     0.029        29      49     151 ..     268     387 ..     263     390 .. 0.78
   4 ?    0.8  14.0      0.63   6.2e+02      36     141 ..     347     448 ..     334     464 .. 0.75
   5 ?    5.2   2.3     0.026        26      59      93 ..     461     495 ..     437     505 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           T3SSipB  21 sqLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaada 78 
                                        +L+n+l  + +++k +++++  l ++l++ ++  k++     + iek+d+ ks+ ++
  gi|298676224|ref|YP_003727973.1| 143 PDLKNQLSKYDSQIKDNENQLNTLENKLKNETELYKNLS-ITRNEIEKLDEEKSKLEK 199
                                       5799************************99998888875.567788888888888654 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT------ CS
                           T3SSipB  22 qLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdeP 98 
                                       +L ++l + +  ++   e++skl +e  ta +  ++  +++++a++k++++++ ++++++k++  +kr keL   e 
  gi|298676224|ref|YP_003727973.1| 175 ELYKNLSITRNEIEKLDEEKSKLEKEY-TAKKIDDETNKEYKEAVNKLNKIQQSIKELENKINYNKKRYKEL---EE 247
                                       566677777777777777777777665.67777889999*********************************...88 PP

                                       ---CHHHHHHHHH.. CS
                           T3SSipB  99 ekakleaaeqQagaa 113
                                        k+k e++ +Q++  
  gi|298676224|ref|YP_003727973.1| 248 TKQKYENDLEQVQHN 262
                                       889999999998854 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...............HHTT.---------CHHHHHHH CS
                           T3SSipB  49 qtalseakgatddleaaiekadqaksaadaatkkvdeaqk...............rlke.LaPdePekakleaaeqQ 109
                                       +t+ +e k++ ++++  i k+++++  +d  ++ ++  +                +l+  +   + +k kle+++  
  gi|298676224|ref|YP_003727973.1| 268 NTLENEIKNINEKIDSNISKMKTLNTYIDGIDEFINSSLDiadvqgnnsidslaeSLNCpFCGTNCDKSKLEEQKSH 344
                                       67778889999999999999999999999999999999989999999955533222221122467899999999999 PP

                                       HH..HHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHTXXXXX CS
                           T3SSipB 110 agaaadalqadeal.qKkldaasklsekakakekevDdisakv 151
                                       ++   d+l+ +++  + k +  + l +  k+ke+e+ +i +k+
  gi|298676224|ref|YP_003727973.1| 345 LTSIRDSLKEENKSlKQKSSEKQELIDSYKKKENEINKINSKI 387
                                       9999***988776526777778889999999999999999887 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.63
                                       HTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH. CS
                           T3SSipB  36 aqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQaga 112
                                       + ++ +++  + l++  se +++ d ++++ +++++++s++ + ++ ++e  +++k+       + kl+  +qQ  +
  gi|298676224|ref|YP_003727973.1| 347 SIRDSLKEENKSLKQKSSEKQELIDSYKKKENEINKINSKIIDTENLISETNEQIKKA------QNKLRDIKQQKIE 417
                                       5566666777899***********************************9999999999......8888888888887 PP

                                       .HHHHHH.HHHH.HHHHHHHHHHHHHHHHHH CS
                           T3SSipB 113 aadalqa.deal.qKkldaasklsekakake 141
                                       + d  ++ +e + + + d++++ls+   ++e
  gi|298676224|ref|YP_003727973.1| 418 QEDIVSKfKEEVeTETADITNRLSKVNAQLE 448
                                       7776554233335888899988887764433 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           T3SSipB  59 tddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                        ++     ek+d++k ++d+++ k ++ qk+++++
  gi|298676224|ref|YP_003727973.1| 461 IENNRLNKEKYDELKTKIDDLNDKRSNLQKKINNI 495
                                       33344455677777777777777777777777766 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 ?    0.5   9.2      0.67   6.6e+02      17      75 ..     145     203 ..     137     213 .. 0.60
   2 ?    2.8  18.3      0.13   1.3e+02      27     102 ..     179     257 ..     163     259 .. 0.80
   3 ?    7.4  12.1    0.0048       4.8       5      83 ..     212     291 ..     208     313 .. 0.84
   4 ?   10.6  14.9    0.0005       0.5      27     106 ..     334     413 ..     310     421 .. 0.93
   5 ?    5.6   7.6     0.018        18      24      85 ..     429     490 ..     419     510 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.67
                       TMF_TATA_bd  17 lsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekelee 75 
                                       l+ ++ + +++++  +++l++le++ ++ +e   +l+ + +e ++l++e ++leke+++
  gi|298676224|ref|YP_003727973.1| 145 LKNQLSKYDSQIKDNENQLNTLENKLKNETELYKNLSITRNEIEKLDEEKSKLEKEYTA 203
                                       55566666666666666666666666665555556666666666666666666666655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.13
                       TMF_TATA_bd  27 Elaslkeelerleaerdeareeivklm...keneelkelkkeleelekeleelqeryetlLellGeksEeveELraD 100
                                        l+ +++e+e+l +e++++++e  +     ++n e ke+ ++l++++++++el+++ +   + ++e +E  +  ++D
  gi|298676224|ref|YP_003727973.1| 179 NLSITRNEIEKLDEEKSKLEKEYTAKKiddETNKEYKEAVNKLNKIQQSIKELENKINYNKKRYKELEETKQKYEND 255
                                       57889******************99983334444555555666667779*********9999999999999999999 PP

                       TMF_TATA_bd 101 va 102
                                       ++
  gi|298676224|ref|YP_003727973.1| 256 LE 257
                                       87 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0048
                       TMF_TATA_bd   5 ssagpsvqlverlsseirrlEgElaslkeelerleaerdeareeivklm.keneelkelkkeleelekeleelqery 80 
                                       ++ +  v+ +++++++i++lE+ ++  k+++++le+ +++ ++++ ++  +en ++++l++e++++++++++  ++ 
  gi|298676224|ref|YP_003727973.1| 212 KEYKEAVNKLNKIQQSIKELENKINYNKKRYKELEETKQKYENDLEQVQhNENIDVNTLENEIKNINEKIDSNISKM 288
                                       5566778899**********************************988764677789999999999999998877777 PP

                       TMF_TATA_bd  81 etl 83 
                                       +tl
  gi|298676224|ref|YP_003727973.1| 289 KTL 291
                                       665 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.0005
                       TMF_TATA_bd  27 ElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEeveELraDvaD 103
                                       ++++l+e+ + l++ rd+++ee  +l +++ e++el +++++ e+e+++++++   +  l+ e +E+++  ++ + D
  gi|298676224|ref|YP_003727973.1| 334 DKSKLEEQKSHLTSIRDSLKEENKSLKQKSSEKQELIDSYKKKENEINKINSKIIDTENLISETNEQIKKAQNKLRD 410
                                       678999*********************************************************************** PP

                       TMF_TATA_bd 104 lKe 106
                                       +K+
  gi|298676224|ref|YP_003727973.1| 411 IKQ 413
                                       **8 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.018
                       TMF_TATA_bd  24 lEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLe 85 
                                        E+E a + ++l++++a+ ++ ++   ++ k+ e+++ +k++++el++++++l+++ ++l +
  gi|298676224|ref|YP_003727973.1| 429 VETETADITNRLSKVNAQLESYKNKEDQINKSIENNRLNKEKYDELKTKIDDLNDKRSNLQK 490
                                       58899999999999999999999999999999999999999999999999999998877654 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4  26.4     0.094        94      13     147 ..     150     284 ..     126     293 .. 0.75
   2 ?    4.7  11.0     0.037        37      25     101 ..     213     290 ..     208     325 .. 0.52
   3 ?   11.3  24.0   0.00035      0.35      28     163 ..     340     466 ..     334     471 .. 0.82
   4 ?    1.7  11.1       0.3     3e+02      35     106 ..     435     502 ..     417     529 .. 0.46

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.094
                              Fez1  13 slLKqQLkdsqaevt...qklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellr 86 
                                       s   +Q+kd  ++++   +kl++  +l  +l  +r+++e+ +ee ++le++++ k+ + ++ ++e +++ ++ + ++
  gi|298676224|ref|YP_003727973.1| 150 SKYDSQIKDNENQLNtleNKLKNETELYKNLSITRNEIEKLDEEKSKLEKEYTAKKID-DETNKEYKEAVNKLNKIQ 225
                                       4455677777766542225777777788888888888888888888888888888887.566778888888888888 PP

                              Fez1  87 ekvekleeelkelreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeLkee 147
                                       + +++le++++  +++++el+  e+++++e d  ++q++e+ ++++l++e++++++++  +
  gi|298676224|ref|YP_003727973.1| 226 QSIKELENKINYNKKRYKELE--ETKQKYENDLEQVQHNENIDVNTLENEIKNINEKIDSN 284
                                       888888888888888888754..45555788888888888899999999998888887665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.037
                              Fez1  25 evtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrk.kseaellrekvekleeelkelr 100
                                       e  + ++ + +++ +++el++k++ + ++ kelee+ ++ +++le+++++ +   ++ ++ +++  ek+++++++++
  gi|298676224|ref|YP_003727973.1| 213 EYKEAVNKLNKIQQSIKELENKINYNKKRYKELEETKQKYENDLEQVQHNENIDvNTLENEIKNINEKIDSNISKMK 289
                                       33344444444555555555555555555555555555555555555433332212222223333334444444444 PP

                              Fez1 101 e 101
                                       +
  gi|298676224|ref|YP_003727973.1| 290 T 290
                                       3 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00035
                              Fez1  28 qklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreels 104
                                       ++ s + +++ +l+e +++l++k +e +el +s+++k++e++++++++  +++  + ++e+++k++++l++++++  
  gi|298676224|ref|YP_003727973.1| 340 EQKSHLTSIRDSLKEENKSLKQKSSEKQELIDSYKKKENEINKINSKIIDTENLISETNEQIKKAQNKLRDIKQQKI 416
                                       566778899***********************************************9***99999999999999444 PP

                              Fez1 105 elsleeeeaalesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqassFeqERr 163
                                       e    +e+       +k +++ ++e+++ ++++ +++a+L+  ++k+++ ++s e+ R 
  gi|298676224|ref|YP_003727973.1| 417 E----QEDI-----VSKFKEEVETETADITNRLSKVNAQLESYKNKEDQINKSIENNRL 466
                                       4....2222.....233444455678888889999999999999999999999998886 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.3
                              Fez1  35 alkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelsel 106
                                        + ++l  ++a+le+  ++ +++++s+e+  l+ e++    ++ k++ + l++k ++l+++++++ ++++e+
  gi|298676224|ref|YP_003727973.1| 435 DITNRLSKVNAQLESYKNKEDQINKSIENNRLNKEKY----DELKTKIDDLNDKRSNLQKKINNIEQNVREN 502
                                       2223333444444444444444444444333333322....2224444444444444444444444444332 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7  31.1       8.3   8.3e+03       4     130 ..     143     263 ..     138     290 .. 0.74
   2 ?   14.3  31.3   2.7e-05     0.027      11     141 ..     353     479 ..     339     506 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 8.3
                            TACC_C   4 kdldaalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvl.eekeq 79 
                                        dl ++l k + +++++e++++ l++k +++++ +++++ + +e ek   +  e+++ +ke + k+i+  + +e ++
  gi|298676224|ref|YP_003727973.1| 143 PDLKNQLSKYDSQIKDNENQLNTLENKLKNETELYKNLSITRNEIEKL-DE--EKSKLEKEYTAKKIDDETnKEYKE 216
                                       58899999************************9999999887777773.22..233345555666665544489999 PP

                            TACC_C  80 lladlnsveksfsdlfkryekqkevlegykkneeslkkcaeeylarvkkee 130
                                       + ++ln++++s+++l ++++  k+    yk+ ee+ +k  +  l++v+++e
  gi|298676224|ref|YP_003727973.1| 217 AVNKLNKIQQSIKELENKINYNKK---RYKELEETKQKYEN-DLEQVQHNE 263
                                       9******************98887...79999998666555.455555544 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.7e-05
                            TACC_C  11 ekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqlladlnsv 87 
                                       ++ ++  ++k +e qel ++++++++e ++++  + + e+ i+++ e+ +k +++ +   q+ +e+++ +++  ++v
  gi|298676224|ref|YP_003727973.1| 353 KEENKSLKQKSSEKQELIDSYKKKENEINKINSKIIDTENLISETNEQIKKAQNKLRDIKQQKIEQEDIVSKFKEEV 429
                                       3334445568889999****************9999********99988666665555555556666677777789* PP

                            TACC_C  88 eksfsdlfkryekqkevlegykkneeslkkcaeeylarvkkeeqRYqaLkahae 141
                                       e++ +d+ +r+ k    le yk++e++ +k++e   +r++k  ++Y++Lk++ +
  gi|298676224|ref|YP_003727973.1| 430 ETETADITNRLSKVNAQLESYKNKEDQINKSIE--NNRLNK--EKYDELKTKID 479
                                       *********************************..567765..58*****7654 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6  32.1     0.014        14     477     628 ..     146     295 ..     135     307 .. 0.85
   2 ?    8.0  36.0   0.00068      0.68     396     600 ..     337     533 ..     320     537 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.014
                              HOOK 477 eekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkleehleklkevqeel 553
                                       +++l++  +++ d+++++n+Le++ + +++  ++L+   +e++k l+e++sk e   + kk  +e  ++ ke+ ++l
  gi|298676224|ref|YP_003727973.1| 146 KNQLSKYDSQIKDNENQLNTLENKLKNETELYKNLSITRNEIEK-LDEEKSKLEKEYTAKKIDDETNKEYKEAVNKL 221
                                       567889999999************************99777765.6777899998666666667888999******* PP

                              HOOK 554 qkkkeqleelepklssnkqkieeleeaLkkkdedlkameerYkkyveKAksViktLdpkqnpaspaevqalknql 628
                                       +k ++ + ele+k++ nk++ +elee+ +k ++dl+++++     v+   + ik ++ k +++  + +++l++ +
  gi|298676224|ref|YP_003727973.1| 222 NKIQQSIKELENKINYNKKRYKELEETKQKYENDLEQVQHNENIDVNTLENEIKNINEKIDSNI-SKMKTLNTYI 295
                                       **************************************99999999999999999999996555.7777776655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00068
                              HOOK 396 alqkekerllaerdaLketneELkcaqlqqkelsqadalaskss..ssgenlaaellpaevreklirLqhENKmLkl 470
                                        l+ +k  l++ rd+Lke n  Lk    +++el  + + ++++    +++ + +e l +e+ e++ + q  NK   +
  gi|298676224|ref|YP_003727973.1| 337 KLEEQKSHLTSIRDSLKEENKSLKQKSSEKQELIDSYKKKENEInkINSKIIDTENLISETNEQIKKAQ--NKLRDI 411
                                       5788999*****************988888886655433333331122333444444455555554433..444444 PP

                              HOOK 471 kqegseeekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkleehleklk 547
                                       kq++          e+ +   + k+e+ete    ++r+++++aq+e  +++ ++ +   e+  l k+k +e+  k+ 
  gi|298676224|ref|YP_003727973.1| 412 KQQKI---------EQEDIVSKFKEEVETETADITNRLSKVNAQLESYKNKEDQINKSIENNRLNKEKYDELKTKID 479
                                       44444.........33444567778999*****************99988888878888889999************ PP

                              HOOK 548 evqeelqkkkeqleelepklssnk.qkieeleeaLkkkdedlkameerYkkyve 600
                                       ++++++++ ++ ++++e+++++n  + i+e+ + L   + d+  + + Y  y+ 
  gi|298676224|ref|YP_003727973.1| 480 DLNDKRSNLQKKINNIEQNVRENFnNHIKEVYDELGFENIDNIELSSDYNLYIT 533
                                       ***********************999********99999999888888888875 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   4.9   4.9e-05     0.049      50     107 ..     145     202 ..     130     210 .. 0.89
   2 ?    4.1   7.2     0.052        52       2      49 ..     223     272 ..     208     296 .. 0.63
   3 ?    3.0  11.5      0.11   1.1e+02      13      89 ..     337     415 ..     334     434 .. 0.72
   4 ?    2.6   4.6      0.15   1.5e+02       2      77 ..     428     501 ..     427     514 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.9e-05
                              FliJ  50 yqafisaldeaiaqqkqelaqaekqvekareewqearqerkklekLkerekkeeqkee 107
                                       +++++s+ d++i+  +++l+ +e+++++  e ++   + r+ +ekL+e++ k e +  
  gi|298676224|ref|YP_003727973.1| 145 LKNQLSKYDSQIKDNENQLNTLENKLKNETELYKNLSITRNEIEKLDEEKSKLEKEYT 202
                                       67899*******************************************9988776555 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.052
                              FliJ   2 eaareLaeaqrelqqaeekleeleqyrqeyqkqlsgea.q.glsaaelrn 49 
                                       ++++  +e +++++ ++++  ele++ q+y++ l++ + + +++++ l n
  gi|298676224|ref|YP_003727973.1| 223 KIQQSIKELENKINYNKKRYKELEETKQKYENDLEQVQhNeNIDVNTLEN 272
                                       44566666677777777777777777777777777776544555544443 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.11
                              FliJ  13 elqqaeekleeleqyrqeyqkqlsgea.q.glsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearq 87 
                                       +l++++++l+++++ ++e  k+l++++ +    +  +++ ++ i++++++i  +++ ++  ++q++ka++++   +q
  gi|298676224|ref|YP_003727973.1| 337 KLEEQKSHLTSIRDSLKEENKSLKQKSsEkQELIDSYKKKENEINKINSKIIDTENLISETNEQIKKAQNKLRDIKQ 413
                                       56777777777777777777777777766666678999999999999999999999999999999999998876555 PP

                              FliJ  88 er 89 
                                       ++
  gi|298676224|ref|YP_003727973.1| 414 QK 415
                                       54 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.15
                              FliJ   2 eaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvek 77 
                                       e ++e a + ++l + +++le+ ++  ++  k+++++   l+ +++  ++  i+ l+++ + +++++++ e++v +
  gi|298676224|ref|YP_003727973.1| 428 EVETETADITNRLSKVNAQLESYKNKEDQINKSIENNR--LNKEKYDELKTKIDDLNDKRSNLQKKINNIEQNVRE 501
                                       56677777777788888888888888888888888887..889999999999999999999999999999988865 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 ?    0.4  13.9      0.23   2.3e+02     180     255 ..     149     223 ..     138     237 .. 0.66
   2 ?    9.8   9.3   0.00031      0.31     173     244 ..     235     306 ..     224     344 .. 0.82
   3 ?   -0.5  16.2      0.41   4.1e+02     172     251 ..     348     426 ..     309     436 .. 0.71
   4 ?   10.8  11.9   0.00016      0.16     167     285 ..     427     549 ..     418     553 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.23
                        Fmp27_WPPW 180 leeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseesseeeeskskelsa 255
                                       l++ ++qi+++e++l++le+k ++ ++el ++++ +++ei++l+e+++ le+ ++  k+++e+++e ++  ++l++
  gi|298676224|ref|YP_003727973.1| 149 LSKYDSQIKDNENQLNTLENKLKN-ETELYKNLSITRNEIEKLDEEKSKLEKEYTAKKIDDETNKEYKEAVNKLNK 223
                                       555567888888888888888888.688888888888888888888888888887777777755533332222222 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00031
                        Fmp27_WPPW 173 kelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseesse 244
                                        ++ ++R +elee  +k e++le+++++++ + ++l++ei++++++i++  +k+++l+t+++ ++e  +ss 
  gi|298676224|ref|YP_003727973.1| 235 INYNKKRYKELEETKQKYENDLEQVQHNENIDVNTLENEIKNINEKIDSNISKMKTLNTYIDGIDEFINSSL 306
                                       56779********************************************************99998877555 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.41
                        Fmp27_WPPW 172 qkelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseesseeees 248
                                        ++ l+e  ++l+++ ++++e ++++++k+++  ++++++i ++e+ i+e++e+++  ++ l+d+k+++ ++e+  s
  gi|298676224|ref|YP_003727973.1| 348 IRDSLKEENKSLKQKSSEKQELIDSYKKKENE-INKINSKIIDTENLISETNEQIKKAQNKLRDIKQQKIEQEDIVS 423
                                       45567777888999999999999999999888.78999999999999999999999999999999998876663333 PP

                        Fmp27_WPPW 249 ksk 251
                                       k k
  gi|298676224|ref|YP_003727973.1| 424 KFK 426
                                       333 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00016
                        Fmp27_WPPW 167 dpervqkelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseess 243
                                       +  ++ +  + +Rl+++++q+e+ ++k ++++++ e+ ++  ke+++el+++i++l++k++ l++ +++++++ +++
  gi|298676224|ref|YP_003727973.1| 427 EEVETETADITNRLSKVNAQLESYKNKEDQINKSIEN-NRLNKEKYDELKTKIDDLNDKRSNLQKKINNIEQNVREN 502
                                       45567777899********************999999.789999****************************99854 PP

                        Fmp27_WPPW 244 eeeeskskelsaastsesfselde..........lasseesaseFknRFiih 285
                                             +++ ++  ++  f+++d+          ++++++  + + +R+ i+
  gi|298676224|ref|YP_003727973.1| 503 F-----NNHIKEVYDELGFENIDNielssdynlyITRTSDEGKGYFDRYSIM 549
                                       3.....3333333333333333333334456666666666666666677665 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 ?    4.1  35.9     0.026        25      50     195 ..     143     286 ..     137     291 .. 0.76
   2 ?   -2.0  18.4       1.9   1.9e+03      37     114 ..     337     414 ..     332     419 .. 0.76
   3 ?    9.2  23.2   0.00069      0.69      28     145 ..     405     519 ..     397     520 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.026
                               GAS  50 seisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdely 126
                                        +++++ +++  ++k  e++++ L+++lkn  +  + l  +++++++l++e ++l+ e+  ++   ++  ke++e  
  gi|298676224|ref|YP_003727973.1| 143 PDLKNQLSKYDSQIKDNENQLNTLENKLKNETELYKNLSITRNEIEKLDEEKSKLEKEYTAKKID-DETNKEYKEAV 218
                                       56777888888888999999999999999999999999999999999999999999988876654.66777888888 PP

                               GAS 127 kkfeaaiqevqqktglknllLekklkalqeelEkkeaqleevlaaanldpaalsavsekleevlesKnq 195
                                       +k ++ iq+  ++ ++k    +k+ k+l+e+ +k e  le+v  + n+d ++l++  ++++e ++s  +
  gi|298676224|ref|YP_003727973.1| 219 NKLNK-IQQSIKELENKINYNKKRYKELEETKQKYENDLEQVQHNENIDVNTLENEIKNINEKIDSNIS 286
                                       88877.555555677888888899999999999999999999999999977776666666665555444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.9
                               GAS  37 elkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleq 113
                                       +l++++ + +   + +++enk+lk++  + +e ++  +k+ ++ +k  +++  +++ ++e+++++k+ + + +  +q
  gi|298676224|ref|YP_003727973.1| 337 KLEEQKSHLTSIRDSLKEENKSLKQKSSEKQELIDSYKKKENEINKINSKIIDTENLISETNEQIKKAQNKLRDIKQ 413
                                       56677777777778888888888888888888888888888888888888888888888888888888877666555 PP

                               GAS 114 r 114
                                       +
  gi|298676224|ref|YP_003727973.1| 414 Q 414
                                       4 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00069
                               GAS  28 IkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdl 104
                                       +++l++  +++ ++e+  +k  +e+++e  +++  L k+++++e  +++  + +k  +  +  k+++ el+ ++ dl
  gi|298676224|ref|YP_003727973.1| 405 QNKLRDIKQQKIEQEDIVSKFKEEVETETADITNRLSKVNAQLESYKNKEDQINKSIENNRLNKEKYDELKTKIDDL 481
                                       33444444444556666778888899999999999999999999999999999999999999999999999999999 PP

                               GAS 105 kwehevleqrfekvekerdelykkfeaaiqevqqktglknl 145
                                         +  +l+++++++e+    ++++f++ i+ev  + g++n+
  gi|298676224|ref|YP_003727973.1| 482 NDKRSNLQKKINNIEQN---VRENFNNHIKEVYDELGFENI 519
                                       99999999999999875...567888889999888888885 PP

>> MHB  Haemophore, haem-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.4   1.4e+03      60      75 ..     219     234 ..     202     261 .. 0.67
   2 ?   -1.0   0.1       2.2   2.2e+03      42      73 ..     360     391 ..     343     392 .. 0.71
   3 ?    9.0   0.5    0.0017       1.6       5      71 ..     433     501 ..     431     505 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.4
                               MHB  60 adLrgIrqPltdlknr 75 
                                       + L++I+q +++l+n+
  gi|298676224|ref|YP_003727973.1| 219 NKLNKIQQSIKELENK 234
                                       4566666666666553 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.2
                               MHB  42 dqaraavkaYfdanPqvaadLrgIrqPltdlk 73 
                                       +q++++ ++ +d+  + ++++++I+  + d++
  gi|298676224|ref|YP_003727973.1| 360 KQKSSEKQELIDSYKKKENEINKINSKIIDTE 391
                                       67777777777777888888888888877776 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0017
                               MHB   5 aadlarvvsgVaastsaYLdthPdvnqalt..slkgqprdqaraavkaYfdanPqvaadLrgIrqPltd 71 
                                        ad+++  s+V+a+ ++Y ++  ++n+ +    l++++ d+ ++++++  d++ + ++ +++I+q +++
  gi|298676224|ref|YP_003727973.1| 433 TADITNRLSKVNAQLESYKNKEDQINKSIEnnRLNKEKYDELKTKIDDLNDKRSNLQKKINNIEQNVRE 501
                                       57889999*********************8334566666*************************98765 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   4.2      0.35   3.5e+02      30      97 ..     146     185 ..     115     206 .. 0.47
   2 ?    7.2  11.8    0.0047       4.7       5      80 ..     214     293 ..     203     308 .. 0.81
   3 ?    2.0   0.4       0.2     2e+02      25      52 ..     337     364 ..     335     373 .. 0.81
   4 ?    8.1  10.8    0.0025       2.5       4      77 ..     351     427 ..     348     428 .. 0.88
   5 ?    8.1  11.3    0.0025       2.5      12      83 ..     426     500 ..     420     514 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.35
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHHH CS
                        Laminin_II  30 keklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseike 97 
                                       k++ls+ +++                            + + +++l++l+++ +++  l +n+s  ++
  gi|298676224|ref|YP_003727973.1| 146 KNQLSKYDSQ----------------------------IKDNENQLNTLENKLKNETELYKNLSITRN 185
                                       2222222222............................222222222222222222222222222222 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0047
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXX--TTTTTGGGHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvk....dankairdArrsvkkLeklapqLldklke 77 
                                        +ea ++++++++ +++l+++++  k+ ++e++++ ++ +++++    + n  ++  ++++k+++++++  ++k+k+
  gi|298676224|ref|YP_003727973.1| 214 YKEAVNKLNKIQQSIKELENKINYNKKRYKELEETKQKYENDLEqvqhNENIDVNTLENEIKNINEKIDSNISKMKT 290
                                       57899999999999999999999999999999999998888877552344444567789999999999999999999 PP

                                       HHH CS
                        Laminin_II  78 lkq 80 
                                       l++
  gi|298676224|ref|YP_003727973.1| 291 LNT 293
                                       986 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.2
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  25 nlentkeklseinrsveetnekvkdank 52 
                                       +le+ k+ l +i++s++e n+ +k+++ 
  gi|298676224|ref|YP_003727973.1| 337 KLEEQKSHLTSIRDSLKEENKSLKQKSS 364
                                       6899999999999999999999997664 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0025
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--T...TTTTGGGHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLekl...apqLldklke 77 
                                        ++e n+++k+  + +++l    ++ ++++++in+++  t++++++ n++i+ A+++ ++++++    +++++k+ke
  gi|298676224|ref|YP_003727973.1| 351 SLKEENKSLKQKSSEKQELIDSYKKKENEINKINSKIIDTENLISETNEQIKKAQNKLRDIKQQkieQEDIVSKFKE 427
                                       56788999999999********************************************9998763225889999875 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0025
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHH CS
                        Laminin_II  12 akevleqlaplsqnlentkeklseinrsveetnekvk...dankairdArrsvkkLeklapqLldklkelkqlee 83 
                                        +ev+  +a++ ++l++++++l++ +++ +++n+ ++     ++  ++ ++++ +L+ +  +L +k+++++q   
  gi|298676224|ref|YP_003727973.1| 426 KEEVETETADITNRLSKVNAQLESYKNKEDQINKSIEnnrLNKEKYDELKTKIDDLNDKRSNLQKKINNIEQNVR 500
                                       468999999999999999999999999966666666533112234445555555555555555555555555433 PP

>> LTXXQ  LTXXQ motif family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.7      0.62   6.1e+02      36      80 ..     186     230 ..     146     260 .. 0.70
   2 ?    9.9   1.2    0.0012       1.2      17      85 ..     339     408 ..     338     414 .. 0.69
   3 ?   -0.4   0.2       1.9   1.9e+03      28      89 ..     399     458 ..     389     464 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.62
                                       --..-HHHHHHHHHHHTSSS--HHHHHHHH..HHHHHHHHHHHHH CS
                             LTXXQ  36 plkakkeemramrkkvlaanfdetaperlarmeamlearleavkk 80 
                                       + ++  ee+ ++ k+++a+++d+++ ++     + l++ +++ k+
  gi|298676224|ref|YP_003727973.1| 186 EIEKLDEEKSKLEKEYTAKKIDDETNKEYKEAVNKLNKIQQSIKE 230
                                       224556777777777788888877777776555555555555554 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHHHS---..-HHHHHHHHHHHTSSS--HHHHH.HHH..HHHHHHHHHHHHHHHHHH CS
                             LTXXQ  17 daQkaalkalaeaaraeakplkakkeemramrkkvlaanfdetape.rlarmeamlearleavkkraeal 85 
                                       ++Qk +l++++++ ++e+k+lk+k  e++++ + + +++   ++++ ++   e+ +++ +e+ kk +++l
  gi|298676224|ref|YP_003727973.1| 339 EEQKSHLTSIRDSLKEENKSLKQKSSEKQELIDSYKKKENEINKINsKIIDTENLISETNEQIKKAQNKL 408
                                       79*******************9999999988876633333333332133346666667666666666665 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.9
                                       HHHHHHS---..-HHHHHHHHHHHTSSS--HHHHHHHH..HHHHHHHHHHHHHHHHHHHHHH CS
                             LTXXQ  28 eaaraeakplkakkeemramrkkvlaanfdetaperlarmeamlearleavkkraealkqfy 89 
                                       e+ ++++++l++ k+++ ++ +  + ++f+e+  ++ a   ++l++ ++++++ +++ +q+ 
  gi|298676224|ref|YP_003727973.1| 399 EQIKKAQNKLRDIKQQKIEQED--IVSKFKEEVETETADITNRLSKVNAQLESYKNKEDQIN 458
                                       5666667777777777776666..55666666666666667777777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4702  (0.262257); expected 358.6 (0.02)
Passed bias filter:                      776  (0.0432818); expected 358.6 (0.02)
Passed Vit filter:                       312  (0.017402); expected 17.9 (0.001)
Passed Fwd filter:                       180  (0.0100396); 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: 3.02u 0.41s 00:00:03.43 Elapsed: 00:00:00.84
# Mc/sec: 2276.94
//
Query:       gi|298676225|ref|YP_003727974.1|  [L=238]
Description: hypothetical protein Metev_2368 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   15.4   0.6       0.22   12.3   0.0    2.5  2  DUF4373   Domain of unknown function (DUF4373)


Domain annotation for each model (and alignments):
>> DUF4373  Domain of unknown function (DUF4373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.2e-05      0.22      37      90 ..       8      59 ..       5      59 .. 0.92
   2 ?    0.9   0.1     0.045   8.1e+02      57      81 ..     178     204 ..      88     217 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                           DUF4373 37 ykekgyyiewdeeqlllladkaklevdeeevkeiveacveyglFdkelfeedgi 90
                                       +e++y+ e +++ +l +++  +++++ ++ + i+++c  ++l++ +lf+e++i
  gi|298676225|ref|YP_003727974.1|  8 PHENDYVTESEDNLALGISN--NVNIQTDKQEPIISSCRVCNLLKTDLFNEKQI 59
                                      57899*99999999999999..899**************************987 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.045
                           DUF4373  57 ka..klevdeeevkeiveacveyglFd 81 
                                       ++    +++++  ++ +e++++++l +
  gi|298676225|ref|YP_003727974.1| 178 DLkkGFDFSQNVANKALERALNRKLVS 204
                                       222244555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 1337.57
//
Query:       gi|298676226|ref|YP_003727975.1|  [L=161]
Description: hypothetical protein Metev_2369 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-06   27.3   2.0     0.0012   18.8   0.1    2.3  2  HTH_45    Winged helix-turn-helix
     0.0033   17.5   0.1        2.5    8.3   0.0    2.3  2  DUF2250   Uncharacterized protein conserved in archaea (DUF22
  ------ inclusion threshold ------
       0.01   15.9   0.1       0.73    9.9   0.1    2.2  2  HTH_54    ParA helix turn helix domain
      0.027   13.6   0.2      0.036   13.2   0.2    1.2  1  DUF4835   Domain of unknown function (DUF4835)


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 !   18.8   0.1   2.6e-07    0.0012       9      73 ..       8      76 ..       6      79 .. 0.91
   2 !    7.9   0.3   0.00068       3.1       2      65 ..      92     157 ..      91     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.6e-07
                            HTH_45  9 adILeaisegeakkTkimykanLsykllnkYLdmLvekgli......kkskekYvlTekGlelleklkele 73
                                      +d+L++   +  ++T+i   + L+  + ++ ++ L + gli      + ++++++lT+ Gl+++ +++e++
  gi|298676226|ref|YP_003727975.1|  8 LDVLKIF--KILSPTRIKEFSGLTNTRSKQEINDLENLGLIelspqsTPHDKEFKLTDFGLKIYTNFREFN 76
                                      6778877..78899****************************999866699*****************997 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00068
                            HTH_45   2 RskleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekgli.....kkskekYvlTekGlel 65 
                                       R k + i+d Le   +++a+   + +   L +  l+ YL +L+ ++++       +   Y++Tek  ++
  gi|298676226|ref|YP_003727975.1|  92 RKKAKTIIDTLE---DQGASFDYLRKITGLPFLDLKLYLIFLIYREYVdrkliGGDLVYYTTTEKSNKF 157
                                       666666666666...6677777777788899999999*****988876544447788999999997776 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0   0.00056       2.5      11      58 ..       5      52 ..       1      63 [. 0.70
   2 !    7.8   0.0   0.00077       3.5       3      50 ..      58     106 ..      55     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00056
                           DUF2250 11 lkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegk 58
                                      l+vl  lk  +   +  i +   +  ++ ++ +++Le+lGL+e   ++
  gi|298676226|ref|YP_003727975.1|  5 LRVLDVLKIFKILSPTRIKEFSGLTNTRSKQEINDLENLGLIELSPQS 52
                                      45555555555555566666677777889999**********976555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00077
                           DUF2250   3 eleedelalkvlkhlkkanvdYaksiakelei.pleevrellkkLeelG 50 
                                       e + ++  lk+   +++ n +Y k  ++ l++ ++++++ +++ Le+ G
  gi|298676226|ref|YP_003727975.1|  58 EFKLTDFGLKIYTNFREFNYEYFKVSVNTLKKnERKKAKTIIDTLEDQG 106
                                       566778899***************9999988725788999******998 PP

>> HTH_54  ParA helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.01        46      23      71 ..      12      61 ..       5      63 .. 0.79
   2 ?    9.9   0.1   0.00016      0.73      21      59 ..      72     110 ..      45     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.01
                            HTH_54 23 eyyqtyskaalaklpklsrrkvdkavsemeaeG.yefekkeagstekYal 71
                                      + ++  s + ++++++l+    ++ ++++e+ G +e++ +++   ++++l
  gi|298676226|ref|YP_003727975.1| 12 KIFKILSPTRIKEFSGLTNTRSKQEINDLENLGlIELSPQSTPHDKEFKL 61
                                      5688899999*********************9944666666665555555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00016
                            HTH_54  21 edeyyqtyskaalaklpklsrrkvdkavsemeaeGyefe 59 
                                         e+  +y k ++++l k  r+k+++ ++ +e++G +f+
  gi|298676226|ref|YP_003727975.1|  72 FREFNYEYFKVSVNTLKKNERKKAKTIIDTLEDQGASFD 110
                                       567888999**************************9997 PP

>> DUF4835  Domain of unknown function (DUF4835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   7.9e-06     0.036     182     249 ..      67     133 ..      52     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.9e-06
                           DUF4835 182 ekleelrellYeYhrkGLDemaenkekgrkailealeklkevkkkkpnslllqlFfdaKsdElvnifs 249
                                       + ++++re+ YeY++  + ++++n++k  k+i+++le+  + + ++ ++++   F+d K   +  i++
  gi|298676226|ref|YP_003727975.1|  67 KIYTNFREFNYEYFKVSVNTLKKNERKKAKTIIDTLEDQGA-SFDYLRKITGLPFLDLKLYLIFLIYR 133
                                       56899******************************997443.33444445555566666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 948.73
//
Query:       gi|298676227|ref|YP_003727976.1|  [L=33]
Description: hypothetical protein Metev_2370 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       125  (0.00697194); expected 358.6 (0.02)
Passed bias filter:                      117  (0.00652574); 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: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 211.28
//
Query:       gi|298676228|ref|YP_003727977.1|  [L=375]
Description: IS605 OrfB family transposase [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-27   95.6   2.1    5.1e-27   94.5   2.1    1.5  1  OrfB_IS605      Probable transposase
    5.4e-24   83.9   0.4    1.1e-23   82.9   0.4    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.9e-19   68.9   1.4      4e-19   67.8   1.4    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0071   16.5   0.3      0.019   15.1   0.3    1.7  1  zf-piccolo      Piccolo Zn-finger
  ------ inclusion threshold ------
      0.031   14.1   0.9        0.4   10.5   0.2    2.2  2  LemA            LemA family
      0.036   13.9   6.7       0.21   11.4   1.3    2.7  3  Phage_GP20      Phage minor structural protein GP20
       0.37   10.8   1.8        1.3    9.1   0.8    2.2  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.59   10.4   8.1       0.22   11.8   2.0    2.4  2  MapZ_EC1        MapZ extracellular domain 1


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   2.1   2.3e-30   5.1e-27       9     117 ..     168     276 ..     158     278 .. 0.93

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 2.3e-30
                        OrfB_IS605   9 e...lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhr 82 
                                       +   ++k ++ +++g+D+Gi+++a++++++   ++ ++r lk+  ++l+  +++l++k+k+s+ny+k + ++a++h+
  gi|298676228|ref|YP_003727977.1| 168 QlpqKQKFDEVNTVGVDVGIKDFAVTSDGE---KIDNPRYLKNSIERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHE 241
                                       34447788899*******************...******************************************** PP

                        OrfB_IS605  83 krsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       k++++r +++hkl+++li ++++v++e Lnv+++ 
  gi|298676228|ref|YP_003727977.1| 242 KIANQREDFQHKLSSRLISENQAVALECLNVKGLL 276
                                       ********************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.4   4.8e-27   1.1e-23       1      68 [.     290     359 ..     290     360 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 4.8e-27
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpay.TSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++++ ++leyka++yG++++++ ++  +Sk C++Cg+ +++ +l++r+++Cp+C++e+drD+nA++Ni k
  gi|298676228|ref|YP_003727977.1| 290 WSSFVQKLEYKAEWYGKNIIKIGRFDpSSKICHVCGYYHQDlELKDREWECPDCKTEHDRDINASVNIKK 359
                                       99******************************************************************87 PP

>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   1.4   1.8e-22     4e-19       1      47 []       1      46 [.       1      46 [. 0.98

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 1.8e-22
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lkaykyr yP++ Q+e++a+++G++Rf+YN+aL+ + + ye+ gk
  gi|298676228|ref|YP_003727977.1|  1 M-LKAYKYRMYPNQIQQELIAKHIGACRFIYNWALENKLKSYEQDGK 46
                                      8.******************************************997 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   8.6e-06     0.019      28      56 ..     318     346 ..     314     348 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.6e-06
                        zf-piccolo  28 kqvCnlCGFnptphltekkeWlclnCQtq 56 
                                       +++C +CG+  ++   + +eW c  C t+
  gi|298676228|ref|YP_003727977.1| 318 SKICHVCGYYHQDLELKDREWECPDCKTE 346
                                       79***********999**********985 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.11   2.4e+02      37      82 ..      59     104 ..      44     108 .. 0.80
   2 ?   10.5   0.2   0.00018       0.4      58     107 ..     203     253 ..     190     260 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.11
                              LemA  37 vteaRakaaeaesveekaeaenqlssalsrllavaEnYPdLkanen 82 
                                       v +  ++  ++ + ++ + a  +l++a+ +++     +P++k+++n
  gi|298676228|ref|YP_003727977.1|  59 VLKEDHEWLNEINSQSLQGATLNLENAFTKFFREKSGFPKFKSKKN 104
                                       55555566778889999999***********************987 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00018
                              LemA  58 nqlssalsrllavaEnY.PdLkanenfleLqeelegtEnriavaRrrYnea 107
                                       + l+++++rl +++ +   + k ++n+++L++++++  ++ia++R++++++
  gi|298676228|ref|YP_003727977.1| 203 RYLKNSIERLKVLQKRLsRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHK 253
                                       5667777777777666414557899**********************9876 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 ?    4.6   0.0     0.012        26     112     138 ..      42      71 ..      14      79 .. 0.77
   2 ?   -2.4   0.0       1.7   3.8e+03       9      25 ..     163     180 ..     160     181 .. 0.75
   3 ?   11.4   1.3   9.2e-05      0.21      32      90 ..     210     268 ..     196     278 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.012
                        Phage_GP20 112 kedgelkg...LdeqikkLkesdkyLFeee 138
                                       ++dg+ +    L++qi  Lke++++L e +
  gi|298676228|ref|YP_003727977.1|  42 EQDGKAISrfeLNKQIRVLKEDHEWLNEIN 71 
                                       456666644459************998733 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.7
                        Phage_GP20   9 aengkdit.kakldevee 25 
                                       ++++k ++ k+k+dev++
  gi|298676228|ref|YP_003727977.1| 163 VDDDKQLPqKQKFDEVNT 180
                                       556677888999999986 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 9.2e-05
                        Phage_GP20  32 eqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldnaielaLk 90 
                                       e+lk  +k L+  kk +++  +L+ qi+++ +k++++ ++ + k++ + +++    aL+
  gi|298676228|ref|YP_003727977.1| 210 ERLKVLQKRLSRKKKGSNNYRKLKHQIAKYHEKIANQREDFQHKLSSRLISENQAVALE 268
                                       6788889999999********************************99888776666666 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.4   3.1e+03      18      34 ..     169     186 ..     160     191 .. 0.80
   2 ?    9.1   0.8   0.00057       1.3      68      96 ..     316     347 ..     306     361 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                                       H.CCTT..EEEEEEEEEE CS
                              HypA  18 a.keaaarkvtkvkvevG 34 
                                       + +++++++v++v v+vG
  gi|298676228|ref|YP_003727977.1| 169 LpQKQKFDEVNTVGVDVG 186
                                       43668899*******999 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00057
                                       --EEEETTTS-EEE.CHH.H.HHS-TTTSSS- CS
                              HypA  68 pvkvrCreCgkefe.lee.k.alrCpkCgsad 96 
                                       p +  C++Cg+  + le  + + +Cp+C++++
  gi|298676228|ref|YP_003727977.1| 316 PSSKICHVCGYYHQdLELkDrEWECPDCKTEH 347
                                       55678*****8887444333588*****9874 PP

>> MapZ_EC1  MapZ extracellular domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.5      0.12   2.8e+02      48      84 ..      34      73 ..      30      85 .. 0.78
   2 ?   11.8   2.0   9.7e-05      0.22      22      78 ..     184     246 ..     163     269 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.12
                          MapZ_EC1 48 LekkLeklk.gskeYk..klkkkldslkkqisaieavNsq 84
                                      Le+kL+ ++ + k  +  +l+k++  lk+  + ++++Nsq
  gi|298676228|ref|YP_003727977.1| 34 LENKLKSYEqDGKAISrfELNKQIRVLKEDHEWLNEINSQ 73
                                      777788777544443323799*****************97 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 9.7e-05
                          MapZ_EC1  22 ekeyaafftddketflkn.....sefaklseLekkLeklk.gskeYkklkkkldslkkqisai 78 
                                       +  +++f ++++ +++ n     + ++ l+ L+k L   k gs++Y+klk+++++  ++i+ +
  gi|298676228|ref|YP_003727977.1| 184 DVGIKDFAVTSDGEKIDNprylkNSIERLKVLQKRLSRKKkGSNNYRKLKHQIAKYHEKIANQ 246
                                       5566666666666666652222223578999*****98777*****************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1446  (0.0806515); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2266.73
//
Query:       gi|298676229|ref|YP_003727978.1|  [L=1028]
Description: hypothetical protein Metev_2372 [Methanohalobium evestigatum Z-7303]
Scores for 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-05   22.3  37.7    0.00013   21.7   1.7    6.6  7  Big_3_3   Bacterial Ig-like domain (group 3)
    0.00058   20.1  31.0      0.093   13.0   0.8    7.0  8  DUF4625   Domain of unknown function (DUF4625)
  ------ inclusion threshold ------
       0.22   11.5   9.1       0.41   10.6   0.3    4.6  3  Y_Y_Y     Y_Y_Y domain


Domain annotation for each model (and alignments):
>> Big_3_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.5      0.12   7.4e+02      14      99 ..      99     181 ..      87     191 .. 0.58
   2 !   21.7   1.7   2.1e-08   0.00013       6      71 ..     189     257 ..     184     274 .. 0.76
   3 !   10.4   0.8   6.2e-05      0.37       3      60 ..     293     348 ..     291     357 .. 0.78
   4 ?   -0.9   0.3      0.19   1.1e+03      53      81 ..     426     456 ..     381     481 .. 0.61
   5 ?   -0.8   0.3      0.17     1e+03      57      81 ..     430     456 ..     414     532 .. 0.55
   6 !    6.1   0.8    0.0014       8.1       2      62 ..     604     669 ..     603     678 .. 0.76
   7 !    7.0   0.8   0.00072       4.3      21      95 ..     733     804 ..     724     813 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.12
                           Big_3_3  14 eGkynlvlaakdtfnn....qvtksllstilvdntpPtvsisegkkisdgavvkglenlritladaldkskltsial 86 
                                       +G+y + ++ + t+n+      + ++++t+++d   P+vs      i+     k+ e++ ++ + + d++  +s+ +
  gi|298676229|ref|YP_003727978.1|  99 DGEYDVYAYDSATVNDgddlSNNANISTTLTIDDDNPSVSS-----ITTPIYTKSSEDVPVEFTYTEDNP--SSVDI 168
                                       56666666555554444444555666667777777787764.....455555555566666665555554..34444 PP

                           Big_3_3  87 sGGpasDkVelsw 99 
                                         G+  ++  ls+
  gi|298676229|ref|YP_003727978.1| 169 IIGSNTESFTLST 181
                                       4455555555555 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.1e-08
                           Big_3_3   6 tfdlkelp..eGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkki.sdgavvkglenlrit 71 
                                       tf+  +lp  eGkyn++++++d+ +n+ +k++ ++++vd t P+v+ ++ + +  d+  vk+ + ++i+
  gi|298676229|ref|YP_003727978.1| 189 TFSSTNLPssEGKYNITVKITDQAGNTGNKKCENEVTVDDTKPSVTNVQITDVtDDNGFVKSGDTVKIE 257
                                       67777776338*********************************9975544440556677777777664 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 6.2e-05
                           Big_3_3   3 ytvtfdlke.lpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdga 60 
                                       y+ tf +++   +G+ +l+++a+d+ +n   ++++ t+++d+t Pt++    ++  d++
  gi|298676229|ref|YP_003727978.1| 293 YNATFTVDSgANDGEESLTINATDKAGNSNDTETSGTLTIDTTEPTLED---AESVDKT 348
                                       6667777652568******************99999**********975...4444444 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.19
                           Big_3_3  53 gkkisdgavvkglenlritl..adaldkskl 81 
                                       ++++s++++v g++++  tl  a++++++k+
  gi|298676229|ref|YP_003727978.1| 426 NSNNSGSVTVTGMDSVAPTLdhASKINATKI 456
                                       3345566666777776666622233333344 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 0.17
                           Big_3_3  57 sdgavvkglenlritl..adaldkskl 81 
                                       s++++v g++++  tl  a++++++k+
  gi|298676229|ref|YP_003727978.1| 430 SGSVTVTGMDSVAPTLdhASKINATKI 456
                                       334444444444444411122222222 PP

  == domain 6  score: 6.1 bits;  conditional E-value: 0.0014
                           Big_3_3   2 nytvtfdlkelpeGkynlvl.aakdtfnn..qvtksllstilvdntpPtvsi..segkkisdgavv 62 
                                       nyt++  ++  ++G y+++l +a+d ++n      ++ s  +vd+t P+++   ++++ ++d+  v
  gi|298676229|ref|YP_003727978.1| 604 NYTYNATYEFSSDGWYKVELvTANDSNDNngSSGDEYISGAVVDTTKPVIDSvtPNNTMVTDDQKV 669
                                       788888889999*****999888888888334456778899*********8546666677776655 PP

  == domain 7  score: 7.0 bits;  conditional E-value: 0.00072
                           Big_3_3  21 laakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvkglenlritladaldks..kltsialsGGpasDkV 95 
                                       +  +d ++n  tk+ +  ++vd t+P+v+    + i +g   +++ +++++  + +++s  +  s+++s G ++ ++
  gi|298676229|ref|YP_003727978.1| 733 VEVTDMYDNIQTKQWN--FTVDATSPSVEY---AVIDNGFSTNDMTGVNVKFSEGINTSvpEDISMVISNGETQKQI 804
                                       4678999998877766..99********99...8999999*************999998776668888888887665 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   8.5e-05      0.51     105     127 ..     198     220 ..     173     224 .. 0.77
   2 !   13.0   0.8   1.6e-05     0.093       3      48 ..     220     264 ..     218     272 .. 0.90
   3 !   10.6   0.1   8.6e-05      0.51      92     128 ..     291     327 ..     269     333 .. 0.86
   4 ?   -2.3   0.0       0.8   4.8e+03      35      62 ..     345     372 ..     329     378 .. 0.67
   5 ?   -2.2   0.1      0.74   4.4e+03      32      70 ..     386     426 ..     355     439 .. 0.69
   6 ?    1.8   0.2     0.043   2.6e+02      11      84 ..     542     612 ..     532     621 .. 0.60
   7 !    4.2   0.6    0.0078        47      10      58 ..     642     687 ..     625     752 .. 0.75
   8 ?   -2.2   0.1      0.75   4.5e+03     114     131 ..     842     859 ..     834     860 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.5e-05
                           DUF4625 105 eaGdYhlvirvtDasGneteesr 127
                                        +G+Y++++++tD++Gn+ +++ 
  gi|298676229|ref|YP_003727978.1| 198 SEGKYNITVKITDQAGNTGNKKC 220
                                       59***************988776 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.6e-05
                           DUF4625   3 cssddeeedtekPvidllevsaepeeeevlkiGetlhfeaklsdne 48 
                                       c+++ +  d +kP+++ ++++   +++  +k G+t+++ea+++dn 
  gi|298676229|ref|YP_003727978.1| 220 CENEVT-VDDTKPSVTNVQITDVTDDNGFVKSGDTVKIEANIIDNF 264
                                       766655.9************999*********************95 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 8.6e-05
                           DUF4625  92 yelheeieiPadaeaGdYhlvirvtDasGneteesre 128
                                        + + ++++++ a++G+  l+i +tD++Gn++ ++++
  gi|298676229|ref|YP_003727978.1| 291 DTYNATFTVDSGANDGEESLTINATDKAGNSNDTETS 327
                                       5678899************************998876 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 0.8
                           DUF4625  35 Getlhfeaklsdn.ealasykvdihnnfD 62 
                                        ++ +++++lsd+   +++ ++d  n+fD
  gi|298676229|ref|YP_003727978.1| 345 VDKTTINVTLSDDgSGINKSSIDT-NDFD 372
                                       355677888887635688888887.7777 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 0.74
                           DUF4625  32 lkiGet..lhfeaklsdnealasykvdihnnfDhhshssea 70 
                                       ++ G t    ++++l d ++ +s+ v +++  D+ +++  +
  gi|298676229|ref|YP_003727978.1| 386 VTDGATsqQIIQIELRDPVDSESVDVVLNSSNDGIKDKAGN 426
                                       44444433557788888888888888887777777666554 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.043
                           DUF4625  11 dtekPvidllevsaepeeeevlkiGetlhfeaklsdnealasykvdihnnfDhhshsseakeg......ekewsfek 81 
                                       d  +P+i++++v +           ++ ++ ++++  e+l +++ di +  D+   ++ ++        e++++++ 
  gi|298676229|ref|YP_003727978.1| 542 DGVAPTISDYKVVN--------PNKDNRNLTIEFNSTEKLTNITADI-KTDDGSPITTINESNfneftsESNYTYNA 609
                                       55666666663333........2223356777888899999999999.44455555555444455666666666666 PP

                           DUF4625  82 syd 84 
                                       +y+
  gi|298676229|ref|YP_003727978.1| 610 TYE 612
                                       665 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.0078
                           DUF4625  10 e....dtekPvidllevsaepeeeevlkiGetlhfeaklsdnealasykvdih 58 
                                       +    dt+kPvid +      + ++++ ++++  + +++sd   l+ ++v+i 
  gi|298676229|ref|YP_003727978.1| 642 SgavvDTTKPVIDSV------TPNNTMVTDDQKVISFNVSDTYPLK-LSVKIG 687
                                       045559*******99......4456777788888888899988886.444443 PP

  == domain 8  score: -2.2 bits;  conditional E-value: 0.75
                           DUF4625 114 rvtDasGneteesreiki 131
                                        v D++Gn   ++ +i+i
  gi|298676229|ref|YP_003727978.1| 842 NVSDKNGNDVSVNEDIEI 859
                                       5889****9999999988 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   6.9e-05      0.41      26      65 ..     184     226 ..     169     227 .. 0.79
   2 ?    0.7   0.0     0.084     5e+02      43      65 ..     310     332 ..     305     333 .. 0.90
   3 ?    0.4   1.7      0.11   6.4e+02      22      55 ..     600     633 ..     593     637 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.9e-05
                                       STS...EEEEES--S..EEEEEEEEEEETTS-B-SS-EEEEEEE CS
                             Y_Y_Y  26 dysq..easytnlpp..GdYtlkVkakdndgqwnyditslsfti 65 
                                       ++    ++s tnlp+  G+Y ++Vk++d  g+  ++  + ++t+
  gi|298676229|ref|YP_003727978.1| 184 SS-EtkTFSSTNLPSseGKYNITVKITDQAGNTGNKKCENEVTV 226
                                       33.24799999999555***************999988888877 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.084
                                       EEEEEEETTS-B-SS-EEEEEEE CS
                             Y_Y_Y  43 lkVkakdndgqwnyditslsfti 65 
                                       l++ a+d+ g++n+ +ts ++ti
  gi|298676229|ref|YP_003727978.1| 310 LTINATDKAGNSNDTETSGTLTI 332
                                       7899***********9*999998 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.11
                                       EEESSTS.EEEEES--SEEEEEEEEEEETTS-B- CS
                             Y_Y_Y  22 veasdysqeasytnlppGdYtlkVkakdndgqwn 55 
                                       +++s+y+++a+y   + G Y++++ + ++++++n
  gi|298676229|ref|YP_003727978.1| 600 TSESNYTYNATYEFSSDGWYKVELVTANDSNDNN 633
                                       56677777**************988877666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1028 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.87u 0.36s 00:00:01.23 Elapsed: 00:00:00.65
# Mc/sec: 4797.57
//
Query:       gi|298676230|ref|YP_003727979.1|  [L=369]
Description: Gram-positive anchor protein [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0003   20.6   0.2    0.00065   19.6   0.2    1.6  1  Gram_pos_anchor  LPXTG cell wall anchor motif
    0.00086   19.5   0.8    0.00086   19.5   0.8    2.3  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0056   16.7   0.2     0.0056   16.7   0.2    3.2  4  Big_1            Bacterial Ig-like domain (group 1)
     0.0091   16.1   1.6        1.9    8.7   0.2    2.8  2  MG4              Macroglobulin domain MG4
  ------ inclusion threshold ------
      0.047   14.3   2.0       0.25   11.9   0.6    2.5  2  SEP              SEP domain
       0.13   12.3   0.2        1.2    9.2   0.0    2.2  2  DUF617           Protein of unknown function, DUF617
       0.14   11.3   2.7       0.33   10.0   2.7    1.6  1  ABC2_membrane_3  ABC-2 family transporter protein
       0.74   10.6   3.7        1.6    9.4   0.2    2.8  3  TTR-52           Transthyretin-like family
        2.5    8.0   5.8         13    5.7   0.0    3.2  4  Glyco_hydro2_C5  Glycoside hydrolase family 2 C-terminal doma
        4.5    8.3   6.3        2.2    9.3   0.3    3.0  3  Pilin_N          Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   3.6e-07   0.00065      13      38 ..     340     366 ..     340     369 .] 0.82

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.6e-07
                                       XX.XXXXXXXXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor  13 Ge.ngnifltaaGllallggllLlvkr 38 
                                       Ge +g++++ta Glla+ +g+++l+++
  gi|298676230|ref|YP_003727979.1| 340 GEsQGMPGFTAIGLLAAGAGAAFLKRK 366
                                       6449*********99999999996666 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.8   4.8e-07   0.00086       2      46 ..      35      86 ..      34     117 .. 0.71
   2 ?   -2.2   0.1         3   5.4e+03      16      36 ..     202     221 ..     195     222 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.8e-07
                   CarboxypepD_reg  2 isGrVtdasgapiagatVtvtnadtg......tvastttdadGafrlr..glp 46
                                      + G+++d +g++++g +V+++++d++      t+ +t td++G++ l+  gl+
  gi|298676230|ref|YP_003727979.1| 35 VYGYIKD-DGNGVSGIQVEIRTDDGTklsndkTSVTTSTDSEGYYELKpnGLQ 86
                                      5688887.899**********7665456666689************9733444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3
                   CarboxypepD_reg  16 gatVtvtnadtgtvastttda 36 
                                        +++++t+  ++t+ +t+td+
  gi|298676230|ref|YP_003727979.1| 202 DVNIEITD-HGETKPETVTDS 221
                                       57777773.455666777775 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   3.1e-06    0.0056      17      50 ..      42      80 ..      38      90 .. 0.85
   2 ?   -3.4   0.0       5.6     1e+04      45      56 ..     156     167 ..     155     170 .. 0.73
   3 ?   -1.2   0.1       1.2   2.1e+03      24      44 ..     201     221 ..     196     222 .. 0.75
   4 ?   -2.1   0.1       2.2     4e+03      21      43 ..     245     268 ..     241     269 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.1e-06
                             Big_1 17 ngnpvagatVtfsvsggals.....assgtTdanGkatv 50
                                      +gn v+g++V +++++g+ +     + ++ Td++G ++ 
  gi|298676230|ref|YP_003727979.1| 42 DGNGVSGIQVEIRTDDGTKLsndktSVTTSTDSEGYYEL 80
                                      8***************66666*99999999*****9876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.6
                             Big_1  45 nGkatvtltstk 56 
                                       nGka ++++  +
  gi|298676230|ref|YP_003727979.1| 156 NGKANTNIKQIN 167
                                       899999887655 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.2
                             Big_1  24 atVtfsvsg.galsassgtTda 44 
                                       + V++++++ g +  ++++Td+
  gi|298676230|ref|YP_003727979.1| 201 QDVNIEITDhGET-KPETVTDS 221
                                       6789999996666.66777775 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2.2
                             Big_1  21 vagatVtfsvsggals.assgtTd 43 
                                       +  a++tf+v+++ +  ++ g Td
  gi|298676230|ref|YP_003727979.1| 245 IDSASITFEVDKDWVKeNNAGPTD 268
                                       567889999998544446666666 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.1    0.0087        16      25      78 ..      41      98 ..      38     117 .. 0.82
   2 !    8.7   0.2    0.0011       1.9      42      88 ..     143     189 ..     126     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0087
                               MG4 25 pdgspaknvpVkiealk.....seteekeslttdedGtakfsintpedaksltitvktk 78
                                       dg+ +++++V i++ +     s+++   ++ td++G  ++  n  +d+k+l++ v  +
  gi|298676230|ref|YP_003727979.1| 41 DDGNGVSGIQVEIRT-DdgtklSNDKTSVTTSTDSEGYYELKPNGLQDGKTLSLYVDGD 98
                                      689999*********.445657778888888899***9999999999999998887655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0011
                               MG4  42 seteekeslttdedGtakfsintpedaksltitvktkdpslpeenqa 88 
                                       s++e k+ + + ++G a+++i   +++ +++i+ + +d++ +e+++ 
  gi|298676230|ref|YP_003727979.1| 143 SDKETKQLKAELKNGKANTNIKQINKGDEVSIELESEDKDQEEQQSI 189
                                       4455666667889*************************999877765 PP

>> SEP  SEP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6   0.00014      0.25      19      75 ..     143     198 ..     140     199 .. 0.85
   2 ?    0.5   0.0      0.53   9.5e+02      45      65 ..     279     299 ..     246     306 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                               SEP  19 ddpenaeflesikkGevPeelekvekgeevevnledrrneeykppkkpkfkaFsGsG 75 
                                       +d+e++++ +++k+G++  ++++++kg+ev+++le  ++++ +++++ k  +F+ +G
  gi|298676230|ref|YP_003727979.1| 143 SDKETKQLKAELKNGKANTNIKQINKGDEVSIELE-SEDKDQEEQQSIKSISFKSNG 198
                                       689999****************************9.667777776666777898877 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.53
                               SEP  45 geevevnledrrneeykppkk 65 
                                        +evev++ d+++ +y  + k
  gi|298676230|ref|YP_003727979.1| 279 WDEVEVSMFDETEDKYIYKAK 299
                                       47899******9999987654 PP

>> DUF617  Protein of unknown function, DUF617
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00066       1.2     134     161 ..      67      95 ..      47      96 .. 0.91
   2 ?    0.3   0.1      0.36   6.5e+02      36      64 ..     160     189 ..     143     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00066
                            DUF617 134 rvvgskdsesfylinpdg.sggqeLsifl 161
                                        v+ s+dse +y ++p+g ++g+ Ls+++
  gi|298676230|ref|YP_003727979.1|  67 SVTTSTDSEGYYELKPNGlQDGKTLSLYV 95 
                                       6899*************9999*****995 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.36
                            DUF617  36 salvkem.asglvriaLecekkkekkkkke 64 
                                       ++ +k++ + + v i Le+e k+++++++ 
  gi|298676230|ref|YP_003727979.1| 160 NTNIKQInKGDEVSIELESEDKDQEEQQSI 189
                                       556677745567999999999998887654 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 ?   10.0   2.7   0.00019      0.33       2      95 ..       5     186 ..       4     257 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                   ABC2_membrane_3   2 sfliitlllPiilvlllglifsnsveddentpiavvdedn...............sslsqqlv.............. 49 
                                        +l ++l+  +++v ++g +   ++++++++ ++++ +d+               +                     
  gi|298676230|ref|YP_003727979.1|   5 QTL-TILITIFLFVSMVGAASAETSKTPPHMVYGYIKDDGngvsgiqveirtddgT------Klsndktsvttstds 74 
                                       566.77777777777777775555559************97765555555544441......044455566777777 PP

                   ABC2_membrane_3  50 ............................................ealeaspsve...........lvyevdseeeak 71 
                                                                                   ++l+ s++ +           + ++ + ++++k
  gi|298676230|ref|YP_003727979.1|  75 egyyelkpnglqdgktlslyvdgddtgndityttgkveqvnhegNYLSDSSDDDggssggisapgTGKSDKETKQLK 151
                                       78888888888888888888888888888888888888888888555555554455556666887777888888888 PP

                   ABC2_membrane_3  72 kalkngdidg.ilvipkgfskdll..........k 95 
                                         lkng++++ i +i+kg++ +++          +
  gi|298676230|ref|YP_003727979.1| 152 AELKNGKANTnIKQINKGDEVSIElesedkdqeeQ 186
                                       88888888875666777777776666666664442 PP

>> TTR-52  Transthyretin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   0.00091       1.6       8      45 ..      43      82 ..      37     119 .. 0.84
   2 ?    0.9   0.1      0.41   7.4e+02      11      38 ..     200     227 ..     196     252 .. 0.77
   3 ?   -1.9   0.0       3.2   5.8e+03       9      35 ..     277     300 ..     275     324 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00091
                                      T-GGSS-EEEEEEHHHH..TS--EEEEEE--TTSEEEEEE CS
                            TTR-52  8 gkpaknvkVkLwekdtl..dpddlldetkTdedGnFelsg 45
                                      g+ +++++V++  +d +   +d++  +t+Td++G++el+ 
  gi|298676230|ref|YP_003727979.1| 43 GNGVSGIQVEIRTDDGTklSNDKTSVTTSTDSEGYYELKP 82
                                      6778999999999876566899999999**********94 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.41
                                       GSS-EEEEEEHHHHTS--EEEEEE--TT CS
                            TTR-52  11 aknvkVkLwekdtldpddlldetkTded 38 
                                       a++v+++++++  ++p+++ d+  +d +
  gi|298676230|ref|YP_003727979.1| 200 AQDVNIEITDHGETKPETVTDSGDSDTE 227
                                       7889999999877788888888888764 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.2
                                       -GGSS-EEEEEEHHHHTS--EEEEEE- CS
                            TTR-52   9 kpaknvkVkLwekdtldpddlldetkT 35 
                                       +   +v+V+++++    +d+ + ++kT
  gi|298676230|ref|YP_003727979.1| 277 DDWDEVEVSMFDET---EDKYIYKAKT 300
                                       56678899999973...5666666666 PP

>> Glyco_hydro2_C5  Glycoside hydrolase family 2 C-terminal domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0074        13      10      47 ..      39      76 ..      37      85 .. 0.92
   2 ?    3.8   0.3     0.029        52      48      97 ..     134     181 ..     129     187 .. 0.78
   3 ?   -3.1   0.0       3.8   6.8e+03      37      47 ..     201     211 ..     194     226 .. 0.60
   4 ?   -3.2   0.0       4.4   7.8e+03      14      28 ..     276     290 ..     273     294 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0074
                   Glyco_hydro2_C5 10 lkadgkDlafvtvevvDknGnlvpnadnevtfeveGpG 47
                                      +k dg+ ++ ++ve+  ++G+ ++n++  vt + + +G
  gi|298676230|ref|YP_003727979.1| 39 IKDDGNGVSGIQVEIRTDDGTKLSNDKTSVTTSTDSEG 76
                                      789****************************9987766 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.029
                   Glyco_hydro2_C5  48 elvgvdngdptslesfksnerkafnGkalaivrstkeaGkitltasaegl 97 
                                        + + + g++   ++ k+ + ++ nGka   +++ ++  +++++ ++e+ 
  gi|298676230|ref|YP_003727979.1| 134 GISAPGTGKS--DKETKQLKAELKNGKANTNIKQINKGDEVSIELESEDK 181
                                       5566665554..455678888999********************999875 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.8
                   Glyco_hydro2_C5  37 nevtfeveGpG 47 
                                       ++v++e+++ G
  gi|298676230|ref|YP_003727979.1| 201 QDVNIEITDHG 211
                                       33444444444 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 4.4
                   Glyco_hydro2_C5  14 gkDlafvtvevvDkn 28 
                                       g+D   v+v+++D+ 
  gi|298676230|ref|YP_003727979.1| 276 GDDWDEVEVSMFDET 290
                                       788899999999986 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.3    0.0012       2.2      15      79 ..       7      73 ..       5      75 .. 0.74
   2 ?    0.3   0.3      0.79   1.4e+03      45      59 ..     177     194 ..     136     214 .. 0.54
   3 ?   -0.3   0.3       1.2   2.2e+03      63      63 ..     211     211 ..     176     257 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                           Pilin_N 15 itvIlaAviaafvlgl.asneekapqasievkidssastgkna..vslehkgGdsidtkdlkivlnse 79
                                      +t+++  ++ ++++g  + +++k+p  ++   i+++++  +    v+++ ++G  +++++++++++ +
  gi|298676230|ref|YP_003727979.1|  7 LTILITIFLFVSMVGAaSAETSKTPPHMVYGYIKDDGNGVS-GiqVEIRTDDGTKLSNDKTSVTTSTD 73
                                      67777778888888886667777777778555555555433.258******************98876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.79
                           Pilin_N  45 kidssastgkna...vsl 59 
                                       ++++++++++++   +s+
  gi|298676230|ref|YP_003727979.1| 177 ESEDKDQEEQQSiksISF 194
                                       222222222222222333 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.2
                           Pilin_N  63 g 63 
                                       g
  gi|298676230|ref|YP_003727979.1| 211 G 211
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1236  (0.0689386); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.57
# Mc/sec: 1941.39
//
Query:       gi|298676231|ref|YP_003727980.1|  [L=129]
Description: transcriptional regulator TrmB [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.2e-06   25.5   0.0    1.5e-05   24.8   0.0    1.3  1  TrmB         Sugar-specific transcriptional regulator TrmB
      3e-05   23.8   0.0    4.5e-05   23.2   0.0    1.3  1  MarR_2       MarR family
    4.2e-05   23.4   0.1    7.8e-05   22.5   0.0    1.5  1  MarR         MarR family
    0.00082   19.0   0.1     0.0012   18.5   0.1    1.2  1  SMC_ScpB     Segregation and condensation complex subunit Scp
     0.0072   16.3   0.1      0.011   15.7   0.1    1.3  1  HTH_36       Helix-turn-helix domain
  ------ inclusion threshold ------
      0.016   15.2   0.1       0.02   14.9   0.1    1.2  1  DUF327       Protein of unknown function (DUF327)
      0.022   15.3   0.1      0.036   14.7   0.1    1.3  1  Phage_rep_O  Bacteriophage replication protein O
      0.046   13.7   0.1       0.11   12.5   0.0    1.7  2  HTH_37       Helix-turn-helix domain
        0.1   12.8   0.2       0.41   10.8   0.1    2.0  2  DUF2582      Winged helix-turn-helix domain (DUF2582)


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 !   24.8   0.0   7.5e-09   1.5e-05       1      67 [.      19      93 ..      19      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 7.5e-09
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST........TTEEEE--H CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr........pklYravdp 67
                                      L+ lGL+ + + + + L   ++++ +ei  ++g+ ++ v ++ + L++kG++e+++++        +klY  v p
  gi|298676231|ref|YP_003727980.1| 19 LKNLGLTRTVSMTLACLSDGQELSSKEIETISGLRQPEVSSATKYLIEKGWIEIREEKittnkgrpTKLYTLVAP 93
                                      778999999999999999999************************************999999996668887765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   2.3e-08   4.5e-05       1      54 [.      22      73 ..      22      81 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.3e-08
                                      TT--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  1 lgltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      lglt++  + La L ++ +  l+ +e++   gl ++ vs + k L ++G++e r
  gi|298676231|ref|YP_003727980.1| 22 LGLTRTVSMTLACLSDGQE--LSSKEIETISGLRQPEVSSATKYLIEKGWIEIR 73
                                      69***************99..******************************987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   3.9e-08   7.8e-05       1      48 [.      24      71 ..      24      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.9e-08
                                      --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      lt+t  ++L++l++ ++ls +e+   +g+ ++ v+ +++ L++kG+ie
  gi|298676231|ref|YP_003727980.1| 24 LTRTVSMTLACLSDGQELSSKEIETISGLRQPEVSSATKYLIEKGWIE 71
                                      67888899***************************************8 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 !   18.5   0.1     6e-07    0.0012      79     140 ..      22      88 ..       6      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6e-07
                          SMC_ScpB  79 trLsqaaletLaiIaykqpvtraeieeiRGvn...sdsvvrtLlerglieekgrkee..pgrpilYg 140
                                         L++    tLa+    q ++++eie i G +   ++s+ + L+e+g+ie +++k +  +grp+ + 
  gi|298676231|ref|YP_003727980.1|  22 LGLTRTVSMTLACLSDGQELSSKEIETISGLRqpeVSSATKYLIEKGWIEIREEKITtnKGRPTKLY 88 
                                       568999999*****************99776444499***********9988877554489997654 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   5.5e-06     0.011       3      55 .]      22      70 ..      20      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.5e-06
                            HTH_36  3 LspsaklllgslasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                      L+   +++ ++la ++++ +    s + + + +gl    vs+a k L+++G+i
  gi|298676231|ref|YP_003727980.1| 22 LGL-TRTVSMTLACLSDGQEL---SSKEIETISGLRQPEVSSATKYLIEKGWI 70
                                      566.77888899999977777...99999999********************9 PP

>> DUF327  Protein of unknown function (DUF327)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1     1e-05      0.02      72     128 ..      57     115 ..      28     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHHH.HHHHT..-----H.HHHHHHHHHHHHHHHHHHHHHHHTTSTTCHHH CS
                            DUF327  72 vkeflkevvkns.lklkkersldrkg.rsrvykivkeiDekldeLteellkeekealdi 128
                                       v++  k++++++ +++ +e+ ++ kg  ++ y++v  iD+  +++  ++l+++++ ld 
  gi|298676231|ref|YP_003727980.1|  57 VSSATKYLIEKGwIEIREEKITTNKGrPTKLYTLVAPIDKITKDIEADILSQNRNILDN 115
                                       6666666665542789999999999999************************9987664 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.8e-05     0.036      34      90 ..      25      81 ..      12      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                       Phage_rep_O 34 lavirktYgfkkksdwisnsqlveltgisrtkvskalkeLirekviikegrkvgvnk 90
                                        ++++t+ +    + +s +++ ++ g+ + +vs+a k+Li+++ i ++++k+  nk
  gi|298676231|ref|YP_003727980.1| 25 TRTVSMTLACLSDGQELSSKEIETISGLRQPEVSSATKYLIEKGWIEIREEKITTNK 81
                                      56789999999999**************************************99997 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.5e-05      0.11      21      54 ..      30      63 ..      11      67 .. 0.86
   2 ?   -2.6   0.0       2.8   5.6e+03      22      34 ..      96     108 ..      87     110 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.5e-05
                                      HHHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT CS
                            HTH_37 21 laiaeliekrelsqseaaqllgiaqPkvsrllrg 54
                                      +++a l +++els +e+ ++ g  qP+vs+  ++
  gi|298676231|ref|YP_003727980.1| 30 MTLACLSDGQELSSKEIETISGLRQPEVSSATKY 63
                                      56888999*********************98876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.8
                                       HHHHHHHHCT--H CS
                            HTH_37  22 aiaeliekrelsq 34 
                                       +i++ ie+  lsq
  gi|298676231|ref|YP_003727980.1|  96 KITKDIEADILSQ 108
                                       5778888887877 PP

>> DUF2582  Winged helix-turn-helix domain (DUF2582)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.93   1.9e+03      21      36 ..      11      26 ..       8      34 .. 0.73
   2 ?   10.8   0.1    0.0002      0.41      16      56 ..      34      81 ..      30      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.93
                                      SSEEHHHHHHHCT-SC CS
                           DUF2582 21 geislkelkrktglsd 36
                                      ++i ++e+ ++ gl++
  gi|298676231|ref|YP_003727980.1| 11 KKIEMSEILKNLGLTR 26
                                      7889999999999865 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0002
                                      HHCCSSSEEHHHHHHHCT-SCHHHHHHH......HHH.HCTTSEEEEE CS
                           DUF2582 16 lLnengeislkelkrktglsdkelalAi......GWL.aREdKivier 56
                                       L++ +e+s ke++  +gl + e+ +A       GW   RE+Ki +++
  gi|298676231|ref|YP_003727980.1| 34 CLSDGQELSSKEIETISGLRQPEVSSATkyliekGWIeIREEKITTNK 81
                                      69999*****************99999655566699856999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.60u 0.72s 00:00:01.31 Elapsed: 00:00:00.64
# Mc/sec: 603.90
//
Query:       gi|298676232|ref|YP_003727981.1|  [L=328]
Description: hypothetical protein Metev_2378 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-13   51.3   0.1    5.2e-13   49.4   0.0    1.9  2  AAA_22    AAA domain
    7.2e-06   26.5   0.3    0.00015   22.2   0.0    2.5  2  AAA_16    AAA ATPase domain
     0.0011   18.9   0.8      0.015   15.2   0.5    2.7  2  ATPase_2  ATPase domain predominantly from Archaea
      0.007   16.7   0.1      0.036   14.4   0.0    2.1  2  AAA_19    AAA domain
  ------ inclusion threshold ------
       0.01   16.3   0.6      0.025   15.0   0.1    1.9  2  AAA       ATPase family associated with various cellular acti
      0.011   14.5   0.1      0.017   13.9   0.1    1.2  1  SNF2_N    SNF2 family N-terminal domain
      0.012   14.8   1.2        2.7    7.1   0.1    2.5  2  NB-ARC    NB-ARC domain


Domain annotation for each model (and alignments):
>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.0     2e-16   5.2e-13       5     135 ..      71     200 ..      66     202 .. 0.85
   2 ?   -1.6   0.0       1.2   3.1e+03      52      70 ..     300     318 ..     250     326 .. 0.63

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 2e-16
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelkaerlsseell. 79 
                                        +i v+++++G+GK+      l++l+e       +++++   ++++  ++ ++l+++lr+++ e k+   ++ +l+ 
  gi|298676232|ref|YP_003727981.1|  71 SSIFVIHAPVGMGKSSIRDFTLKTLNE-------SDDYYITVINNPRlTPLQILKQILRDITAEEKT--PRTMDLVw 138
                                       6799*************9999999975.......555543333344458*************99999..88888886 PP

                            AAA_22  80 ealeqalrarav...ielliiDEaqhlrseealeeLrsllnl....srkgvqliLvGtpelrk 135
                                       ++  + l++ +      ++ iDEa++l  ++ l+ Lr l+++    ++k ++++L Gtp l k
  gi|298676232|ref|YP_003727981.1| 139 NKAKNILSELKEtgiSTIIWIDEAEKL-DNKKLSLLRALADVktfdGEKVCKIVLTGTPTLKK 200
                                       888888888888999999*********.999999999999999999*************9977 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                            AAA_22  52 sskdllrellralglelka 70 
                                       s++d+l++l  ++++e+++
  gi|298676232|ref|YP_003727981.1| 300 SQDDVLNALSTQIQEENSE 318
                                       4455555555555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0     6e-08   0.00015      21     161 ..      68     179 ..      53     186 .. 0.73
   2 ?   -1.9   0.1       1.4   3.7e+03      89     106 ..     300     317 ..     257     327 .. 0.52

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6e-08
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqalareellrqlldeaesaelea 96 
                                        +++++ +++ + G+GKss+ +  l+ l++++  + +  ++ +l   +p           ++l+q+l++ ++ e   
  gi|298676232|ref|YP_003727981.1|  68 LSESSIFVIHAPVGMGKSSIRDFTLKTLNESDdYYITVINNPRL---TP----------LQILKQILRDITA-E--- 127
                                       3455999***********************97466677777777...33..........3666666666222.1... PP

                            AAA_16  97 wrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslqllaaLlrl 161
                                         ek ++++             ++++ k++l+ l++++  +++++D+++++d   l+ll+aL++ 
  gi|298676232|ref|YP_003727981.1| 128 --EKTPRTMD-----------LVWNKAKNILSELKETGISTIIWIDEAEKLDNKKLSLLRALADV 179
                                       ..22222233...........5688888999666666666**********************986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                            AAA_16  89 aesaeleawrekleeala 106
                                       ++++ l+a +++++e+ +
  gi|298676232|ref|YP_003727981.1| 300 SQDDVLNALSTQIQEENS 317
                                       333444444444444443 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.5     6e-06     0.015      13     148 ..      64     179 ..      58     204 .. 0.69
   2 ?   -1.1   0.0      0.57   1.5e+03     212     232 ..     257     277 ..     224     278 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6e-06
                          ATPase_2  13 eilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpka 89 
                                       + l+ ++++i +i  p g GK+++    ++ l+++d+y  y++ +++ +++ l+        k+ l++ ++      
  gi|298676232|ref|YP_003727981.1|  64 RFLSLSESSIFVIHAPVGMGKSSIRDFTLKTLNESDDY--YITVINNPRLTPLQIL------KQILRDITA------ 126
                                       56666777888888888888888777777777666653..4444444444444443......223333332...... PP

                          ATPase_2  90 eleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnl 148
                                         ee   ++  lv+++ +++l ++k++g   ii iDe+ kl     n++ +l+ +L+++
  gi|298676232|ref|YP_003727981.1| 127 --EEKTPRTMDLVWNKAKNILSELKETGISTIIWIDEAEKLD----NKKLSLLRALADV 179
                                       ..2222345699******************************....7777788888765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.57
                          ATPase_2 212 skedfeeiyryvGGkPkalve 232
                                       +k   +e+ ++ +GkP+ + +
  gi|298676232|ref|YP_003727981.1| 257 TKGAADEVIEFSDGKPRTITQ 277
                                       67778999999*****99987 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.4e-05     0.036       9     127 ..      70     178 ..      64     188 .. 0.76
   2 ?   -1.6   0.0       1.2     3e+03      50      77 ..     256     280 ..     240     325 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlalldfddllt 85 
                                       +++++++ a+ G+GK+ +    ++ l+e  +      ++  +     + l++ l+ ++ae +T   + l+ +++ + 
  gi|298676232|ref|YP_003727981.1|  70 ESSIFVIHAPVGMGKSSIRDFTLKTLNESDDY--YITVINNPRLTPLQILKQILRDITAEEKTPRTMDLV-WNKAK- 142
                                       67788999999999999999999999999965..455555666667888899999999999999888333.33333. PP

                            AAA_19  86 ealelleeaeeekklqeeellivDEfqdvdelqyrLlkallg 127
                                       + l+ l+e    + +   +++++DE+  +d    +Ll+al++
  gi|298676232|ref|YP_003727981.1| 143 NILSELKE----TGI--STIIWIDEAEKLDNKKLSLLRALAD 178
                                       34444443....444..5699******************984 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                            AAA_19  50 ftgrAakelrerlaalgaeatTiHrlal 77 
                                       ft+ Aa+e+ e     +++ +Ti +++ 
  gi|298676232|ref|YP_003727981.1| 256 FTKGAADEVIEFS---DGKPRTITQITQ 280
                                       5666666666655...444455544433 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   9.7e-06     0.025       3      88 ..      76     172 ..      74     206 .. 0.66
   2 ?   -1.6   0.1       1.4   3.5e+03      81      99 ..     300     318 ..     272     323 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.7e-06
                                       EESSTTSSHHHHHHHHHHHHT....HEEEEEETTTCSSS..................STTHHHHHHHHHHHHHHHTS CS
                               AAA   3 lyGppGtGKTllakavakelg....vefleisgsellsk..................yvgesekkirelfkeakeka 57 
                                       ++ p G+GK+++     k+l+     ++  i+ ++l+                    ++    +k +++++e+ke  
  gi|298676232|ref|YP_003727981.1|  76 IHAPVGMGKSSIRDFTLKTLNesddYYITVINNPRLTPLqilkqilrditaeektprTMDLVWNKAKNILSELKETG 152
                                       7899***************9654556677777777773357777777777555555566666666666666666666 PP

                                       TS.EEEEEETGGGHHHHHTTCCCHHHHHHHHH CS
                               AAA  58 kp.silfiDEidalaksrsgseseeeervvnq 88 
                                          +i++iDE+++l +++           ++ 
  gi|298676232|ref|YP_003727981.1| 153 -IsTIIWIDEAEKLDNKK-----------LSL 172
                                       .559**********8887...........333 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHHTTTS CS
                               AAA  81 eeervvnqLlteldgvkkk 99 
                                       ++++v+n+L t++++++++
  gi|298676232|ref|YP_003727981.1| 300 SQDDVLNALSTQIQEENSE 318
                                       5678999999999988775 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   6.6e-06     0.017     168     220 ..     143     202 ..     111     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.6e-06
                                       ...TTS-S-S-SEEE.ES-GGGT--TTSHHHHHHHH--.....-S-EEEE-S--SSS.-H CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx.xx RF
                            SNF2_N 168 kkrsvlkqvewkrvv.lDEghtlknstskaaeavskLs.....tsnrwiltGTPiqn.sl 220
                                       ++ s+lk+  +  ++ +DE+ +l n++ ++  a+ + +        +++ltGTP+   ++
  gi|298676232|ref|YP_003727981.1| 143 NILSELKETGISTIIwIDEAEKLDNKKLSLLRALADVKtfdgeKVCKIVLTGTPTLKkKV 202
                                       67788899887776659*********988888877765333445679*******987344 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.002       5.1       8     111 ..      62     161 ..      55     208 .. 0.78
   2 ?    7.1   0.1     0.001       2.7     163     208 ..     237     282 ..     224     324 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.002
                                       HHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSS CS
                            NB-ARC   8 viekLlekdelqslvvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseeiletilkeLslseddle 84 
                                       +   L+   e+   +  ++   G+GK+ +    l+    +++  d ++ v      +  +il++il+++  +e+   
  gi|298676232|ref|YP_003727981.1|  62 LTRFLS-LSESS--IFVIHAPVGMGKSSIRDFTLKT---LNESDDYYITVINNPRLTPLQILKQILRDITAEEKTPR 132
                                       444555.44555..899************9988888...66666888999999999999**********99999999 PP

                                       SS-STTSHHHHHHHHCCCT..TEEEEEEE CS
                            NB-ARC  85 ekeeveslkrklvrlLltk..rfllvlDD 111
                                        ++ v ++++++   L++    +++ +D 
  gi|298676232|ref|YP_003727981.1| 133 TMDLVWNKAKNILSELKETgiSTIIWIDE 161
                                       99999888999988888776777777775 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.001
                                       HHHHHHHHCCTS-GGCHH..CHHHHHHHHHHCTT-HHHHHHHHHHH CS
                            NB-ARC 163 eawellenkvfekkleekesleevakeivekckGlPlalkvlggll 208
                                       e well+++    +   ++  +  a e++e + G P ++  + +++
  gi|298676232|ref|YP_003727981.1| 237 EWWELLCEYCSTDDNAINPFTKGAADEVIEFSDGKPRTITQITQMV 282
                                       67*********999999999********************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1315  (0.0733449); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); 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: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 1865.98
//
Query:       gi|298676233|ref|YP_003727982.1|  [L=177]
Description: hypothetical protein Metev_2379 [Methanohalobium evestigatum Z-7303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1344  (0.0749624); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1123.27
//
[ok]
